TileDB provides the -Universal Data Engine that can be accessed in a variety of -ways. Users sometimes wonder how to transfer data from existing -databases. This short vignettes shows an example relying on the DBI package for R. It -offers a powerful and convenient abstraction layer on top a number of -database backends with connection packages that adhere to, and utilise, -the DBI framework. Some examples are the packages (listed in -alphabetical order) duckdb, RClickhouse, -RGreenplum, -RJDBC, RMariaDB, RMySQL, ROracle, RPostgres, RPostgreSQL, -RPresto, RRedshiftSQL, -RSQLite, and -many more as seen via the CRAN page.
We provide a simple example using RPostgreSQL -and an existing database of historical stockmarket price data.
TileDB provides the Universal Data Engine that can be accessed in a variety of ways. Users sometimes wonder how to transfer data from existing databases. This short vignettes shows an example relying on the DBI package for R. It offers a powerful and convenient abstraction layer on top a number of database backends with connection packages that adhere to, and utilise, the DBI framework. Some examples are the packages (listed in alphabetical order) duckdb, RClickhouse, RGreenplum, RJDBC, RMariaDB, RMySQL, ROracle, RPostgres, RPostgreSQL, RPresto, RRedshiftSQL, RSQLite, and many more as seen via the CRAN page.
We provide a simple example using RPostgreSQL and an existing database of historical stockmarket price data.
The basic setup is straightforward. We load the required package RPostgreSQL -which in turn imports DBI as well as tiledb. We use data.table for -its print method, the tibble package -offers an alternative):
The basic setup is straightforward. We load the required package RPostgreSQL which in turn imports DBI as well as tiledb. We use data.table for its print method, the tibble package offers an alternative):
library(RPostgreSQL) library(data.table) @@ -121,16 +104,7 @@ Load Required Packages Connect to Database -This step uses the DBI abstraction. A compliant backend driver can be -loaded via dbDriver, and a connection can be established -via dbConnect using appropriate arguments -dbname, user, password, -host, and port, as needed, with proper -dispatching the implementation provided by the driver. The details -depend on the chosen backend, this can be as simple as -con <- dbConnect(RSQLite::SQLite(), ":memory:") in the -case of RSQLite -and an in-memory (and likely transient) database. +This step uses the DBI abstraction. A compliant backend driver can be loaded via dbDriver, and a connection can be established via dbConnect using appropriate arguments dbname, user, password, host, and port, as needed, with proper dispatching the implementation provided by the driver. The details depend on the chosen backend, this can be as simple as con <- dbConnect(RSQLite::SQLite(), ":memory:") in the case of RSQLite and an in-memory (and likely transient) database. ## a local SQL db we have here -- about 617k rows dbSetup <- function() { @@ -145,11 +119,7 @@ Connect to Database Fetch Data -In the next step we fetch the data—and for simplicity issue just one -select statement returning a single data.frame -(or here a data.table variant). In larger-than-memory -settings the SQL query could easily bucket by symbols, or date range, or -… +In the next step we fetch the data—and for simplicity issue just one select statement returning a single data.frame (or here a data.table variant). In larger-than-memory settings the SQL query could easily bucket by symbols, or date range, or … getDataFromSQL <- function() { con <- dbSetup() @@ -163,12 +133,7 @@ Fetch Data Writing Data to TileDB -Having read the data into memory we can use the TileDB R function -fromDataFrame. It has numerous option to configure, as well -as sensible defaults (to for example enable ZSTD compression). Here we -select the first two columns for symbol and data as dimensions. Symbols, -being text, do not set a domain set. For the date we set two ‘safe’ -outer values for the range. +Having read the data into memory we can use the TileDB R function fromDataFrame. It has numerous option to configure, as well as sensible defaults (to for example enable ZSTD compression). Here we select the first two columns for symbol and data as dimensions. Symbols, being text, do not set a domain set. For the date we set two ‘safe’ outer values for the range. storeDataTDB <- function(dat, uri) { fromDataFrame(dat, uri, @@ -176,16 +141,11 @@ Writing Data to TileDB tile_domain=list(date=c(as.numeric(as.Date("1985-01-01")), as.numeric(as.Date("2030-12-31"))))) } -The mode="append" argument of fromDataFrame -can be used to append to an existing array to support chunked -operation. +The mode="append" argument of fromDataFrame can be used to append to an existing array to support chunked operation. Reading Data Back In -Reading data from TileDB is a very standard operation of opening the -URI, possibly specifying the return type and possibly subsetting by -dimension values, or attributes. Here, for simplicity, we just read -everything. +Reading data from TileDB is a very standard operation of opening the URI, possibly specifying the return type and possibly subsetting by dimension values, or attributes. Here, for simplicity, we just read everything. getDataTDB <- function(uri) { set_allocation_size_preference(1e7) # larger than local default value @@ -206,21 +166,13 @@ Reading Data Back In See Also -The vignette TileDB MariaDB -Examples shows to use MariaDB via the MyTile integration of TileDB -as a direct backend. -The TileDB -R Tutorial at useR! 2021 contained a worked example of writing -much larger data set in chunks. The process is very similar to -the simple example we showed here – and in addition requires a suffient -domain range for the dimension along with a (sequential or parallel) -loop of reading chunks and writing them to TileDB. +The vignette TileDB MariaDB Examples shows to use MariaDB via the MyTile integration of TileDB as a direct backend. +The TileDB R Tutorial at useR! 2021 contained a worked example of writing much larger data set in chunks. The process is very similar to the simple example we showed here – and in addition requires a suffient domain range for the dimension along with a (sequential or parallel) loop of reading chunks and writing them to TileDB. Summary -This vignette provides a commented walk-through of a worked example -of a SQL-to-TileDB data ingestion. +This vignette provides a commented walk-through of a worked example of a SQL-to-TileDB data ingestion. @@ -229,11 +181,11 @@ Summary diff --git a/docs/articles/data-ingestion-from-sql_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/data-ingestion-from-sql_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 0000000000..ca349fd6a5 --- /dev/null +++ b/docs/articles/data-ingestion-from-sql_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. + +document.addEventListener('DOMContentLoaded', function() { + const codeList = document.getElementsByClassName("sourceCode"); + for (var i = 0; i < codeList.length; i++) { + var linkList = codeList[i].getElementsByTagName('a'); + for (var j = 0; j < linkList.length; j++) { + if (linkList[j].innerHTML === "") { + linkList[j].setAttribute('aria-hidden', 'true'); + } + } + } +}); diff --git a/docs/articles/documentation.html b/docs/articles/documentation.html index 48c90de3c6..3ec793d97e 100644 --- a/docs/articles/documentation.html +++ b/docs/articles/documentation.html @@ -12,7 +12,7 @@ - + @@ -26,7 +26,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -68,8 +68,7 @@ - - + TileDB API Documentation @@ -86,15 +85,11 @@ TileDB API Documentation %\VignetteEngine{simplermarkdown::mdweave_to_html} %\VignetteEncoding{UTF-8} --> -This document follows the TileDB API usage -examples. A shorter introductory -vignette is also available. +This document follows the TileDB API usage examples. A shorter introductory vignette is also available. Prelimaries -We will show two initial and basic examples for a dense and sparse -array simply to create array data on disk to refer to later in examples -that follow. +We will show two initial and basic examples for a dense and sparse array simply to create array data on disk to refer to later in examples that follow. library(tiledb) @@ -1304,11 +1299,11 @@ Catching Errors diff --git a/docs/articles/documentation_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/documentation_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 0000000000..ca349fd6a5 --- /dev/null +++ b/docs/articles/documentation_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. + +document.addEventListener('DOMContentLoaded', function() { + const codeList = document.getElementsByClassName("sourceCode"); + for (var i = 0; i < codeList.length; i++) { + var linkList = codeList[i].getElementsByTagName('a'); + for (var j = 0; j < linkList.length; j++) { + if (linkList[j].innerHTML === "") { + linkList[j].setAttribute('aria-hidden', 'true'); + } + } + } +}); diff --git a/docs/articles/index.html b/docs/articles/index.html index e74f7844ec..6eb1a0a5b5 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -1,5 +1,5 @@ -Articles • tiledb +Articles • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -75,11 +75,11 @@ Working with SQL diff --git a/docs/articles/installation-options.html b/docs/articles/installation-options.html index e82d52aade..40b28296d9 100644 --- a/docs/articles/installation-options.html +++ b/docs/articles/installation-options.html @@ -12,7 +12,7 @@ - + @@ -26,7 +26,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -68,8 +68,7 @@ - - + Installation Options for the TileDB R Package @@ -90,53 +89,30 @@ 2022-01-25 Overview -This vignette discusses different options for installing the TileDB R -package. +This vignette discusses different options for installing the TileDB R package. CRAN Binaries -The TileDB R package is released via the Comprehensive R Archive -Network, or CRAN. CRAN generally provides binaries for the two most -widely operating systems, Windows and macOS. So issueing the command +The TileDB R package is released via the Comprehensive R Archive Network, or CRAN. CRAN generally provides binaries for the two most widely operating systems, Windows and macOS. So issueing the command install.packages("tiledb") -will, on those two operating system, default to -type="binary" and install a ready-to-run binary -package. +will, on those two operating system, default to type="binary" and install a ready-to-run binary package. Source -On other operating systems such as Linux, or by explicitly selecting -type="source" on Windows or macOS, an installation from source is attempted when usinginstall.packages(“tiledb”)`. -On Linux or macOS, this invokes the standard R build process which -will rely on configure. If pkg-config is -found, it is used to query the system about a possible TileDB -installation. If one is found, it used. Otherwise, on all three main -operating systems a prebuilt archive with the TileDB Embedded library is -downloaded from GitHub and unpacked. Each build of the R package will -have one matching build of TileDB Embedded associated with it via file -the tools/tiledbVersion.txt specifying a version and -release commit sha1. These two values are used to find the corresponding -binary artifacts from a release at GitHub. -The location of an existing installed version of TileDB Embedded can -also be provided to the configure script which supplies an -argument --with-tiledb=PATH. So on the command-line, one -could say -R CMD INSTALL --configure-args='--with-tiledb=/some/path' tiledb_*.tar.gz -to pass the configure argument on. From within R, the -equivalent command is +On other operating systems such as Linux, or by explicitly selecting type="source" on Windows or macOS, an installation from source is attempted when usinginstall.packages(“tiledb”)`. +On Linux or macOS, this invokes the standard R build process which will rely on configure. If pkg-config is found, it is used to query the system about a possible TileDB installation. If one is found, it used. Otherwise, on all three main operating systems a prebuilt archive with the TileDB Embedded library is downloaded from GitHub and unpacked. Each build of the R package will have one matching build of TileDB Embedded associated with it via file the tools/tiledbVersion.txt specifying a version and release commit sha1. These two values are used to find the corresponding binary artifacts from a release at GitHub. +The location of an existing installed version of TileDB Embedded can also be provided to the configure script which supplies an argument --with-tiledb=PATH. So on the command-line, one could say +R CMD INSTALL --configure-args='--with-tiledb=/some/path' tiledb_*.tar.gz +to pass the configure argument on. From within R, the equivalent command is install.packages("tiledb", repos=NULL, configure.args="--with-tiledb=/some/path") -Lastly, one can also override the default download location -(otherwise inferred via tools/tiledbVersion.txt. The -configure script supports an option ---with-download=URL so the two calls become, -respectively -R CMD INSTALL --configure-args='--with-download=https://some.where.net/file.tgz' tiledb_*.tar.gz +Lastly, one can also override the default download location (otherwise inferred via tools/tiledbVersion.txt. The configure script supports an option --with-download=URL so the two calls become, respectively +R CMD INSTALL --configure-args='--with-download=https://some.where.net/file.tgz' tiledb_*.tar.gz and install.packages("tiledb_0.11.0.tar.gz", repos=NULL, @@ -147,30 +123,23 @@ Source Conda -Using for example the current condaforge/mambaforge -container from the conda-forge project, -we can do -mamba install -y r-tiledb # installs R, tiledb and deps without extra prompt -# ...several lines of installation detail omitted -R -# ... several lines of R startup output omitted -> library(tiledb) -which installs R, the tiledb package and all respective -dependencies. +Using for example the current condaforge/mambaforge container from the conda-forge project, we can do +mamba install -y r-tiledb # installs R, tiledb and deps without extra prompt +# ...several lines of installation detail omitted +R +# ... several lines of R startup output omitted +> library(tiledb) +which installs R, the tiledb package and all respective dependencies. Docker -Builds of the TileDB package could also be provided via Docker -containers. At present, no official TileDB R containers are provided by -TileDB. However, the discussion of installation from source above -describes how to create such containers. +Builds of the TileDB package could also be provided via Docker containers. At present, no official TileDB R containers are provided by TileDB. However, the discussion of installation from source above describes how to create such containers. Summary -This note described several installation options for the TileDB R -package. +This note described several installation options for the TileDB R package. @@ -179,11 +148,11 @@ Summary diff --git a/docs/articles/installation-options_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/installation-options_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 0000000000..ca349fd6a5 --- /dev/null +++ b/docs/articles/installation-options_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. + +document.addEventListener('DOMContentLoaded', function() { + const codeList = document.getElementsByClassName("sourceCode"); + for (var i = 0; i < codeList.length; i++) { + var linkList = codeList[i].getElementsByTagName('a'); + for (var j = 0; j < linkList.length; j++) { + if (linkList[j].innerHTML === "") { + linkList[j].setAttribute('aria-hidden', 'true'); + } + } + } +}); diff --git a/docs/articles/introduction.html b/docs/articles/introduction.html index b87009f33d..bf485522d9 100644 --- a/docs/articles/introduction.html +++ b/docs/articles/introduction.html @@ -12,7 +12,7 @@ - + @@ -26,7 +26,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -68,8 +68,7 @@ - - + First Steps with TileDB @@ -86,29 +85,14 @@ First Steps with TileDB %\VignetteEngine{simplermarkdown::mdweave_to_html} %\VignetteEncoding{UTF-8} --> -This document introduces TileDB via several simple examples. A -corresponding document with more complete API documentation is also available. +This document introduces TileDB via several simple examples. A corresponding document with more complete API documentation is also available. Getting started -Once the TileDB R package is installed, it can be loaded via -library(tiledb). Installation is supported for Windows, -Linux and macOS via the official CRAN -package, on Linux and macOS via the conda package as well as -from source. -Documentation for the TileDB R package is available via the -help() function from within R as well as via the package documentation -and an introductory -notebook. Documentation about TileDB itself is also available. -Several “quickstart” examples that are discussed on the website are -available in the examples -directory. This vignette discusses similar examples. -In the following examples, the URIs describing arrays point to local -file system object. When TileDB has been built with S3 support, and with -proper AWS credentials in the usual environment variables, URIs such as -s3://some/data/bucket can be used where a local file would -be used. See the script ex_S3.R -for an example. +Once the TileDB R package is installed, it can be loaded via library(tiledb). Installation is supported for Windows, Linux and macOS via the official CRAN package, on Linux and macOS via the conda package as well as from source. +Documentation for the TileDB R package is available via the help() function from within R as well as via the package documentation and an introductory notebook. Documentation about TileDB itself is also available. +Several “quickstart” examples that are discussed on the website are available in the examples directory. This vignette discusses similar examples. +In the following examples, the URIs describing arrays point to local file system object. When TileDB has been built with S3 support, and with proper AWS credentials in the usual environment variables, URIs such as s3://some/data/bucket can be used where a local file would be used. See the script ex_S3.R for an example. Dense Arrays @@ -116,104 +100,72 @@ Dense Arrays Preliminaries -These illustrations use the array created by the file ex_1.R -which one can run from within R, or on the command-line. To follow along -with discussion that follows, it helps to run the example once to create -the array after possibly adjusting the array location path from its -default value (using the current directory or, if set as an option, an -override). +These illustrations use the array created by the file ex_1.R which one can run from within R, or on the command-line. To follow along with discussion that follows, it helps to run the example once to create the array after possibly adjusting the array location path from its default value (using the current directory or, if set as an option, an override). Basic Reading of Dense Arrays -The file ex_1.R -in the examples directory is a simple yet complete example extending quickstart_dense.R -by adding a second and third attribute. In this as well as the following -examples we will use tiledb_array() to access the array; -the older variants tiledb_dense() and -tiledb_sparse() remain supported but are deprecated and may -be removed at some point in the future. +The file ex_1.R in the examples directory is a simple yet complete example extending quickstart_dense.R by adding a second and third attribute. In this as well as the following examples we will use tiledb_array() to access the array; the older variants tiledb_dense() and tiledb_sparse() remain supported but are deprecated and may be removed at some point in the future. Read 1-D -The first example extracts rows 1 to 2 and column 2 from an array. It -also limits the selection to just one attribute (via -attrs), asks for the return to be a data.frame -(instead of a simpler list) and for the (row and column, if present as -here) indices to not be printed (via extended=FALSE). -> A <- tiledb_array(uri = uri, attrs = "b", -+ return_as = "data.frame", extended=FALSE)) -> A[1:2,2] -[1] 101.5 104.0 -> -Note that the examples create three two-dimensional attributes. The -attributes can be selected via the attrs argument, or the -attrs() method on the array object. The square-bracket -indexing then selects with in the 2-d attribute object. -If multiple objects are returned (as list or -data.frame), subsetting on the returned object works via -[[var]] or $var. A numeric index also works -(but needs to account for rows and cols). -> A <- tiledb_array(uri = uri, attrs = c("a","b"), -+ return_as = "data.frame") -> A[1:2,2][["a"]] -[1] 2 7 -> A[1:2,2]$a -[1] 2 7 -> +The first example extracts rows 1 to 2 and column 2 from an array. It also limits the selection to just one attribute (via attrs), asks for the return to be a data.frame (instead of a simpler list) and for the (row and column, if present as here) indices to not be printed (via extended=FALSE). +> A <- tiledb_array(uri = uri, attrs = "b", ++ return_as = "data.frame", extended=FALSE)) +> A[1:2,2] +[1] 101.5 104.0 +> +Note that the examples create three two-dimensional attributes. The attributes can be selected via the attrs argument, or the attrs() method on the array object. The square-bracket indexing then selects with in the 2-d attribute object. +If multiple objects are returned (as list or data.frame), subsetting on the returned object works via [[var]] or $var. A numeric index also works (but needs to account for rows and cols). +> A <- tiledb_array(uri = uri, attrs = c("a","b"), ++ return_as = "data.frame") +> A[1:2,2][["a"]] +[1] 2 7 +> A[1:2,2]$a +[1] 2 7 +> Read 2-D -This works analogously. Note that the results are generally returned -as vectors, or as a columns of a data.frame object in case -that option was set. -> A[6:9,3:4] -$a -[1] 28 29 33 34 38 39 43 44 - -$b -[1] 114.5 115.0 117.0 117.5 119.5 120.0 122.0 122.5 - -$c -[1] "fox" "A" "E" "F" "J" "K" "O" "P" -> +This works analogously. Note that the results are generally returned as vectors, or as a columns of a data.frame object in case that option was set. +> A[6:9,3:4] +$a +[1] 28 29 33 34 38 39 43 44 + +$b +[1] 114.5 115.0 117.0 117.5 119.5 120.0 122.0 122.5 + +$c +[1] "fox" "A" "E" "F" "J" "K" "O" "P" +> Read 2-D with attribute selection -We can restrict the selection to a subset of attributes when opening -the array. -> A <- tiledb_dense(uri = uri, attrs = c("b","c"), -+ return_as = "data.frame", extended=FALSE) -> A[6:9,2:4] - b c -1 114.0 brown -2 114.5 fox -3 115.0 A -4 116.5 D -5 117.0 E -6 117.5 F -7 119.0 I -8 119.5 J -9 120.0 K -10 121.5 N -11 122.0 O -12 122.5 P -> -This also illustrated the effect of setting -as.data.frame=TRUE when opening the array. -This scheme can be generalized to variable cells, or cells where -N>1, as we can expand each (atomistic) value over corresponding row -and column indices. -The column types correspond to the attribute typed in the array -schema, subject to the constraint mentioned above on R types. (The char -comes in as a factor variable as is still the R 3.6.* default which is -about to change. We can also override, users can too.) -> A <- tiledb_array("/tmp/tiledb/ex_1/", attrs=c("b","c"), -+ return_as = "data.frame", extended=TRUE) -> sapply(A[6:9, 3:4], "class") - rows cols b c - "integer" "integer" "numeric" "character" -> -Consistent with the data.frame semantics, now -requesting a named column reduces to a vector as this happens -at the R side: +We can restrict the selection to a subset of attributes when opening the array. +> A <- tiledb_dense(uri = uri, attrs = c("b","c"), ++ return_as = "data.frame", extended=FALSE) +> A[6:9,2:4] + b c +1 114.0 brown +2 114.5 fox +3 115.0 A +4 116.5 D +5 117.0 E +6 117.5 F +7 119.0 I +8 119.5 J +9 120.0 K +10 121.5 N +11 122.0 O +12 122.5 P +> +This also illustrated the effect of setting as.data.frame=TRUE when opening the array. +This scheme can be generalized to variable cells, or cells where N>1, as we can expand each (atomistic) value over corresponding row and column indices. +The column types correspond to the attribute typed in the array schema, subject to the constraint mentioned above on R types. (The char comes in as a factor variable as is still the R 3.6.* default which is about to change. We can also override, users can too.) +> A <- tiledb_array("/tmp/tiledb/ex_1/", attrs=c("b","c"), ++ return_as = "data.frame", extended=TRUE) +> sapply(A[6:9, 3:4], "class") + rows cols b c + "integer" "integer" "numeric" "character" +> +Consistent with the data.frame semantics, now requesting a named column reduces to a vector as this happens at the R side: > A[6:9, 3:4]$b [1] 114.5 115.0 117.0 117.5 119.5 120.0 122.0 122.5 > @@ -226,96 +178,78 @@ Sparse ArraysBasic Reading and Writing of Sparse Arrays Simple Examples -Basic reading returns the coordinates and any attributes. The -following examples use the array created by the quickstart_sparse -example. -> A <- tiledb_array(uri = uri, is.sparse = TRUE) -> A[] -$rows -[1] 1 2 2 - -$cols -[1] 1 3 4 - -$a -[1] 1 3 2 - -> -We can also request a data.frame object, either when -opening or by changing this object characteristic on the fly: -> return.data.frame(A) <- TRUE -> A[] - a rows cols -1 1 1 1 -2 3 2 3 -3 2 2 4 -For sparse arrays, the return type is by default ‘extended’ showing -rows and column but this can be overridden. +Basic reading returns the coordinates and any attributes. The following examples use the array created by the quickstart_sparse example. +> A <- tiledb_array(uri = uri, is.sparse = TRUE) +> A[] +$rows +[1] 1 2 2 + +$cols +[1] 1 3 4 + +$a +[1] 1 3 2 + +> +We can also request a data.frame object, either when opening or by changing this object characteristic on the fly: +> return.data.frame(A) <- TRUE +> A[] + a rows cols +1 1 1 1 +2 3 2 3 +3 2 2 4 +For sparse arrays, the return type is by default ‘extended’ showing rows and column but this can be overridden. Assignment works similarly: -> A[4,2] <- 42L -> A[] -> A[] - rows cols a -1 1 1 1 -2 2 3 3 -3 2 4 2 -4 4 2 42 -> +> A[4,2] <- 42L +> A[] +> A[] + rows cols a +1 1 1 1 +2 2 3 3 +3 2 4 2 +4 4 2 42 +> Reads can select rows and or columns: -> A[2,] - rows cols a -1 2 3 3 -2 2 4 2 -> A[,2] - rows cols a -1 4 2 42 -> +> A[2,] + rows cols a +1 2 3 3 +2 2 4 2 +> A[,2] + rows cols a +1 4 2 42 +> Attributes can be selected similarly. Date(time) Attributes -Similar to the dense array case described earlier, the file ex_2.R -illustrates some basic operations on sparse arrays. It also shows date -and datetime types instead of just integer and double precision -floats. -> A <- tiledb_array(uri = uri, return_as = "data.frame") -> A[1577858403:1577858408] - rows cols a b d e -1 1577858403 1 3 103 2020-01-11 2020-01-02 18:24:33.844 -2 1577858404 1 4 104 2020-01-15 2020-01-05 02:28:36.214 -3 1577858405 1 5 105 2020-01-19 2020-01-05 00:44:04.805 -4 1577858406 1 6 106 2020-01-21 2020-01-06 12:58:51.770 -5 1577858407 1 7 107 2020-01-25 2020-01-09 04:29:56.309 -6 1577858408 1 8 108 2020-01-26 2020-01-07 13:55:10.240 -> -The row coordinate is currently a floating point representation of -the underlying time type. We can both select attributes (here we -excluded the “a” column) and select rows by time (as the time stamps get -converted to the required floating point value). -> attrs(A) <- c("b", "d", "e") -> A[as.POSIXct("2020-01-01"):as.POSIXct("2020-01-01 00:00:03")] - rows cols b d e -1 1577858401 1 101 2020-01-05 2020-01-01 03:03:07.548 -2 1577858402 1 102 2020-01-10 2020-01-02 21:02:19.747 -3 1577858403 1 103 2020-01-11 2020-01-02 18:24:33.844 -> -More extended examples are available showing indexing by date(time) -as well as character dimension. +Similar to the dense array case described earlier, the file ex_2.R illustrates some basic operations on sparse arrays. It also shows date and datetime types instead of just integer and double precision floats. +> A <- tiledb_array(uri = uri, return_as = "data.frame") +> A[1577858403:1577858408] + rows cols a b d e +1 1577858403 1 3 103 2020-01-11 2020-01-02 18:24:33.844 +2 1577858404 1 4 104 2020-01-15 2020-01-05 02:28:36.214 +3 1577858405 1 5 105 2020-01-19 2020-01-05 00:44:04.805 +4 1577858406 1 6 106 2020-01-21 2020-01-06 12:58:51.770 +5 1577858407 1 7 107 2020-01-25 2020-01-09 04:29:56.309 +6 1577858408 1 8 108 2020-01-26 2020-01-07 13:55:10.240 +> +The row coordinate is currently a floating point representation of the underlying time type. We can both select attributes (here we excluded the “a” column) and select rows by time (as the time stamps get converted to the required floating point value). +> attrs(A) <- c("b", "d", "e") +> A[as.POSIXct("2020-01-01"):as.POSIXct("2020-01-01 00:00:03")] + rows cols b d e +1 1577858401 1 101 2020-01-05 2020-01-01 03:03:07.548 +2 1577858402 1 102 2020-01-10 2020-01-02 21:02:19.747 +3 1577858403 1 103 2020-01-11 2020-01-02 18:24:33.844 +> +More extended examples are available showing indexing by date(time) as well as character dimension. Additional Information -The TileDB R package is documented via R help functions -(e.g. help("tiledb_array") shows information for -the tiledb_array() function) as well as via a website regrouping all -documentation. Extended API -documentation is available, as is a examples/ -directory. -TileDB itself has extensive installation, -and overall -documentation as well as a support forum. +The TileDB R package is documented via R help functions (e.g. help("tiledb_array") shows information for the tiledb_array() function) as well as via a website regrouping all documentation. Extended API documentation is available, as is a examples/ directory. +TileDB itself has extensive installation, and overall documentation as well as a support forum. @@ -324,11 +258,11 @@ Additional Information diff --git a/docs/articles/introduction_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/introduction_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 0000000000..ca349fd6a5 --- /dev/null +++ b/docs/articles/introduction_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. + +document.addEventListener('DOMContentLoaded', function() { + const codeList = document.getElementsByClassName("sourceCode"); + for (var i = 0; i < codeList.length; i++) { + var linkList = codeList[i].getElementsByTagName('a'); + for (var j = 0; j < linkList.length; j++) { + if (linkList[j].innerHTML === "") { + linkList[j].setAttribute('aria-hidden', 'true'); + } + } + } +}); diff --git a/docs/articles/tiledb-mariadb-examples.html b/docs/articles/tiledb-mariadb-examples.html index 849627c0bf..866cf34a7c 100644 --- a/docs/articles/tiledb-mariadb-examples.html +++ b/docs/articles/tiledb-mariadb-examples.html @@ -12,7 +12,7 @@ - + @@ -26,7 +26,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -68,8 +68,7 @@ - - + TileDB and (R)MariaDB Examples @@ -89,43 +88,26 @@ TileDB and (R)MariaDB Examples Introduction -TileDB provides the -Universal Data Engine that can be accessed in a variety of -ways. The C/C++ library offered by TileDB Embedded is one -approach, and the R -package, as well as the Python package and -other language bindings use it. Another interface is provided by the MariaDB Integration via the -MyTile storage plugin. -This provides TileDB integration with any frontend that interfaces -with MariaDB—such as the RMariaDB package -for R. So this vignette illustrates the use of TileDB via MariaDB using -R and the RMariaDB packages. +TileDB provides the Universal Data Engine that can be accessed in a variety of ways. The C/C++ library offered by TileDB Embedded is one approach, and the R package, as well as the Python package and other language bindings use it. Another interface is provided by the MariaDB Integration via the MyTile storage plugin. +This provides TileDB integration with any frontend that interfaces with MariaDB—such as the RMariaDB package for R. So this vignette illustrates the use of TileDB via MariaDB using R and the RMariaDB packages. Installation or Using Docker -In order to use the MyTile storage plugin, one has to compile both -the storage plugin itself and the MariaDB server with consistent -compiler flags. As the build also requires the TileDB Embedded library -and headers, using a Docker container may be easiest. The Dockerfile -also provides a concrete example of the build setup. -So here we will use the tiledb/tiledb-mariadb-r -container. +In order to use the MyTile storage plugin, one has to compile both the storage plugin itself and the MariaDB server with consistent compiler flags. As the build also requires the TileDB Embedded library and headers, using a Docker container may be easiest. The Dockerfile also provides a concrete example of the build setup. +So here we will use the tiledb/tiledb-mariadb-r container. Launch Container in Background -We launch the container ‘tiledb/tiledb-mariadb-r’ as a daemon, -allowing MariaDB to accept an empty password (using an older MySQL -variable setting), and name the running image ‘tiledb-mariadb-r’: -docker run --name tiledb-mariadb-r -it -d --rm \ - -e MYSQL_ALLOW_EMPTY_PASSWORD=1 tiledb/tiledb-mariadb-r +We launch the container ‘tiledb/tiledb-mariadb-r’ as a daemon, allowing MariaDB to accept an empty password (using an older MySQL variable setting), and name the running image ‘tiledb-mariadb-r’: +docker run --name tiledb-mariadb-r -it -d --rm \ + -e MYSQL_ALLOW_EMPTY_PASSWORD=1 tiledb/tiledb-mariadb-r Access Container Once to Write via TileDB -Using the name given to the running instance, we start an R session -to write data with TileDB: -docker exec -it -u root tiledb-mariadb-r R +Using the name given to the running instance, we start an R session to write data with TileDB: +docker exec -it -u root tiledb-mariadb-r R @@ -134,220 +116,200 @@ Examples Palmer Penguins -With the sessions started as in the previous section, we start an R -session. -> library(tiledb) -> library(palmerpenguins) -> praw <- penguins_raw -> fromDataFrame(praw, "/tmp/penguinsraw") +With the sessions started as in the previous section, we start an R session. +> library(tiledb) +> library(palmerpenguins) +> praw <- penguins_raw +> fromDataFrame(praw, "/tmp/penguinsraw") Access Container Again to Read via RMariaDB -In another shell, we can access the container once more and launch -another R process: -docker exec -it -u root tiledb-mariadb-r R -where we use RMariaDB to access the data via a tibble -object and magrittr pipe -> library(RMariaDB) -> library(dplyr, warn.conflicts=FALSE) -> con <- DBI::dbConnect(RMariaDB::MariaDB(), dbname="test") -> tbl(con, "/tmp/penguinsraw") %>% -+ dplyr::select(contains("Length")) -# Source: lazy query [?? x 2] -# Database: mysql [@localhost:NA/test] - `Culmen Length (mm)` `Flipper Length (mm)` - <dbl> <dbl> - 1 39.1 181 - 2 39.5 186 - 3 40.3 195 - 4 NA NA - 5 36.7 193 - 6 39.3 190 - 7 38.9 181 - 8 39.2 195 - 9 34.1 193 -10 42 190 -# ... with more rows -Note that this R session uses TileDB only via the MyTile plugin which -is activated implicitly via the ‘table location’ (here -/tmp/penguinsraw) of the test database enabling -plugins. -Also note that the query is still ‘lazy’: only column names and the -first ten observations have been retrieved, and the total size is still -unknown as indicated by lazy query [?? x 2]. Adding a -collect() verb materialized the full subset. -> tbl(con, "/tmp/penguinsraw") %>% -+ dplyr::select(contains("Length")) %>% -+ collect() -# A tibble: 344 x 2 - `Culmen Length (mm)` `Flipper Length (mm)` - <dbl> <dbl> - 1 39.1 181 - 2 39.5 186 - 3 40.3 195 - 4 NA NA - 5 36.7 193 - 6 39.3 190 - 7 38.9 181 - 8 39.2 195 - 9 34.1 193 -10 42 190 -# ... with 334 more rows -> -We now see that all 344 rows of this particular result set have been -accessed. +In another shell, we can access the container once more and launch another R process: +docker exec -it -u root tiledb-mariadb-r R +where we use RMariaDB to access the data via a tibble object and magrittr pipe +> library(RMariaDB) +> library(dplyr, warn.conflicts=FALSE) +> con <- DBI::dbConnect(RMariaDB::MariaDB(), dbname="test") +> tbl(con, "/tmp/penguinsraw") %>% ++ dplyr::select(contains("Length")) +# Source: lazy query [?? x 2] +# Database: mysql [@localhost:NA/test] + `Culmen Length (mm)` `Flipper Length (mm)` + <dbl> <dbl> + 1 39.1 181 + 2 39.5 186 + 3 40.3 195 + 4 NA NA + 5 36.7 193 + 6 39.3 190 + 7 38.9 181 + 8 39.2 195 + 9 34.1 193 +10 42 190 +# ... with more rows +Note that this R session uses TileDB only via the MyTile plugin which is activated implicitly via the ‘table location’ (here /tmp/penguinsraw) of the test database enabling plugins. +Also note that the query is still ‘lazy’: only column names and the first ten observations have been retrieved, and the total size is still unknown as indicated by lazy query [?? x 2]. Adding a collect() verb materialized the full subset. +> tbl(con, "/tmp/penguinsraw") %>% ++ dplyr::select(contains("Length")) %>% ++ collect() +# A tibble: 344 x 2 + `Culmen Length (mm)` `Flipper Length (mm)` + <dbl> <dbl> + 1 39.1 181 + 2 39.5 186 + 3 40.3 195 + 4 NA NA + 5 36.7 193 + 6 39.3 190 + 7 38.9 181 + 8 39.2 195 + 9 34.1 193 +10 42 190 +# ... with 334 more rows +> +We now see that all 344 rows of this particular result set have been accessed. Similarly, we can also run summaries on selected column: -> tbl(con, "/tmp/penguinsraw") %>% -+ group_by(Species) %>% -+ summarise(across(starts_with("Flipper"), -+ list(~mean(.x, na.rm=TRUE), ~sd(.x, na.rm=TRUE)))) -# Source: lazy query [?? x 3] -# Database: mysql [@localhost:NA/test] - Species `\`Flipper Length (mm)\`_~me~ `\`Flipper Length (mm)\`_~~ - <chr> <dbl> <dbl> -1 Adelie Penguin (Pyg~ 190. 6.54 -2 Chinstrap penguin (~ 196. 7.13 -3 Gentoo penguin (Pyg~ 217. 6.48 -> +> tbl(con, "/tmp/penguinsraw") %>% ++ group_by(Species) %>% ++ summarise(across(starts_with("Flipper"), ++ list(~mean(.x, na.rm=TRUE), ~sd(.x, na.rm=TRUE)))) +# Source: lazy query [?? x 3] +# Database: mysql [@localhost:NA/test] + Species `\`Flipper Length (mm)\`_~me~ `\`Flipper Length (mm)\`_~~ + <chr> <dbl> <dbl> +1 Adelie Penguin (Pyg~ 190. 6.54 +2 Chinstrap penguin (~ 196. 7.13 +3 Gentoo penguin (Pyg~ 217. 6.48 +> DBI -We can connect directly using the DBI package along with -the RMariaDB package and its MyTile bindings: +We can connect directly using the DBI package along with the RMariaDB package and its MyTile bindings: library(DBI) -con <- dbConnect(RMariaDB::MariaDB(), dbname="test") -res <- dbSendQuery(con, "select * from `/work/penguins` as `q91` limit 10") -df <- dbFetch(res, n = 10) -dbClearResult(res) +con <- dbConnect(RMariaDB::MariaDB(), dbname="test") +res <- dbSendQuery(con, "select * from `/work/penguins` as `q91` limit 10") +df <- dbFetch(res, n = 10) +dbClearResult(res) print(df) -dbDisconnect(con) +dbDisconnect(con) S3 -When using Docker, the container setup needs to be modified to -include the required AWS access environment variables: -docker run --name tiledb-mariadb-r \ - -it -d --rm \ - -v $PWD:/work -w /work \ - -e MYSQL_ALLOW_EMPTY_PASSWORD=1 \ - -e AWS_SECRET_ACCESS_KEY=${AWS_SECRET_ACCESS_KEY} \ - -e AWS_ACCESS_KEY_ID=${AWS_ACCESS_KEY_ID} \ - tiledb/tiledb-mariadb-r -This exports the current working directory (accessed as -$PWD in the shell) as /work inside the -container (via the -v switch), and instructs the container -to start in directory /work (via the -w -switch). -In the following example we also set a TileDB configuration option to -switch AWS regions. -> library(dplyr, warn.conflicts=FALSE) -> # connect as usual -> con <- DBI::dbConnect(RMariaDB::MariaDB(), dbname="test") -> # use connection to update config in order to switch s3 regions -> res1 <- DBI::dbSendQuery(con, "set mytile_tiledb_config=\"vfs.s3.region=us-west-1\";") -> DBI::dbClearResult(res1) -> # run simple query -> tbl(con, "s3://tiledb-public-us-west-1/test-array-4x4") %>% collect() -# A tibble: 16 x 3 - `__dim_0` `__dim_1` `__attr` - <int64> <int64> <dbl> - 1 0 0 0.397 - 2 0 1 0.432 - 3 0 2 0.617 - 4 0 3 0.403 - 5 1 0 0.837 - 6 1 1 0.670 - 7 1 2 0.235 - 8 1 3 0.841 - 9 2 0 0.222 -10 2 1 0.468 -11 2 2 0.970 -12 2 3 0.551 -13 3 0 0.628 -14 3 1 0.0149 -15 3 2 0.0540 -16 3 3 0.445 -> -> DBI::dbDisconnect(con) # close connection +When using Docker, the container setup needs to be modified to include the required AWS access environment variables: +docker run --name tiledb-mariadb-r \ + -it -d --rm \ + -v $PWD:/work -w /work \ + -e MYSQL_ALLOW_EMPTY_PASSWORD=1 \ + -e AWS_SECRET_ACCESS_KEY=${AWS_SECRET_ACCESS_KEY} \ + -e AWS_ACCESS_KEY_ID=${AWS_ACCESS_KEY_ID} \ + tiledb/tiledb-mariadb-r +This exports the current working directory (accessed as $PWD in the shell) as /work inside the container (via the -v switch), and instructs the container to start in directory /work (via the -w switch). +In the following example we also set a TileDB configuration option to switch AWS regions. +> library(dplyr, warn.conflicts=FALSE) +> # connect as usual +> con <- DBI::dbConnect(RMariaDB::MariaDB(), dbname="test") +> # use connection to update config in order to switch s3 regions +> res1 <- DBI::dbSendQuery(con, "set mytile_tiledb_config=\"vfs.s3.region=us-west-1\";") +> DBI::dbClearResult(res1) +> # run simple query +> tbl(con, "s3://tiledb-public-us-west-1/test-array-4x4") %>% collect() +# A tibble: 16 x 3 + `__dim_0` `__dim_1` `__attr` + <int64> <int64> <dbl> + 1 0 0 0.397 + 2 0 1 0.432 + 3 0 2 0.617 + 4 0 3 0.403 + 5 1 0 0.837 + 6 1 1 0.670 + 7 1 2 0.235 + 8 1 3 0.841 + 9 2 0 0.222 +10 2 1 0.468 +11 2 2 0.970 +12 2 3 0.551 +13 3 0 0.628 +14 3 1 0.0149 +15 3 2 0.0540 +16 3 3 0.445 +> +> DBI::dbDisconnect(con) # close connection NYC Taxis -We can write the New York taxi data into TileDB (in the current -directory) after reading it as a csv: -> nyc <- data.table::fread("trip_data_1.csv") -> tiledb::fromDataFrame(nyc, "trip_data_1") -Then we can access it via the path /work/trip_data_1 via -RMariaDB. -> library(dplyr, warn.conflicts=FALSE) -> con <- DBI::dbConnect(RMariaDB::MariaDB(), dbname="test") -> # list column names -> tbl(con, "/work/trip_data_1") %>% colnames() -> tbl(con, "/work/trip_data_1") %>% colnames() - [1] "__tiledb_rows" "dropoff_latitude" "medallion" - [4] "hack_license" "dropoff_longitude" "vendor_id" - [7] "rate_code" "store_and_fwd_flag" "pickup_datetime" -[10] "dropoff_datetime" "trip_time_in_secs" "pickup_latitude" -[13] "passenger_count" "trip_distance" "pickup_longitude" -> # extract one column (here passenger_count) completely and tabulate in R -> tbl(con, "/work/trip_data_1") %>% select(passenger_count) %>% collect() %>% table() -. - 0 1 2 3 4 5 6 9 - 166 10471701 1986196 597485 280992 920006 520066 1 - 208 255 - 1 1 -> # alternatively, run a lazy query -> tbl(con, "/work/trip_data_1") %>% group_by(passenger_count) %>% summarize(nobs = n()) -# Source: lazy query [?? x 2] -# Database: mysql [@localhost:NA/test] - passenger_count nobs - <int> <int64> - 1 0 166 - 2 1 10471701 - 3 2 1986196 - 4 3 597485 - 5 4 280992 - 6 5 920006 - 7 6 520066 - 8 9 1 - 9 208 1 -10 255 1 -> # here the request is actually sent as SQL and the computation is done in the SQL layer -> tbl(con, "/work/trip_data_1") %>% -+ group_by(passenger_count) %>% -+ summarize(nobs = n()) %>% -+ show_query() -<SQL> -SELECT `passenger_count`, COUNT(*) AS `nobs` -FROM `/work/trip_data_1` -GROUP BY `passenger_count` -> # naturally we can also send the query directly to the SQL backend -> sql <- "SELECT passenger_count, count(*) AS n FROM `/work/trip_data_1` GROUP BY passenger_count;" -> DBI::dbGetQuery(con, sql) - passenger_count n -1 0 166 -2 1 10471701 -3 2 1986196 -4 3 597485 -5 4 280992 -6 5 920006 -7 6 520066 -8 9 1 -9 208 1 -10 255 1 -> -> DBI::dbDisconnect(con) # close connection +We can write the New York taxi data into TileDB (in the current directory) after reading it as a csv: +> nyc <- data.table::fread("trip_data_1.csv") +> tiledb::fromDataFrame(nyc, "trip_data_1") +Then we can access it via the path /work/trip_data_1 via RMariaDB. +> library(dplyr, warn.conflicts=FALSE) +> con <- DBI::dbConnect(RMariaDB::MariaDB(), dbname="test") +> # list column names +> tbl(con, "/work/trip_data_1") %>% colnames() +> tbl(con, "/work/trip_data_1") %>% colnames() + [1] "__tiledb_rows" "dropoff_latitude" "medallion" + [4] "hack_license" "dropoff_longitude" "vendor_id" + [7] "rate_code" "store_and_fwd_flag" "pickup_datetime" +[10] "dropoff_datetime" "trip_time_in_secs" "pickup_latitude" +[13] "passenger_count" "trip_distance" "pickup_longitude" +> # extract one column (here passenger_count) completely and tabulate in R +> tbl(con, "/work/trip_data_1") %>% select(passenger_count) %>% collect() %>% table() +. + 0 1 2 3 4 5 6 9 + 166 10471701 1986196 597485 280992 920006 520066 1 + 208 255 + 1 1 +> # alternatively, run a lazy query +> tbl(con, "/work/trip_data_1") %>% group_by(passenger_count) %>% summarize(nobs = n()) +# Source: lazy query [?? x 2] +# Database: mysql [@localhost:NA/test] + passenger_count nobs + <int> <int64> + 1 0 166 + 2 1 10471701 + 3 2 1986196 + 4 3 597485 + 5 4 280992 + 6 5 920006 + 7 6 520066 + 8 9 1 + 9 208 1 +10 255 1 +> # here the request is actually sent as SQL and the computation is done in the SQL layer +> tbl(con, "/work/trip_data_1") %>% ++ group_by(passenger_count) %>% ++ summarize(nobs = n()) %>% ++ show_query() +<SQL> +SELECT `passenger_count`, COUNT(*) AS `nobs` +FROM `/work/trip_data_1` +GROUP BY `passenger_count` +> # naturally we can also send the query directly to the SQL backend +> sql <- "SELECT passenger_count, count(*) AS n FROM `/work/trip_data_1` GROUP BY passenger_count;" +> DBI::dbGetQuery(con, sql) + passenger_count n +1 0 166 +2 1 10471701 +3 2 1986196 +4 3 597485 +5 4 280992 +6 5 920006 +7 6 520066 +8 9 1 +9 208 1 +10 255 1 +> +> DBI::dbDisconnect(con) # close connection Summary -This short vignette demonstrates the use of TileDB-stored data from R -using RMariaDB via the MyTile storage extension to MariaBD. +This short vignette demonstrates the use of TileDB-stored data from R using RMariaDB via the MyTile storage extension to MariaBD. @@ -356,11 +318,11 @@ Summary diff --git a/docs/articles/tiledb-mariadb-examples_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/tiledb-mariadb-examples_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 0000000000..ca349fd6a5 --- /dev/null +++ b/docs/articles/tiledb-mariadb-examples_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. + +document.addEventListener('DOMContentLoaded', function() { + const codeList = document.getElementsByClassName("sourceCode"); + for (var i = 0; i < codeList.length; i++) { + var linkList = codeList[i].getElementsByTagName('a'); + for (var j = 0; j < linkList.length; j++) { + if (linkList[j].innerHTML === "") { + linkList[j].setAttribute('aria-hidden', 'true'); + } + } + } +}); diff --git a/docs/authors.html b/docs/authors.html index 145a22f84f..0eef9fee6c 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -1,5 +1,5 @@ -Authors and Citation • tiledb +Authors and Citation • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -49,11 +49,7 @@ Authors and Citation Authors - . Author, copyright holder. - - - - Dirk Eddelbuettel. Author. + . Author, copyright holder. @@ -66,15 +62,15 @@ Authors Citation Source: DESCRIPTION - TileDB, Inc., Eddelbuettel D (2024). + TileDB, Inc. (2025). tiledb: Modern Database Engine for Complex Data Based on Multi-Dimensional Arrays. -R package version 0.31.0, https://tiledb-inc.github.io/TileDB-R/, https://github.com/TileDB-Inc/TileDB-R. +R package version 0.31.0.1, https://tiledb-inc.github.io/TileDB-R/, https://github.com/TileDB-Inc/TileDB-R. @Manual{, title = {tiledb: Modern Database Engine for Complex Data Based on Multi-Dimensional Arrays}, - author = {{TileDB, Inc.} and Dirk Eddelbuettel}, - year = {2024}, - note = {R package version 0.31.0, https://tiledb-inc.github.io/TileDB-R/}, + author = {{TileDB, Inc.}}, + year = {2025}, + note = {R package version 0.31.0.1, https://tiledb-inc.github.io/TileDB-R/}, url = {https://github.com/TileDB-Inc/TileDB-R}, } @@ -84,11 +80,11 @@ Citation diff --git a/docs/deps/data-deps.txt b/docs/deps/data-deps.txt index 1b877ae225..ca4dfd9c5c 100644 --- a/docs/deps/data-deps.txt +++ b/docs/deps/data-deps.txt @@ -1,4 +1,4 @@ - + diff --git a/docs/index.html b/docs/index.html index cd8955108a..8ebb804b44 100644 --- a/docs/index.html +++ b/docs/index.html @@ -12,7 +12,7 @@ - + @@ -28,7 +28,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -71,7 +71,7 @@ - + The TileDB R package offers an R interface to the modern database by TileDB. @@ -84,19 +84,19 @@ InstallationCRAN and be installed directly via -> install.packages("tiledb") +> install.packages("tiledb") as usual. The most recent released version can be installed from Github using the package remotes. -> if (!requireNamespace("remotes",quietly=TRUE)) install.packages("remotes") -> remotes::install_github("TileDB-Inc/TileDB-R") -... -> library(tiledb) -TileDB R 0.31.0 with TileDB Embedded 2.27.0 on Ubuntu 24.04. -See https://tiledb.com for more information about TileDB. -> help(package=tiledb) +> if (!requireNamespace("remotes",quietly=TRUE)) install.packages("remotes") +> remotes::install_github("TileDB-Inc/TileDB-R") +... +> library(tiledb) +TileDB R 0.31.0 with TileDB Embedded 2.27.0 on Ubuntu 24.04. +See https://tiledb.com for more information about TileDB. +> help(package=tiledb) If the TileDB library is installed in a custom location, you need to pass the explicit path: -> remotes::install_github("TileDB-Inc/TileDB-R", - args="--configure-args='--with-tiledb=/path/to/tiledb'") +> remotes::install_github("TileDB-Inc/TileDB-R", + args="--configure-args='--with-tiledb=/path/to/tiledb'") Note that the TileDB R package is always developed and tested against the latest stable version of TileDB, but should also build against the newest development version. @@ -150,8 +150,7 @@ Citation Developers - Author, copyright holder -Dirk Eddelbuettel Author + Author, copyright holder Isaiah Norton Maintainer @@ -173,11 +172,11 @@ Dev status diff --git a/docs/news/index.html b/docs/news/index.html index 2d9f731da9..ca226604ed 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -1,5 +1,5 @@ -Changelog • tiledb +Changelog • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -53,7 +53,7 @@ tiledb 0.31.0Update unit tests to expect dense current domain Support parentheses in query conditions memory alloc: Accomodate zero buffer size estimate v2 -Apply styler::style_pkg() +Apply styler::style_pkg() Expose include/linking flags for re-using libtiledb in downstream packages Use TileDB Core 2.27.0 @@ -66,12 +66,10 @@ tiledb 0.30.2 tiledb 0.30.1 -This release of the R package builds against TileDB 2.26.1, and has also been tested against earlier releases as well as the development version (#757) - +This release of the R package builds against TileDB 2.26.1, and has also been tested against earlier releases as well as the development version (#757) tiledb 0.30.0 -This release of the R package builds against TileDB 2.26.0, and has also been tested against earlier releases as well as the development version (#745, #749, #750, #754, #755) - +This release of the R package builds against TileDB 2.26.0, and has also been tested against earlier releases as well as the development version (#745, #749, #750, #754, #755) Improvements Error messages displayed when a mismatched external pointer is detected now show both expected and encountered types (#740) NDRectangle objects can now instantiate from more domain data types (#741, #742) @@ -80,8 +78,7 @@ Improvements Documentation -The documentation website now uses favicon symbols for all pages rendered (#739) - +The documentation website now uses favicon symbols for all pages rendered (#739) Build and Test Systems The nighly valgrind matrix now includes release 2.26.0 (#744) @@ -89,17 +86,14 @@ Build and Test Systems Removals -Boolean arguments as.data.frame, as.matrix and as.array to the tiledb_array() accessor, deprecated in release 0.20.0 in July 2023 in favor of the more general return_as="..." form, have been removed. (#751) - +Boolean arguments as.data.frame, as.matrix and as.array to the tiledb_array() accessor, deprecated in release 0.20.0 in July 2023 in favor of the more general return_as="..." form, have been removed. (#751) Deprecation -As BioConductor package still relies on as.data.frame it was temporarily re-admitted as an argument. It is expected to be removed following the upcoming 3.20 release of BioConducto.r (#752) - +As BioConductor package still relies on as.data.frame it was temporarily re-admitted as an argument. It is expected to be removed following the upcoming 3.20 release of BioConducto.r (#752) tiledb 0.29.0 -This release of the R package builds against TileDB 2.25.0, and has also been tested against earlier releases as well as the development version (#728, #736) - +This release of the R package builds against TileDB 2.25.0, and has also been tested against earlier releases as well as the development version (#728, #736) Improvements Three deprecated calls to dump() methods for TileDB Embedded objects now use the preferred streaming alternatives (#727) Two already deprecated functions that are removed in TileDB 2.26.0 are no longer used (#732) @@ -109,20 +103,16 @@ Improvements Build and Test Systems -The nighly valgrind matrix now includes release 2.25.0 (#729) - +The nighly valgrind matrix now includes release 2.25.0 (#729) tiledb 0.28.2 -This release of the R package builds against TileDB 2.24.2, and has also been tested against earlier releases as well as the development version (#725) - +This release of the R package builds against TileDB 2.24.2, and has also been tested against earlier releases as well as the development version (#725) tiledb 0.28.1 -This release of the R package builds against TileDB 2.24.1, and has also been tested against earlier releases as well as the development version (#714, #715, #717, #724) - +This release of the R package builds against TileDB 2.24.1, and has also been tested against earlier releases as well as the development version (#714, #715, #717, #724) Improvements -When creating arrays with fromDataFrame, start and/or end timestamps can now be specified (#719) - +When creating arrays with fromDataFrame, start and/or end timestamps can now be specified (#719) Build and Test Systems The nighly continuous integration matrix now included Core release 2.24.0 and 2.22.0 is dropped (#721) @@ -131,8 +121,7 @@ Build and Test Systems tiledb 0.28.0 -This release of the R package builds against TileDB 2.24.0, and has also been tested against earlier releases as well as the development version (#714, #715, #717) - +This release of the R package builds against TileDB 2.24.0, and has also been tested against earlier releases as well as the development version (#714, #715, #717) Improvements Three internal and unexported helper functions now document more clearly how they can be called explicitly. (#709) Reading and writing of text- and binary files supported by a VFS backend is now supported. (#710) @@ -145,8 +134,7 @@ Build and Test Systems tiledb 0.27.0 -This release of the R package builds against TileDB 2.23.0, and has also been tested against earlier releases as well as the development version (#701, #704) - +This release of the R package builds against TileDB 2.23.0, and has also been tested against earlier releases as well as the development version (#701, #704) Improvements Group elements can now be deleted (#702) Two error messages now show the human-readable type representation instead of the enum counter value (#705) @@ -158,17 +146,14 @@ Build and Test Systems Deprecations -Function libtiledb_array_create_with_key, accessing a deprecated Core function, is now in src/deprecated.cpp and will be removed at later point (#699) - +Function libtiledb_array_create_with_key, accessing a deprecated Core function, is now in src/deprecated.cpp and will be removed at later point (#699) Removals -Functions libtiledb_query_add_range_with_type and libtiledb_query_add_range, deprecated in release 0.17.1 in January 2023, have been now removed (#700). - +Functions libtiledb_query_add_range_with_type and libtiledb_query_add_range, deprecated in release 0.17.1 in January 2023, have been now removed (#700). tiledb 0.26.0 -This release of the R package builds against TileDB 2.22.0, and has also been tested against earlier releases as well as the development version (#679, #686, #693, #696) - +This release of the R package builds against TileDB 2.22.0, and has also been tested against earlier releases as well as the development version (#679, #686, #693, #696) Improvements The display of a filter_list is now labeled correctly as a filter list (@cgiachalis in #681 addressing #678) The Arrow integration has been simplified using nanoarrow returning a single nanoarrow object; an unexported helper function nanoarrow2list() is provided to matching the previous interface (#682, #685) @@ -177,8 +162,7 @@ Improvements Bug Fixes -The column headers now correspond to the column content in the two-column data.frame returns by tiledb_object_walk (#684 closing #683) - +The column headers now correspond to the column content in the two-column data.frame returns by tiledb_object_walk (#684 closing #683) Build and Test Systems The configure and Makevars.in received a minor update correcting small issues (#680) @@ -186,8 +170,7 @@ Build and Test Systems Documentation -A number of minor typographical and grammar errors in the function documentation has been corrected (@cgiachalis in #681) - +A number of minor typographical and grammar errors in the function documentation has been corrected (@cgiachalis in #681) Deprecations Functions tiledb_arrow_array_ptr(), tiledb_arrow_schmea_ptr(), tiledb_arrow_array_del() and tiledb_arrow_schema_del() are deprecated (in favor of using the corresponding nanoarrow functions) and will be removed in a future release (#685) @@ -196,8 +179,7 @@ Deprecations tiledb 0.25.0 -This release of the R package builds against TileDB 2.21.0, and has also been tested against earlier releases as well as the development version (#661, #666, #668, #676, #677) - +This release of the R package builds against TileDB 2.21.0, and has also been tested against earlier releases as well as the development version (#661, #666, #668, #676, #677) Improvements The vendored nanoarrow sources have been update to release 0.4.0, and use of its facilities has been extended (#663) Query conditions can be expressed against non-existing enumeration (i.e., factor) values when TileDB Core 2.21.0 or later is used (#674) @@ -219,8 +201,7 @@ Build and Test Systems tiledb 0.24.0 -This release of the R package builds against TileDB 2.20.0, and has also been tested against earlier releases as well as the development version (#651,#654,#658,#659) - +This release of the R package builds against TileDB 2.20.0, and has also been tested against earlier releases as well as the development version (#651,#654,#658,#659) Improvements Factor level additions now check for possible over in the index type (#645, #646) Aggregate operations can now be performed on dense arrays via a query object with appropriate subarray settings (#650) @@ -233,17 +214,14 @@ Bug Fixes Build and Test Systems -The nightly valgrind run was updated to include release 2.20 (#649) - +The nightly valgrind run was updated to include release 2.20 (#649) Documentation -The DESCRIPTION file now contains a reference to the documentation site in its URL field (#656) - +The DESCRIPTION file now contains a reference to the documentation site in its URL field (#656) tiledb 0.23.0 -This release of the R package builds against TileDB 2.19.0, and has also been tested against earlier releases as well as the development version (#641) - +This release of the R package builds against TileDB 2.19.0, and has also been tested against earlier releases as well as the development version (#641) Improvements A TileDB Array can now be opened in ‘keep open’ mode for subsequent use without re-opening (#630) Arrays with factor (or ordered) variables now grow their factor levels in appending writes (#639) @@ -252,8 +230,7 @@ Improvements Bug Fixes -The read buffer is now correctly sized when implementing VFS serialization (#631) - +The read buffer is now correctly sized when implementing VFS serialization (#631) Build and Test Systems Builds from TileDB Core non-release tarballs are now supported via new configure option (#627) @@ -265,16 +242,14 @@ Build and Test Systems tiledb 0.22.0 -This release of the R package builds against TileDB 2.18.0, TileDB 2.18.1, TileDB 2.18.2 and has also been tested against earlier releases as well as the development version (#620,#621,#624) - +This release of the R package builds against TileDB 2.18.0, TileDB 2.18.1, TileDB 2.18.2 and has also been tested against earlier releases as well as the development version (#620,#621,#624) Improvements Use of TileDB Embedded was upgraded to release 2.18.0 (#620), 2.18.1 (#621), and 2.18.2 (#624) Support for Aggregates has been added (#623) Bug Fixes -When using serializing via VFS (as added in #608) the filehandles is now properly released (#619) - +When using serializing via VFS (as added in #608) the filehandles is now properly released (#619) Build and Test Systems Some tests were refactored slightly for greater robustness (#618) @@ -282,29 +257,23 @@ Build and Test Systems Documentation -The README now contains a badge for the r-universe version (in addition to CRAN) (#617) - +The README now contains a badge for the r-universe version (in addition to CRAN) (#617) tiledb 0.21.3 -This release of the R package builds against TileDB 2.17.4, and has also been tested against earlier releases as well as the development version (#611) - +This release of the R package builds against TileDB 2.17.4, and has also been tested against earlier releases as well as the development version (#611) Improvements -Query conditioning parsing now supports factor index columns other than the standard integer type (#614) - +Query conditioning parsing now supports factor index columns other than the standard integer type (#614) Build and Test Systems -The nightly valgrind run was updated to include release 2.18 (#615) - +The nightly valgrind run was updated to include release 2.18 (#615) Documentation -The pkgdown documentation has been updated for release 0.21.2 (#613) and release 0.21.3 (#616) - +The pkgdown documentation has been updated for release 0.21.2 (#613) and release 0.21.3 (#616) tiledb 0.21.2 -This release of the R package builds against TileDB 2.17.4, and has also been tested against earlier releases as well as the development version (#611) - +This release of the R package builds against TileDB 2.17.4, and has also been tested against earlier releases as well as the development version (#611) Improvements Set conditions are supported in query condition expressions (#597) Query conditions expression parsing via parse_query_conditions was extended simmilarly (#598) @@ -326,13 +295,11 @@ Bug Fixes Build and Test Systems -The nightly valgrind run was updated to include release 2.17 (#603) - +The nightly valgrind run was updated to include release 2.17 (#603) tiledb 0.21.1 -This release of the R package builds against TileDB 2.17.1, and has also been tested against earlier releases as well as the development version (#593) - +This release of the R package builds against TileDB 2.17.1, and has also been tested against earlier releases as well as the development version (#593) Improvements Array schema evolution has been extended to support enumerations (#590, #591) Conversion to and from integer64 (and nanotime) now use package RcppInt64 (#592) @@ -340,13 +307,11 @@ Improvements Bug Fixes -An added sorting of factor levels insert has been reverted (#594) - +An added sorting of factor levels insert has been reverted (#594) tiledb 0.21.0 -This release of the R package builds against TileDB 2.17.0, and has also been tested against earlier releases as well as the development version (#583, #587) - +This release of the R package builds against TileDB 2.17.0, and has also been tested against earlier releases as well as the development version (#583, #587) Improvements Use of TileDB Embedded was upgraded to release 2.17.0 (#583,#587) Built-time configuration of TileDB Embedded can now be accessed as a JSON string (#584) @@ -356,16 +321,13 @@ Improvements tiledb 0.20.3 -This release of the R package builds against TileDB 2.16.2, and has also been tested against earlier releases as well as the development version (#582) - +This release of the R package builds against TileDB 2.16.2, and has also been tested against earlier releases as well as the development version (#582) Improvements -Use of TileDB Embedded was upgraded to release 2.16.2 (#581) - +Use of TileDB Embedded was upgraded to release 2.16.2 (#581) tiledb 0.20.2 -This release of the R package builds against TileDB 2.16.1, and has also been tested against earlier releases as well as the development version (#579) - +This release of the R package builds against TileDB 2.16.1, and has also been tested against earlier releases as well as the development version (#579) Improvements The column buffer allocation is now robust to container overflow sanitizer checks (#574) The array schema version is now accessible via a function (#575) @@ -374,13 +336,11 @@ Improvements Build and Test Systems -The minimal version of TileDB Embedded that can be used with the R package is now release 2.7.0 (#578) - +The minimal version of TileDB Embedded that can be used with the R package is now release 2.7.0 (#578) tiledb 0.19.1 -This release of the R package builds against TileDB 2.15.2, and has also been tested against earlier releases as well as the development version (#534, #541). - +This release of the R package builds against TileDB 2.15.2, and has also been tested against earlier releases as well as the development version (#534, #541). Improvements Query conditions can now be expressed for attributes of type UTF-8 (#529) The startup message now displays the operating system and version (#532) @@ -399,11 +359,9 @@ Build and Test Systems tiledb 0.19.0 -This release of the R package builds against TileDB 2.15.0, and has also been tested against earlier releases as well as the development version (#516, #521). - +This release of the R package builds against TileDB 2.15.0, and has also been tested against earlier releases as well as the development version (#516, #521). Breaking Changes -The validity map coding of nullable strings has been corrected: validity map values of one are now interpreted as valid/non-null for full compatibility with other TileDB projects. Previously written arrays with nullable strings can be read by setting the config option r.legacy_validity_mode to true; the option also permits to write to an older installation. A conversion helper script is provided in scripts/legacy_validity_convert.r. (#517) - +The validity map coding of nullable strings has been corrected: validity map values of one are now interpreted as valid/non-null for full compatibility with other TileDB projects. Previously written arrays with nullable strings can be read by setting the config option r.legacy_validity_mode to true; the option also permits to write to an older installation. A conversion helper script is provided in scripts/legacy_validity_convert.r. (#517) Improvements Attributes can now be created, written and read from in (explicit) UTF8 types (and CHAR and ASCII already behaved correctly with respect to utf8 data) (#510) @@ -415,48 +373,34 @@ Improvements Bug Fixes -The access to JSON-formatted performance statistics has been simplified (#514) - +The access to JSON-formatted performance statistics has been simplified (#514) Build and Test Systems The TileDB Embedded version is now used to determine whether a dampener is needed for the deprecation warning (#511) One of the test data sets included with #517 has been regenerated under an older TileDB version in order to test on more systems (#523) Documentation for Metadata accessors no longer states URIs strings are accepted (#527) - -Deprecations - - -Removals - +Deprecations +Removals tiledb 0.18.0 -This release of the R package builds against TileDB 2.14.0, and has also been tested against earlier releases as well as the development version (#502). - +This release of the R package builds against TileDB 2.14.0, and has also been tested against earlier releases as well as the development version (#502). Improvements -Use of TileDB Embedded was upgraded to release 2.14.0 (#505) - - -Bug Fixes - +Use of TileDB Embedded was upgraded to release 2.14.0 (#505) +Bug Fixes Build and Test Systems The nightly valgrind job matrix was updated to releases 2.13 and 2.14 as well as the branch (#504) The nightly valgrind job show the most recent commit sha1 after updating from release branches (#507) A query condition test for utf8 attributes has been added (#507, #508) - -Deprecations - - -Removals - +Deprecations +Removals tiledb 0.17.1 -This release of the R package builds against TileDB 2.13.1, and has also been tested against earlier releases as well as the development version (#502). - +This release of the R package builds against TileDB 2.13.1, and has also been tested against earlier releases as well as the development version (#502). Improvements Support for Subarrays to set ranges has been extended (#496) Deprecated Core API functions for Array access and range setting are longer used (#496) @@ -476,17 +420,14 @@ Build and Test Systems Deprecations -Functions libtiledb_query_add_range{,_with_type} relying on depecreated Core functionality are deprecated, and will be removed with the Core functions. Subarray range setters are available. This is a mostly internal change. - +Functions libtiledb_query_add_range{,_with_type} relying on depecreated Core functionality are deprecated, and will be removed with the Core functions. Subarray range setters are available. This is a mostly internal change. Removals -Functions libtiledb_query_set_coordinates() and libtiledb_coords() which have been deprecated since June 2000 have been removed. (#497) - +Functions libtiledb_query_set_coordinates() and libtiledb_coords() which have been deprecated since June 2000 have been removed. (#497) tiledb 0.17.0 -This release of the R package builds against TileDB 2.13.0, and has also been tested against earlier releases as well as the development version (#492). - +This release of the R package builds against TileDB 2.13.0, and has also been tested against earlier releases as well as the development version (#492). Improvements Support for testing group URIs on being relative has been added (#478) Logging support at the R and C++ level has been added (#479, #487, #489) @@ -509,8 +450,7 @@ Build and Test Systems tiledb 0.16.0 -This release of the R package builds against TileDB 2.12.0, and has also been tested against earlier releases as well as the development version (#476). - +This release of the R package builds against TileDB 2.12.0, and has also been tested against earlier releases as well as the development version (#476). Improvements Several deprecated API entry points of TileDB Embedded are no longer used (#452, #453) Support for DELETE queries has been added (requires TileDB Embedded 2.12.0 or later) (#455, #456) @@ -539,8 +479,7 @@ Build and Test Systems tiledb 0.15.0 -This release of the R package builds against TileDB 2.11.0, and has also been tested against earlier releases as well as the development version (#451). - +This release of the R package builds against TileDB 2.11.0, and has also been tested against earlier releases as well as the development version (#451). Improvements Support for query conditions has been extended to dense arrays (#447) Support for filter lists has extended to both the data.frame helper and the dimension object constructor (#448) @@ -548,17 +487,14 @@ Improvements Bug Fixes -Small enhancements have been made to the test suite (#450) - +Small enhancements have been made to the test suite (#450) Build and Test Systems -A small enhancement was made to the test system (#450) - +A small enhancement was made to the test system (#450) tiledb 0.14.1 -This release of the R package builds against TileDB 2.10.2, and has also been tested against earlier releases as well as the development version. - +This release of the R package builds against TileDB 2.10.2, and has also been tested against earlier releases as well as the development version. Improvements Use of TileDB Embedded was upgraded to release 2.10.2 (#443) following an earlier update to 2.10.1 (#434) List columns are now supported in reading and writing of data frames by extending cell variable numbers beyond one (#438, #440) @@ -572,13 +508,11 @@ Bug Fixes Build and Test Systems -The nightly valgrind check was updated to Ubuntu 22.04 (#435, #439, #442) - +The nightly valgrind check was updated to Ubuntu 22.04 (#435, #439, #442) tiledb 0.14.0 -This release of the R package builds against TileDB 2.10.0, and has also been tested against earlier releases as well as the development version. - +This release of the R package builds against TileDB 2.10.0, and has also been tested against earlier releases as well as the development version. Improvements Use of TileDB Embedded was upgraded to release 2.10.0 (#432) following earlier updates to 2.9.1 (#415), 2.9.2 (#419), 2.9.3 (#422), 2.9.4 (#427) and 2.9.5 (#430) The BOOL data type is now supported (#416) @@ -590,8 +524,7 @@ Improvements Bug Fixes -The attr setter for Attributes was corrected to support NA settings (#425) - +The attr setter for Attributes was corrected to support NA settings (#425) Build and Test Systems Filter compression tests are skipped on systems lacking AVX2 support (#418) @@ -602,8 +535,7 @@ Build and Test Systems tiledb 0.13.0 -This release of the R package builds against TileDB 2.9.0, and has also been tested against earlier releases as well as the development version. - +This release of the R package builds against TileDB 2.9.0, and has also been tested against earlier releases as well as the development version. Improvements Support for groups has been added for TileDB 2.8 or later (#404) The group member name retrieval can now also return the optional group member name (#399) @@ -615,12 +547,10 @@ Improvements Bug Fixes -Tests for filters have been made more robust (#407, #412) - +Tests for filters have been made more robust (#407, #412) Deprecations -The check() function is now deprecated and schema_check() is provided (#409) - +The check() function is now deprecated and schema_check() is provided (#409) Build and Test Systems Nightly valgrind checks were updated to use current versions (#397, #402) @@ -629,8 +559,7 @@ Build and Test Systems tiledb 0.12.0 -This release of the R package builds against TileDB 2.8.0, and has also been tested against earlier releases as well as the development version. - +This release of the R package builds against TileDB 2.8.0, and has also been tested against earlier releases as well as the development version. Improvements A schedule nightly continuous action now checks current and release-candidate branches of TileDB with the R package under valgrind (#387) Support for Groups was added (#388, #392, #395) @@ -651,8 +580,7 @@ Bug Fixes tiledb 0.11.1 -This release of the R package builds against TileDB 2.6.4, but has also been tested against earlier releases, and the development version. - +This release of the R package builds against TileDB 2.6.4, but has also been tested against earlier releases, and the development version. Improvements Use of TileDB Embedded was upgraded to release 2.6.4 (#384) following an earlier upgrade to 2.6.2 (#359) Creations of arrays from data.frame objects now supports a mode= argument with values ‘ingest’, ‘schema_only’, and ‘append’ (#360) @@ -684,13 +612,11 @@ Documentation Deprecations -The tiledb_dense and tiledb_sparse functions which were deprecated in February 2021 have been removed after a twelve-month grace period. - +The tiledb_dense and tiledb_sparse functions which were deprecated in February 2021 have been removed after a twelve-month grace period. tiledb 0.11.0 -This release of the R package builds against TileDB 2.6.1, but has also been tested against previous releases, and the development version. - +This release of the R package builds against TileDB 2.6.1, but has also been tested against previous releases, and the development version. Improvements Use of TileDB Embedded was upgraded to release 2.6.1 (#354) following an earlier upgrade to 2.6.0 (#340) A cell value getter for dimension was added (#341) @@ -709,8 +635,7 @@ Bug Fixes tiledb 0.10.2 -This release of the R package builds against TileDB 2.5.3, but has been tested against previous releases, and the development version. - +This release of the R package builds against TileDB 2.5.3, but has been tested against previous releases, and the development version. Improvements The stopifnot() assertions now use consistent error messages across all functions (#331) A helper function matching TileDB data types to R types is now exported (#336) @@ -723,20 +648,16 @@ Bug Fixes tiledb 0.10.1 -This release of the R package builds against TileDB 2.5.2, but has been tested against previous releases, and the development version. - +This release of the R package builds against TileDB 2.5.2, but has been tested against previous releases, and the development version. Improvements -An accessor for the most-recent error message string has been added (#327) - +An accessor for the most-recent error message string has been added (#327) Bug Fixes -On Linux, if a pre-made TileDB Embedded library is used, lack of AVX2 instructions is now detected and a suitable build is deployed (#328) - +On Linux, if a pre-made TileDB Embedded library is used, lack of AVX2 instructions is now detected and a suitable build is deployed (#328) tiledb 0.10.0 -This release of the R package builds against TileDB 2.5.1, but has been tested against previous releases, and the development version. - +This release of the R package builds against TileDB 2.5.1, but has been tested against previous releases, and the development version. Improvements CI tests were expanded to also test refactored TileDB Embedded readers (#310), and now deactivated as this is now part of release 2.5.0 (#321) The minimal version of TileDB Embedded that can be used with the R package is now release 2.0.0 (#313) @@ -757,8 +678,7 @@ Bug Fixes tiledb 0.9.7 -This release of the R package builds against TileDB 2.4.0, but has been tested against previous releases and the development version. - +This release of the R package builds against TileDB 2.4.0, but has been tested against previous releases and the development version. Improvements Accessors for context and query statistics were added (returning easily parseable JSON strings) (#293). Initial support for schema evolution was added to add or drop attributes (#294). @@ -780,8 +700,7 @@ Bug Fixes tiledb 0.9.6 -This release of the R package builds against TileDB 2.3.4, but has been tested against previous releases and the development version. - +This release of the R package builds against TileDB 2.3.4, but has been tested against previous releases and the development version. Improvements When retrieving results via the [ operator, incomplete queries generate a warning (#283) The interface to query element size of queries was extended (#282) @@ -801,8 +720,7 @@ Bug Fixes tiledb 0.9.5 -This release of the R package builds against TileDB 2.3.3, but has also been tested against previous releases and the development version. - +This release of the R package builds against TileDB 2.3.3, but has also been tested against previous releases and the development version. Improvements A query condition parser was added for use with standard (non-quoted) R expressions (#267) Windows UCRT builds at CRAN are now supported (#268) @@ -824,8 +742,7 @@ Bug Fixes tiledb 0.9.4 -This release of the R package builds against TileDB 2.3.1, but has also been tested against previous releases and the development version. - +This release of the R package builds against TileDB 2.3.1, but has also been tested against previous releases and the development version. Improvements The build defaults to TileDB Embedded 2.3.* (unless another version is found during build, or explicitly selected) (#258, #264) Query condition support is available for TileDB 2.3.0 or later, allowing (possibly multiple) numerical constraints on attributes (#261) @@ -834,13 +751,11 @@ Improvements Bug Fixes -Dense arrays with more than two dimensions can now be written (#260) - +Dense arrays with more than two dimensions can now be written (#260) tiledb 0.9.3 -This release of the R package builds against TileDB 2.2.9, but has also been tested against previous releases as well as the development version. - +This release of the R package builds against TileDB 2.2.9, but has also been tested against previous releases as well as the development version. Improvements Continuous integration at GitHub is now faster as suggested packages are no longer installed (#250) Arrays can now be written incrementally via the higher-level replacement function arr[] <- obj (#251) @@ -855,8 +770,7 @@ Bug Fixes tiledb 0.9.2 -This release of the R package builds against TileDB 2.2.9, but has also been tested against previous releases as well as the development version. - +This release of the R package builds against TileDB 2.2.9, but has also been tested against previous releases as well as the development version. Improvements Matrix objects can now be returned under range selections (#247) Matrix return get turned on and off with setter / getter functions (#248) @@ -870,8 +784,7 @@ Bug Fixes tiledb 0.9.1 -This release of the R package builds against TileDB 2.2.9, but has also been tested against previous releases as well as the development version. - +This release of the R package builds against TileDB 2.2.9, but has also been tested against previous releases as well as the development version. Improvements A new vignette show use of TileDB array via RMariaDB and the MyTile extension to MariaDB (#221) Matrices can now be returned directly from suitable two-dimensional TileDB arrays (#225) @@ -897,8 +810,7 @@ Bug Fixes tiledb 0.9.0 -This release of the R package builds against TileDB 2.2.4, but has also been tested against two previous release series as well as the development version. - +This release of the R package builds against TileDB 2.2.4, but has also been tested against two previous release series as well as the development version. Improvements The older implementations tiledb_dense and tiledb_sparse are now marked as deprecated in favor of tiledb_array. No removal date is set or planned yet, but it is recommended to migrate to new code. (#180) Updated the underlying TileDB library to use TileDB 2.1.2 on macOS and Linux (when no system library is found) (#181) @@ -932,8 +844,7 @@ Improvements tiledb 0.8.2 -This release of the R package builds against TileDB 2.1.1, but has also been tested against previous releases as well as the development version. - +This release of the R package builds against TileDB 2.1.1, but has also been tested against previous releases as well as the development version. Bug Fixes The tiledb_stats_reset() function is now exported, and tiledb_stats_print() has been re-added as a wrapper to tiledb_stats_dump() (#174) Configuration options for compute and input/output concurrency set only the new TileDB 2.1 configuration options; documentation on how to checking values has been expanded. (#175) @@ -943,8 +854,7 @@ Bug Fixes tiledb 0.8.1 -This release of the R package supports TileDB 2.1.0, but has also been tested against the previous release TileDB 2.0.8. - +This release of the R package supports TileDB 2.1.0, but has also been tested against the previous release TileDB 2.0.8. Improvements R-based metadata accessors have been extended to also support tiledb_array arrays (#169) configure now also checks the hardware platform before attempting a download of a prebuilt library (#170) @@ -952,13 +862,11 @@ Improvements Bug Fixes -A typo in the manual page source, copied three more times, has been corrected (#167) - +A typo in the manual page source, copied three more times, has been corrected (#167) tiledb 0.8.0 -This release of the R package supports TileDB 2.0.8, but has also been tested against the previous release TileDB 1.7.7. - +This release of the R package supports TileDB 2.0.8, but has also been tested against the previous release TileDB 1.7.7. Improvements A new function limitTileDBCores() controls resource use, it is being used in tests (#139) The function tiledb_get_context() is now exported (#140) @@ -983,8 +891,7 @@ Bug Fixes tiledb 0.7.1 This release of the R package supports TileDB 1.7.7 and TileDB 2.0.5 - - + Improvements Range selection for tiledb_array objects can get/set matrices defining range (#132) The show methods are now consistently exported and documented (#134) @@ -997,14 +904,12 @@ Improvements Bug Fixes -A character conversion when retrieving array metadata resulting in an out-of-bounds reads has been corrected (#137) - +A character conversion when retrieving array metadata resulting in an out-of-bounds reads has been corrected (#137) tiledb 0.7.0 This release of the R package supports TileDB 1.7.7 and TileDB 2.0.5 - - + Improvements All S4 classes are now consistently documented or aliased (#117) If needed, the build system now builds TileDB and its required component (#118) @@ -1019,8 +924,7 @@ Improvements tiledb 0.6.0 This release of the R package supports TileDB 1.7.7 and TileDB 2.0.0 - - + Improvements Added support for heterogenous domains Added support for string dimensions @@ -1036,40 +940,34 @@ Improvements Changes -Dimension attributes must now be named - +Dimension attributes must now be named tiledb 0.5.0 -This release of the R package builds against the 1.7.5 releases of TileDB. - +This release of the R package builds against the 1.7.5 releases of TileDB. Improvements -Added support for i) multi-range subarrays, ii) incomplete queries, -result size estimation and ‘time travel’ at to time-points has been added #105 - - +Added support for i) multi-range subarrays, ii) incomplete queries,result size estimation and ‘time travel’ at to time-points has been added #105 + Added additional support for metadata #106 tiledb 0.4.0 -This release of the R package builds against the 1.7.* releases of tiledb. - +This release of the R package builds against the 1.7.* releases of tiledb. Improvements -This release contains increased coverage of the underlying API, additional documentation as well as unit tests. - +This release contains increased coverage of the underlying API, additional documentation as well as unit tests. diff --git a/docs/pkgdown.js b/docs/pkgdown.js index 9757bf9ef2..1a99c65f5c 100644 --- a/docs/pkgdown.js +++ b/docs/pkgdown.js @@ -152,3 +152,11 @@ async function searchFuse(query, callback) { }); }); })(window.jQuery || window.$) + +document.addEventListener('keydown', function(event) { + // Check if the pressed key is '/' + if (event.key === '/') { + event.preventDefault(); // Prevent any default action associated with the '/' key + document.getElementById('search-input').focus(); // Set focus to the search input + } +}); diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index f50de19444..8098c90ca7 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,5 +1,5 @@ -pandoc: 3.1.3 -pkgdown: 2.1.0 +pandoc: 2.9.2.1 +pkgdown: 2.1.1 pkgdown_sha: ~ articles: data-ingestion-from-sql: data-ingestion-from-sql.html @@ -7,7 +7,7 @@ articles: installation-options: installation-options.html introduction: introduction.html tiledb-mariadb-examples: tiledb-mariadb-examples.html -last_built: 2024-12-12T15:49Z +last_built: 2025-01-14T19:21Z urls: reference: https://tiledb-inc.github.io/TileDB-R/reference article: https://tiledb-inc.github.io/TileDB-R/articles diff --git a/docs/reference/array_consolidate.html b/docs/reference/array_consolidate.html index ceb1e5aba3..776fadc1b4 100644 --- a/docs/reference/array_consolidate.html +++ b/docs/reference/array_consolidate.html @@ -1,5 +1,5 @@ -Consolidate fragments of a TileDB Array — array_consolidate • tiledbConsolidate fragments of a TileDB Array — array_consolidate • tiledbtiledb - 0.31.0 + 0.31.0.1 @@ -103,11 +103,11 @@ Value diff --git a/docs/reference/array_vacuum.html b/docs/reference/array_vacuum.html index cbffc1efe5..d98a4991fa 100644 --- a/docs/reference/array_vacuum.html +++ b/docs/reference/array_vacuum.html @@ -1,5 +1,5 @@ -After consolidation, remove consolidated fragments of a TileDB Array — array_vacuum • tiledbAfter consolidation, remove consolidated fragments of a TileDB Array — array_vacuum • tiledbtiledb - 0.31.0 + 0.31.0.1 @@ -103,11 +103,11 @@ Details diff --git a/docs/reference/as.data.frame.tiledb_config.html b/docs/reference/as.data.frame.tiledb_config.html index 29000b538a..9fcaca314b 100644 --- a/docs/reference/as.data.frame.tiledb_config.html +++ b/docs/reference/as.data.frame.tiledb_config.html @@ -1,5 +1,5 @@ -Convert a tiledb_config object to a R data.frame — as.data.frame.tiledb_config • tiledb +Convert a tiledb_config object to a R data.frame — as.data.frame.tiledb_config • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -392,11 +392,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/as.vector.tiledb_config.html b/docs/reference/as.vector.tiledb_config.html index 5d069349f0..e7a8e16edc 100644 --- a/docs/reference/as.vector.tiledb_config.html +++ b/docs/reference/as.vector.tiledb_config.html @@ -1,5 +1,5 @@ -Convert a tiledb_config object to a R vector — as.vector.tiledb_config • tiledb +Convert a tiledb_config object to a R vector — as.vector.tiledb_config • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -390,11 +390,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/attrs-set-tiledb_array-method.html b/docs/reference/attrs-set-tiledb_array-method.html index bcbc419dd9..2c64564a6e 100644 --- a/docs/reference/attrs-set-tiledb_array-method.html +++ b/docs/reference/attrs-set-tiledb_array-method.html @@ -1,5 +1,5 @@ -Selects attributes for the given TileDB array — attrs<-,tiledb_array-method • tiledb +Selects attributes for the given TileDB array — attrs<-,tiledb_array-method • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -81,11 +81,11 @@ Value diff --git a/docs/reference/attrs-tiledb_array-ANY-method.html b/docs/reference/attrs-tiledb_array-ANY-method.html index f95ab1fa6e..476d9c86ff 100644 --- a/docs/reference/attrs-tiledb_array-ANY-method.html +++ b/docs/reference/attrs-tiledb_array-ANY-method.html @@ -1,5 +1,5 @@ -Retrieve attributes from tiledb_array object — attrs,tiledb_array,ANY-method • tiledbRetrieve attributes from tiledb_array object — attrs,tiledb_array,ANY-method • tiledbtiledb - 0.31.0 + 0.31.0.1 @@ -82,11 +82,11 @@ Value diff --git a/docs/reference/attrs-tiledb_array_schema-ANY-method.html b/docs/reference/attrs-tiledb_array_schema-ANY-method.html index 7c9859a847..08792afc8c 100644 --- a/docs/reference/attrs-tiledb_array_schema-ANY-method.html +++ b/docs/reference/attrs-tiledb_array_schema-ANY-method.html @@ -1,5 +1,5 @@ -Returns a list of all tiledb_attr objects associated with the tiledb_array_schema — attrs,tiledb_array_schema,ANY-method • tiledb +Returns a list of all tiledb_attr objects associated with the tiledb_array_schema — attrs,tiledb_array_schema,ANY-method • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -62,7 +62,7 @@ Argumentsobject -tiledb_array_schema +A TileDB Schema object idx @@ -75,7 +75,7 @@ Arguments Value - a list of tiledb_attr objects + A list of tiledb_attr objects @@ -108,11 +108,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/attrs-tiledb_array_schema-character-method.html b/docs/reference/attrs-tiledb_array_schema-character-method.html index 20b9e0598b..74a2c867ca 100644 --- a/docs/reference/attrs-tiledb_array_schema-character-method.html +++ b/docs/reference/attrs-tiledb_array_schema-character-method.html @@ -1,5 +1,5 @@ -Returns a tiledb_attr object associated with the tiledb_array_schema with a given name. — attrs,tiledb_array_schema,character-method • tiledb +Returns a tiledb_attr object associated with the tiledb_array_schema with a given name. — attrs,tiledb_array_schema,character-method • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -62,7 +62,7 @@ Argumentsobject -tiledb_array_schema +A TileDB Schema object idx @@ -75,7 +75,7 @@ Arguments Value - a tiledb_attr object + A tiledb_attr object @@ -95,11 +95,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/attrs-tiledb_array_schema-numeric-method.html b/docs/reference/attrs-tiledb_array_schema-numeric-method.html index 948b849bc4..6bb04eb131 100644 --- a/docs/reference/attrs-tiledb_array_schema-numeric-method.html +++ b/docs/reference/attrs-tiledb_array_schema-numeric-method.html @@ -1,5 +1,5 @@ -Returns a tiledb_attr object associated with the tiledb_array_schema with a given index — attrs,tiledb_array_schema,numeric-method • tiledb +Returns a tiledb_attr object associated with the tiledb_array_schema with a given index — attrs,tiledb_array_schema,numeric-method • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -62,7 +62,7 @@ Argumentsobject -tiledb_array_schema +A TileDB Schema object idx @@ -75,7 +75,7 @@ Arguments Value - a tiledb_attr object + A tiledb_attr object @@ -95,11 +95,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/cell_order-tiledb_array_schema-method.html b/docs/reference/cell_order-tiledb_array_schema-method.html index b9b9c8eb06..f4a00f530f 100644 --- a/docs/reference/cell_order-tiledb_array_schema-method.html +++ b/docs/reference/cell_order-tiledb_array_schema-method.html @@ -1,5 +1,5 @@ -Returns the cell layout string associated with the tiledb_array_schema — cell_order,tiledb_array_schema-method • tiledb +Returns the cell layout string associated with the tiledb_array_schema — cell_order,tiledb_array_schema-method • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -62,20 +62,24 @@ Argumentsobject -tiledb object +A TileDB Schema object + + Value + A character string with cell's layout, e.g., "COL_MAJOR". + diff --git a/docs/reference/completedBatched.html b/docs/reference/completedBatched.html index 892f682334..01ef8d0da7 100644 --- a/docs/reference/completedBatched.html +++ b/docs/reference/completedBatched.html @@ -1,5 +1,5 @@ -Check ‘batched’ query for completion — completedBatched • tiledbCheck ‘batched’ query for completion — completedBatched • tiledbtiledb - 0.31.0 + 0.31.0.1 @@ -83,11 +83,11 @@ Value diff --git a/docs/reference/config-tiledb_ctx-method.html b/docs/reference/config-tiledb_ctx-method.html index cc94830b61..9cea2b6080 100644 --- a/docs/reference/config-tiledb_ctx-method.html +++ b/docs/reference/config-tiledb_ctx-method.html @@ -1,5 +1,5 @@ -Retrieve the tiledb_config object from the tiledb_ctx — config,tiledb_ctx-method • tiledb +Retrieve the tiledb_config object from the tiledb_ctx — config,tiledb_ctx-method • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -85,11 +85,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/createBatched.html b/docs/reference/createBatched.html index 014038e547..96531fd689 100644 --- a/docs/reference/createBatched.html +++ b/docs/reference/createBatched.html @@ -1,5 +1,5 @@ -Create a ‘batched’ query object — createBatched • tiledbCreate a ‘batched’ query object — createBatched • tiledbtiledb - 0.31.0 + 0.31.0.1 @@ -88,11 +88,11 @@ Details diff --git a/docs/reference/datatype-tiledb_attr-method.html b/docs/reference/datatype-tiledb_attr-method.html index 9721358d38..e55951f01b 100644 --- a/docs/reference/datatype-tiledb_attr-method.html +++ b/docs/reference/datatype-tiledb_attr-method.html @@ -1,5 +1,5 @@ -Return the tiledb_attr datatype — datatype,tiledb_attr-method • tiledb +Return the tiledb_attr datatype — datatype,tiledb_attr-method • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -87,11 +87,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/datatype-tiledb_dim-method.html b/docs/reference/datatype-tiledb_dim-method.html index b287c4e9cc..5e98247df8 100644 --- a/docs/reference/datatype-tiledb_dim-method.html +++ b/docs/reference/datatype-tiledb_dim-method.html @@ -1,5 +1,5 @@ -Return the tiledb_dim datatype — datatype,tiledb_dim-method • tiledb +Return the tiledb_dim datatype — datatype,tiledb_dim-method • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -62,12 +62,12 @@ Argumentsobject -tiledb_dim object +A tiledb_dim object Value - tiledb datatype string + A character string with tiledb's datatype. @@ -83,11 +83,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/datatype-tiledb_domain-method.html b/docs/reference/datatype-tiledb_domain-method.html index 1d4689c4f3..a67fd407ae 100644 --- a/docs/reference/datatype-tiledb_domain-method.html +++ b/docs/reference/datatype-tiledb_domain-method.html @@ -1,5 +1,5 @@ -Returns the tiledb_domain TileDB type string — datatype,tiledb_domain-method • tiledb +Returns the tiledb_domain TileDB type string — datatype,tiledb_domain-method • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -86,11 +86,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/datetimes_as_int64-set-tiledb_array-method.html b/docs/reference/datetimes_as_int64-set-tiledb_array-method.html index a2fdce73eb..5bda59c128 100644 --- a/docs/reference/datetimes_as_int64-set-tiledb_array-method.html +++ b/docs/reference/datetimes_as_int64-set-tiledb_array-method.html @@ -1,5 +1,5 @@ -Set datetimes_as_int64 toggle — datetimes_as_int64<- • tiledbSet datetimes_as_int64 toggle — datetimes_as_int64<- • tiledbtiledb - 0.31.0 + 0.31.0.1 @@ -93,11 +93,11 @@ Value diff --git a/docs/reference/datetimes_as_int64-tiledb_array-method.html b/docs/reference/datetimes_as_int64-tiledb_array-method.html index 16ba610612..aace3a0b41 100644 --- a/docs/reference/datetimes_as_int64-tiledb_array-method.html +++ b/docs/reference/datetimes_as_int64-tiledb_array-method.html @@ -1,5 +1,5 @@ -Retrieve datetimes_as_int64 toggle — datetimes_as_int64 • tiledbRetrieve datetimes_as_int64 toggle — datetimes_as_int64 • tiledbtiledb - 0.31.0 + 0.31.0.1 @@ -90,11 +90,11 @@ Value diff --git a/docs/reference/describe.html b/docs/reference/describe.html index a5e93448b1..5c3333aaa9 100644 --- a/docs/reference/describe.html +++ b/docs/reference/describe.html @@ -1,5 +1,5 @@ -Describe a TileDB array schema via code to create it — describe • tiledbDescribe a TileDB array schema via code to create it — describe • tiledb Skip to contents @@ -9,7 +9,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -78,11 +78,11 @@ Value diff --git a/docs/reference/dim.tiledb_array_schema.html b/docs/reference/dim.tiledb_array_schema.html index 26fcb447ef..e3465c5b77 100644 --- a/docs/reference/dim.tiledb_array_schema.html +++ b/docs/reference/dim.tiledb_array_schema.html @@ -1,5 +1,5 @@ -Retrieve the dimension (domain extent) of the domain — dim.tiledb_array_schema • tiledb +Retrieve the dimension (domain extent) of the domain — dim.tiledb_array_schema • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -62,7 +62,7 @@ Argumentsx -tiledb_array_schema +A TileDB Schema object @@ -87,11 +87,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/dim.tiledb_dim.html b/docs/reference/dim.tiledb_dim.html index baad9d0a84..b4da1bb552 100644 --- a/docs/reference/dim.tiledb_dim.html +++ b/docs/reference/dim.tiledb_dim.html @@ -1,5 +1,5 @@ -Retrieves the dimension of the tiledb_dim domain — dim.tiledb_dim • tiledb +Retrieves the dimension of the tiledb_dim domain — dim.tiledb_dim • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -62,12 +62,12 @@ Argumentsx -tiledb_dim object +A tiledb_dim object Value - a vector of the tile_dim domain type, of the dim domain dimension (extent) + A vector of the tile_dim domain type, of the dim domain dimension (extent) @@ -83,11 +83,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/dim.tiledb_domain.html b/docs/reference/dim.tiledb_domain.html index 9588671f6d..7f98ae09d3 100644 --- a/docs/reference/dim.tiledb_domain.html +++ b/docs/reference/dim.tiledb_domain.html @@ -1,5 +1,5 @@ -Retrieve the dimension (domain extent) of the domain — dim.tiledb_domain • tiledb +Retrieve the dimension (domain extent) of the domain — dim.tiledb_domain • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -86,11 +86,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/dimensions-tiledb_array_schema-method.html b/docs/reference/dimensions-tiledb_array_schema-method.html index 2435fc863b..227ec18c99 100644 --- a/docs/reference/dimensions-tiledb_array_schema-method.html +++ b/docs/reference/dimensions-tiledb_array_schema-method.html @@ -1,5 +1,5 @@ -Returns a list of tiledb_dim objects associated with the tiledb_array_schema — dimensions,tiledb_array_schema-method • tiledb +Returns a list of tiledb_dim objects associated with the tiledb_array_schema — dimensions,tiledb_array_schema-method • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -62,12 +62,12 @@ Argumentsobject -tiledb_array_schema +A TileDB Schema object Value - a list of tiledb_dim objects + A list of tiledb_dim objects @@ -100,11 +100,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/dimensions-tiledb_domain-method.html b/docs/reference/dimensions-tiledb_domain-method.html index bd6e4bc266..40cdc41eb0 100644 --- a/docs/reference/dimensions-tiledb_domain-method.html +++ b/docs/reference/dimensions-tiledb_domain-method.html @@ -1,5 +1,5 @@ -Returns a list of the tiledb_domain dimension objects — dimensions,tiledb_domain-method • tiledb +Returns a list of the tiledb_domain dimension objects — dimensions,tiledb_domain-method • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -99,11 +99,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/domain-tiledb_array_schema-method.html b/docs/reference/domain-tiledb_array_schema-method.html index 1c8f432bfb..6fcbaf3137 100644 --- a/docs/reference/domain-tiledb_array_schema-method.html +++ b/docs/reference/domain-tiledb_array_schema-method.html @@ -1,5 +1,5 @@ -Returns the tiledb_domain object associated with a given tiledb_array_schema — domain,tiledb_array_schema-method • tiledb +Returns the tiledb_domain object associated with a given tiledb_array_schema — domain,tiledb_array_schema-method • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -62,9 +62,13 @@ Argumentsobject -tiledb_array_schema +A TileDB Schema object + + Value + A tiledb_domain object + Examples @@ -82,11 +86,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/domain-tiledb_dim-method.html b/docs/reference/domain-tiledb_dim-method.html index 057c340931..01b7546a27 100644 --- a/docs/reference/domain-tiledb_dim-method.html +++ b/docs/reference/domain-tiledb_dim-method.html @@ -1,5 +1,5 @@ -Return the tiledb_dim domain — domain,tiledb_dim-method • tiledb +Return the tiledb_dim domain — domain,tiledb_dim-method • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -62,7 +62,7 @@ Argumentsobject -tiledb_dim object +A tiledb_dim object @@ -83,11 +83,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/dot-core_info.html b/docs/reference/dot-core_info.html index 50854e5e86..e36f295511 100644 --- a/docs/reference/dot-core_info.html +++ b/docs/reference/dot-core_info.html @@ -1,5 +1,5 @@ -libtiledb Information — .core_info • tiledb +libtiledb Information — .core_info • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -86,11 +86,11 @@ Checking the Examples .core_info() -#> version libtype -#> "2.27.0" "system" +#> version libtype +#> "2.27.0" "vendored" .core_hash() -#> [1] "17c9b4d820870f7c171fccf2be8fdfea" +#> [1] "712cb7e256376af4fbfecc51290a4241" @@ -99,11 +99,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/dot-pkg_config.html b/docs/reference/dot-pkg_config.html index c13faa4c2c..174a0f304d 100644 --- a/docs/reference/dot-pkg_config.html +++ b/docs/reference/dot-pkg_config.html @@ -1,5 +1,5 @@ -Compiler Arguments for Using libtiledb — .pkg_config • tiledbCompiler Arguments for Using libtiledb — .pkg_config • tiledb Skip to contents @@ -9,7 +9,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -79,9 +79,9 @@ Value Examples .pkg_config() -#> [1] "-I/usr/local/include" +#> [1] "-I/tmp/RtmpiRigbQ/temp_libpath556b1464bc75e/tiledb/include -I/tmp/RtmpiRigbQ/temp_libpath556b1464bc75e/tiledb/tiledb/include" .pkg_config("PKG_CXX_LIBS") -#> [1] "-L/usr/local/lib -ltiledb" +#> [1] "-ltiledb -L/tmp/RtmpiRigbQ/temp_libpath556b1464bc75e/tiledb/lib -L/tmp/RtmpiRigbQ/temp_libpath556b1464bc75e/tiledb/tiledb/lib" @@ -90,11 +90,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/extended-set-tiledb_array-method.html b/docs/reference/extended-set-tiledb_array-method.html index 4618988929..0149ea9749 100644 --- a/docs/reference/extended-set-tiledb_array-method.html +++ b/docs/reference/extended-set-tiledb_array-method.html @@ -1,5 +1,5 @@ -Set data.frame extended return columns toggle — extended<- • tiledbSet data.frame extended return columns toggle — extended<- • tiledbtiledb - 0.31.0 + 0.31.0.1 @@ -87,11 +87,11 @@ Value diff --git a/docs/reference/extended-tiledb_array-method.html b/docs/reference/extended-tiledb_array-method.html index fef6d703a6..29ad827156 100644 --- a/docs/reference/extended-tiledb_array-method.html +++ b/docs/reference/extended-tiledb_array-method.html @@ -1,5 +1,5 @@ -Retrieve data.frame extended returns columns toggle — extended • tiledbRetrieve data.frame extended returns columns toggle — extended • tiledbtiledb - 0.31.0 + 0.31.0.1 @@ -84,11 +84,11 @@ Value diff --git a/docs/reference/fetchBatched.html b/docs/reference/fetchBatched.html index f4ce306d49..4d117316bd 100644 --- a/docs/reference/fetchBatched.html +++ b/docs/reference/fetchBatched.html @@ -1,5 +1,5 @@ -Run a ‘batched’ query — fetchBatched • tiledbRun a ‘batched’ query — fetchBatched • tiledbtiledb - 0.31.0 + 0.31.0.1 @@ -92,11 +92,11 @@ Details diff --git a/docs/reference/filter_list-set-tiledb_attr-method.html b/docs/reference/filter_list-set-tiledb_attr-method.html index aba612335b..a803608564 100644 --- a/docs/reference/filter_list-set-tiledb_attr-method.html +++ b/docs/reference/filter_list-set-tiledb_attr-method.html @@ -1,5 +1,5 @@ -Sets the TileDB Filter List for the TileDB Attribute object — filter_list<-,tiledb_attr-method • tiledb +Sets the TileDB Filter List for the TileDB Attribute object — filter_list<-,tiledb_attr-method • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -79,11 +79,11 @@ Value diff --git a/docs/reference/filter_list-set-tiledb_dim-method.html b/docs/reference/filter_list-set-tiledb_dim-method.html index b11f369606..d7a0418c30 100644 --- a/docs/reference/filter_list-set-tiledb_dim-method.html +++ b/docs/reference/filter_list-set-tiledb_dim-method.html @@ -1,5 +1,5 @@ -Sets the TileDB Filter List for the TileDB Dimension object — filter_list<-,tiledb_dim-method • tiledb +Sets the TileDB Filter List for the TileDB Dimension object — filter_list<-,tiledb_dim-method • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -62,7 +62,7 @@ Argumentsx -TileDB Dimension +A tiledb_dim object value @@ -79,11 +79,11 @@ Value diff --git a/docs/reference/filter_list-tiledb_array_schema-method.html b/docs/reference/filter_list-tiledb_array_schema-method.html index 98baffdf54..59f87c52e5 100644 --- a/docs/reference/filter_list-tiledb_array_schema-method.html +++ b/docs/reference/filter_list-tiledb_array_schema-method.html @@ -1,5 +1,5 @@ -Returns the offsets and coordinate filter_lists associated with the tiledb_array_schema — filter_list,tiledb_array_schema-method • tiledb +Returns the offsets and coordinate filter_lists associated with the tiledb_array_schema — filter_list,tiledb_array_schema-method • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -62,12 +62,12 @@ Argumentsobject -tiledb_array_schema +A TileDB Schema object Value - a list of tiledb_filter_list objects + A list of tiledb_filter_list objects diff --git a/docs/reference/filter_list-tiledb_attr-method.html b/docs/reference/filter_list-tiledb_attr-method.html index 12e3dd5797..185b2f164f 100644 --- a/docs/reference/filter_list-tiledb_attr-method.html +++ b/docs/reference/filter_list-tiledb_attr-method.html @@ -1,5 +1,5 @@ -Returns the TileDB Filter List object associated with the given TileDB Attribute — filter_list,tiledb_attr-method • tiledb +Returns the TileDB Filter List object associated with the given TileDB Attribute — filter_list,tiledb_attr-method • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -86,11 +86,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton.
This step uses the DBI abstraction. A compliant backend driver can be -loaded via dbDriver, and a connection can be established -via dbConnect using appropriate arguments -dbname, user, password, -host, and port, as needed, with proper -dispatching the implementation provided by the driver. The details -depend on the chosen backend, this can be as simple as -con <- dbConnect(RSQLite::SQLite(), ":memory:") in the -case of RSQLite -and an in-memory (and likely transient) database.
dbDriver
dbConnect
dbname
user
password
host
port
con <- dbConnect(RSQLite::SQLite(), ":memory:")
This step uses the DBI abstraction. A compliant backend driver can be loaded via dbDriver, and a connection can be established via dbConnect using appropriate arguments dbname, user, password, host, and port, as needed, with proper dispatching the implementation provided by the driver. The details depend on the chosen backend, this can be as simple as con <- dbConnect(RSQLite::SQLite(), ":memory:") in the case of RSQLite and an in-memory (and likely transient) database.
## a local SQL db we have here -- about 617k rows dbSetup <- function() { @@ -145,11 +119,7 @@ Connect to Database Fetch Data -In the next step we fetch the data—and for simplicity issue just one -select statement returning a single data.frame -(or here a data.table variant). In larger-than-memory -settings the SQL query could easily bucket by symbols, or date range, or -… +In the next step we fetch the data—and for simplicity issue just one select statement returning a single data.frame (or here a data.table variant). In larger-than-memory settings the SQL query could easily bucket by symbols, or date range, or … getDataFromSQL <- function() { con <- dbSetup() @@ -163,12 +133,7 @@ Fetch Data Writing Data to TileDB -Having read the data into memory we can use the TileDB R function -fromDataFrame. It has numerous option to configure, as well -as sensible defaults (to for example enable ZSTD compression). Here we -select the first two columns for symbol and data as dimensions. Symbols, -being text, do not set a domain set. For the date we set two ‘safe’ -outer values for the range. +Having read the data into memory we can use the TileDB R function fromDataFrame. It has numerous option to configure, as well as sensible defaults (to for example enable ZSTD compression). Here we select the first two columns for symbol and data as dimensions. Symbols, being text, do not set a domain set. For the date we set two ‘safe’ outer values for the range. storeDataTDB <- function(dat, uri) { fromDataFrame(dat, uri, @@ -176,16 +141,11 @@ Writing Data to TileDB tile_domain=list(date=c(as.numeric(as.Date("1985-01-01")), as.numeric(as.Date("2030-12-31"))))) } -The mode="append" argument of fromDataFrame -can be used to append to an existing array to support chunked -operation. +The mode="append" argument of fromDataFrame can be used to append to an existing array to support chunked operation. Reading Data Back In -Reading data from TileDB is a very standard operation of opening the -URI, possibly specifying the return type and possibly subsetting by -dimension values, or attributes. Here, for simplicity, we just read -everything. +Reading data from TileDB is a very standard operation of opening the URI, possibly specifying the return type and possibly subsetting by dimension values, or attributes. Here, for simplicity, we just read everything. getDataTDB <- function(uri) { set_allocation_size_preference(1e7) # larger than local default value @@ -206,21 +166,13 @@ Reading Data Back In See Also -The vignette TileDB MariaDB -Examples shows to use MariaDB via the MyTile integration of TileDB -as a direct backend. -The TileDB -R Tutorial at useR! 2021 contained a worked example of writing -much larger data set in chunks. The process is very similar to -the simple example we showed here – and in addition requires a suffient -domain range for the dimension along with a (sequential or parallel) -loop of reading chunks and writing them to TileDB. +The vignette TileDB MariaDB Examples shows to use MariaDB via the MyTile integration of TileDB as a direct backend. +The TileDB R Tutorial at useR! 2021 contained a worked example of writing much larger data set in chunks. The process is very similar to the simple example we showed here – and in addition requires a suffient domain range for the dimension along with a (sequential or parallel) loop of reading chunks and writing them to TileDB. Summary -This vignette provides a commented walk-through of a worked example -of a SQL-to-TileDB data ingestion. +This vignette provides a commented walk-through of a worked example of a SQL-to-TileDB data ingestion. @@ -229,11 +181,11 @@ Summary diff --git a/docs/articles/data-ingestion-from-sql_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/data-ingestion-from-sql_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 0000000000..ca349fd6a5 --- /dev/null +++ b/docs/articles/data-ingestion-from-sql_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. + +document.addEventListener('DOMContentLoaded', function() { + const codeList = document.getElementsByClassName("sourceCode"); + for (var i = 0; i < codeList.length; i++) { + var linkList = codeList[i].getElementsByTagName('a'); + for (var j = 0; j < linkList.length; j++) { + if (linkList[j].innerHTML === "") { + linkList[j].setAttribute('aria-hidden', 'true'); + } + } + } +}); diff --git a/docs/articles/documentation.html b/docs/articles/documentation.html index 48c90de3c6..3ec793d97e 100644 --- a/docs/articles/documentation.html +++ b/docs/articles/documentation.html @@ -12,7 +12,7 @@ - + @@ -26,7 +26,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -68,8 +68,7 @@ - - + TileDB API Documentation @@ -86,15 +85,11 @@ TileDB API Documentation %\VignetteEngine{simplermarkdown::mdweave_to_html} %\VignetteEncoding{UTF-8} --> -This document follows the TileDB API usage -examples. A shorter introductory -vignette is also available. +This document follows the TileDB API usage examples. A shorter introductory vignette is also available. Prelimaries -We will show two initial and basic examples for a dense and sparse -array simply to create array data on disk to refer to later in examples -that follow. +We will show two initial and basic examples for a dense and sparse array simply to create array data on disk to refer to later in examples that follow. library(tiledb) @@ -1304,11 +1299,11 @@ Catching Errors diff --git a/docs/articles/documentation_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/documentation_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 0000000000..ca349fd6a5 --- /dev/null +++ b/docs/articles/documentation_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. + +document.addEventListener('DOMContentLoaded', function() { + const codeList = document.getElementsByClassName("sourceCode"); + for (var i = 0; i < codeList.length; i++) { + var linkList = codeList[i].getElementsByTagName('a'); + for (var j = 0; j < linkList.length; j++) { + if (linkList[j].innerHTML === "") { + linkList[j].setAttribute('aria-hidden', 'true'); + } + } + } +}); diff --git a/docs/articles/index.html b/docs/articles/index.html index e74f7844ec..6eb1a0a5b5 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -1,5 +1,5 @@ -Articles • tiledb +Articles • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -75,11 +75,11 @@ Working with SQL diff --git a/docs/articles/installation-options.html b/docs/articles/installation-options.html index e82d52aade..40b28296d9 100644 --- a/docs/articles/installation-options.html +++ b/docs/articles/installation-options.html @@ -12,7 +12,7 @@ - + @@ -26,7 +26,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -68,8 +68,7 @@ - - + Installation Options for the TileDB R Package @@ -90,53 +89,30 @@ 2022-01-25 Overview -This vignette discusses different options for installing the TileDB R -package. +This vignette discusses different options for installing the TileDB R package. CRAN Binaries -The TileDB R package is released via the Comprehensive R Archive -Network, or CRAN. CRAN generally provides binaries for the two most -widely operating systems, Windows and macOS. So issueing the command +The TileDB R package is released via the Comprehensive R Archive Network, or CRAN. CRAN generally provides binaries for the two most widely operating systems, Windows and macOS. So issueing the command install.packages("tiledb") -will, on those two operating system, default to -type="binary" and install a ready-to-run binary -package. +will, on those two operating system, default to type="binary" and install a ready-to-run binary package. Source -On other operating systems such as Linux, or by explicitly selecting -type="source" on Windows or macOS, an installation from source is attempted when usinginstall.packages(“tiledb”)`. -On Linux or macOS, this invokes the standard R build process which -will rely on configure. If pkg-config is -found, it is used to query the system about a possible TileDB -installation. If one is found, it used. Otherwise, on all three main -operating systems a prebuilt archive with the TileDB Embedded library is -downloaded from GitHub and unpacked. Each build of the R package will -have one matching build of TileDB Embedded associated with it via file -the tools/tiledbVersion.txt specifying a version and -release commit sha1. These two values are used to find the corresponding -binary artifacts from a release at GitHub. -The location of an existing installed version of TileDB Embedded can -also be provided to the configure script which supplies an -argument --with-tiledb=PATH. So on the command-line, one -could say -R CMD INSTALL --configure-args='--with-tiledb=/some/path' tiledb_*.tar.gz -to pass the configure argument on. From within R, the -equivalent command is +On other operating systems such as Linux, or by explicitly selecting type="source" on Windows or macOS, an installation from source is attempted when usinginstall.packages(“tiledb”)`. +On Linux or macOS, this invokes the standard R build process which will rely on configure. If pkg-config is found, it is used to query the system about a possible TileDB installation. If one is found, it used. Otherwise, on all three main operating systems a prebuilt archive with the TileDB Embedded library is downloaded from GitHub and unpacked. Each build of the R package will have one matching build of TileDB Embedded associated with it via file the tools/tiledbVersion.txt specifying a version and release commit sha1. These two values are used to find the corresponding binary artifacts from a release at GitHub. +The location of an existing installed version of TileDB Embedded can also be provided to the configure script which supplies an argument --with-tiledb=PATH. So on the command-line, one could say +R CMD INSTALL --configure-args='--with-tiledb=/some/path' tiledb_*.tar.gz +to pass the configure argument on. From within R, the equivalent command is install.packages("tiledb", repos=NULL, configure.args="--with-tiledb=/some/path") -Lastly, one can also override the default download location -(otherwise inferred via tools/tiledbVersion.txt. The -configure script supports an option ---with-download=URL so the two calls become, -respectively -R CMD INSTALL --configure-args='--with-download=https://some.where.net/file.tgz' tiledb_*.tar.gz +Lastly, one can also override the default download location (otherwise inferred via tools/tiledbVersion.txt. The configure script supports an option --with-download=URL so the two calls become, respectively +R CMD INSTALL --configure-args='--with-download=https://some.where.net/file.tgz' tiledb_*.tar.gz and install.packages("tiledb_0.11.0.tar.gz", repos=NULL, @@ -147,30 +123,23 @@ Source Conda -Using for example the current condaforge/mambaforge -container from the conda-forge project, -we can do -mamba install -y r-tiledb # installs R, tiledb and deps without extra prompt -# ...several lines of installation detail omitted -R -# ... several lines of R startup output omitted -> library(tiledb) -which installs R, the tiledb package and all respective -dependencies. +Using for example the current condaforge/mambaforge container from the conda-forge project, we can do +mamba install -y r-tiledb # installs R, tiledb and deps without extra prompt +# ...several lines of installation detail omitted +R +# ... several lines of R startup output omitted +> library(tiledb) +which installs R, the tiledb package and all respective dependencies. Docker -Builds of the TileDB package could also be provided via Docker -containers. At present, no official TileDB R containers are provided by -TileDB. However, the discussion of installation from source above -describes how to create such containers. +Builds of the TileDB package could also be provided via Docker containers. At present, no official TileDB R containers are provided by TileDB. However, the discussion of installation from source above describes how to create such containers. Summary -This note described several installation options for the TileDB R -package. +This note described several installation options for the TileDB R package. @@ -179,11 +148,11 @@ Summary diff --git a/docs/articles/installation-options_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/installation-options_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 0000000000..ca349fd6a5 --- /dev/null +++ b/docs/articles/installation-options_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. + +document.addEventListener('DOMContentLoaded', function() { + const codeList = document.getElementsByClassName("sourceCode"); + for (var i = 0; i < codeList.length; i++) { + var linkList = codeList[i].getElementsByTagName('a'); + for (var j = 0; j < linkList.length; j++) { + if (linkList[j].innerHTML === "") { + linkList[j].setAttribute('aria-hidden', 'true'); + } + } + } +}); diff --git a/docs/articles/introduction.html b/docs/articles/introduction.html index b87009f33d..bf485522d9 100644 --- a/docs/articles/introduction.html +++ b/docs/articles/introduction.html @@ -12,7 +12,7 @@ - + @@ -26,7 +26,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -68,8 +68,7 @@ - - + First Steps with TileDB @@ -86,29 +85,14 @@ First Steps with TileDB %\VignetteEngine{simplermarkdown::mdweave_to_html} %\VignetteEncoding{UTF-8} --> -This document introduces TileDB via several simple examples. A -corresponding document with more complete API documentation is also available. +This document introduces TileDB via several simple examples. A corresponding document with more complete API documentation is also available. Getting started -Once the TileDB R package is installed, it can be loaded via -library(tiledb). Installation is supported for Windows, -Linux and macOS via the official CRAN -package, on Linux and macOS via the conda package as well as -from source. -Documentation for the TileDB R package is available via the -help() function from within R as well as via the package documentation -and an introductory -notebook. Documentation about TileDB itself is also available. -Several “quickstart” examples that are discussed on the website are -available in the examples -directory. This vignette discusses similar examples. -In the following examples, the URIs describing arrays point to local -file system object. When TileDB has been built with S3 support, and with -proper AWS credentials in the usual environment variables, URIs such as -s3://some/data/bucket can be used where a local file would -be used. See the script ex_S3.R -for an example. +Once the TileDB R package is installed, it can be loaded via library(tiledb). Installation is supported for Windows, Linux and macOS via the official CRAN package, on Linux and macOS via the conda package as well as from source. +Documentation for the TileDB R package is available via the help() function from within R as well as via the package documentation and an introductory notebook. Documentation about TileDB itself is also available. +Several “quickstart” examples that are discussed on the website are available in the examples directory. This vignette discusses similar examples. +In the following examples, the URIs describing arrays point to local file system object. When TileDB has been built with S3 support, and with proper AWS credentials in the usual environment variables, URIs such as s3://some/data/bucket can be used where a local file would be used. See the script ex_S3.R for an example. Dense Arrays @@ -116,104 +100,72 @@ Dense Arrays Preliminaries -These illustrations use the array created by the file ex_1.R -which one can run from within R, or on the command-line. To follow along -with discussion that follows, it helps to run the example once to create -the array after possibly adjusting the array location path from its -default value (using the current directory or, if set as an option, an -override). +These illustrations use the array created by the file ex_1.R which one can run from within R, or on the command-line. To follow along with discussion that follows, it helps to run the example once to create the array after possibly adjusting the array location path from its default value (using the current directory or, if set as an option, an override). Basic Reading of Dense Arrays -The file ex_1.R -in the examples directory is a simple yet complete example extending quickstart_dense.R -by adding a second and third attribute. In this as well as the following -examples we will use tiledb_array() to access the array; -the older variants tiledb_dense() and -tiledb_sparse() remain supported but are deprecated and may -be removed at some point in the future. +The file ex_1.R in the examples directory is a simple yet complete example extending quickstart_dense.R by adding a second and third attribute. In this as well as the following examples we will use tiledb_array() to access the array; the older variants tiledb_dense() and tiledb_sparse() remain supported but are deprecated and may be removed at some point in the future. Read 1-D -The first example extracts rows 1 to 2 and column 2 from an array. It -also limits the selection to just one attribute (via -attrs), asks for the return to be a data.frame -(instead of a simpler list) and for the (row and column, if present as -here) indices to not be printed (via extended=FALSE). -> A <- tiledb_array(uri = uri, attrs = "b", -+ return_as = "data.frame", extended=FALSE)) -> A[1:2,2] -[1] 101.5 104.0 -> -Note that the examples create three two-dimensional attributes. The -attributes can be selected via the attrs argument, or the -attrs() method on the array object. The square-bracket -indexing then selects with in the 2-d attribute object. -If multiple objects are returned (as list or -data.frame), subsetting on the returned object works via -[[var]] or $var. A numeric index also works -(but needs to account for rows and cols). -> A <- tiledb_array(uri = uri, attrs = c("a","b"), -+ return_as = "data.frame") -> A[1:2,2][["a"]] -[1] 2 7 -> A[1:2,2]$a -[1] 2 7 -> +The first example extracts rows 1 to 2 and column 2 from an array. It also limits the selection to just one attribute (via attrs), asks for the return to be a data.frame (instead of a simpler list) and for the (row and column, if present as here) indices to not be printed (via extended=FALSE). +> A <- tiledb_array(uri = uri, attrs = "b", ++ return_as = "data.frame", extended=FALSE)) +> A[1:2,2] +[1] 101.5 104.0 +> +Note that the examples create three two-dimensional attributes. The attributes can be selected via the attrs argument, or the attrs() method on the array object. The square-bracket indexing then selects with in the 2-d attribute object. +If multiple objects are returned (as list or data.frame), subsetting on the returned object works via [[var]] or $var. A numeric index also works (but needs to account for rows and cols). +> A <- tiledb_array(uri = uri, attrs = c("a","b"), ++ return_as = "data.frame") +> A[1:2,2][["a"]] +[1] 2 7 +> A[1:2,2]$a +[1] 2 7 +> Read 2-D -This works analogously. Note that the results are generally returned -as vectors, or as a columns of a data.frame object in case -that option was set. -> A[6:9,3:4] -$a -[1] 28 29 33 34 38 39 43 44 - -$b -[1] 114.5 115.0 117.0 117.5 119.5 120.0 122.0 122.5 - -$c -[1] "fox" "A" "E" "F" "J" "K" "O" "P" -> +This works analogously. Note that the results are generally returned as vectors, or as a columns of a data.frame object in case that option was set. +> A[6:9,3:4] +$a +[1] 28 29 33 34 38 39 43 44 + +$b +[1] 114.5 115.0 117.0 117.5 119.5 120.0 122.0 122.5 + +$c +[1] "fox" "A" "E" "F" "J" "K" "O" "P" +> Read 2-D with attribute selection -We can restrict the selection to a subset of attributes when opening -the array. -> A <- tiledb_dense(uri = uri, attrs = c("b","c"), -+ return_as = "data.frame", extended=FALSE) -> A[6:9,2:4] - b c -1 114.0 brown -2 114.5 fox -3 115.0 A -4 116.5 D -5 117.0 E -6 117.5 F -7 119.0 I -8 119.5 J -9 120.0 K -10 121.5 N -11 122.0 O -12 122.5 P -> -This also illustrated the effect of setting -as.data.frame=TRUE when opening the array. -This scheme can be generalized to variable cells, or cells where -N>1, as we can expand each (atomistic) value over corresponding row -and column indices. -The column types correspond to the attribute typed in the array -schema, subject to the constraint mentioned above on R types. (The char -comes in as a factor variable as is still the R 3.6.* default which is -about to change. We can also override, users can too.) -> A <- tiledb_array("/tmp/tiledb/ex_1/", attrs=c("b","c"), -+ return_as = "data.frame", extended=TRUE) -> sapply(A[6:9, 3:4], "class") - rows cols b c - "integer" "integer" "numeric" "character" -> -Consistent with the data.frame semantics, now -requesting a named column reduces to a vector as this happens -at the R side: +We can restrict the selection to a subset of attributes when opening the array. +> A <- tiledb_dense(uri = uri, attrs = c("b","c"), ++ return_as = "data.frame", extended=FALSE) +> A[6:9,2:4] + b c +1 114.0 brown +2 114.5 fox +3 115.0 A +4 116.5 D +5 117.0 E +6 117.5 F +7 119.0 I +8 119.5 J +9 120.0 K +10 121.5 N +11 122.0 O +12 122.5 P +> +This also illustrated the effect of setting as.data.frame=TRUE when opening the array. +This scheme can be generalized to variable cells, or cells where N>1, as we can expand each (atomistic) value over corresponding row and column indices. +The column types correspond to the attribute typed in the array schema, subject to the constraint mentioned above on R types. (The char comes in as a factor variable as is still the R 3.6.* default which is about to change. We can also override, users can too.) +> A <- tiledb_array("/tmp/tiledb/ex_1/", attrs=c("b","c"), ++ return_as = "data.frame", extended=TRUE) +> sapply(A[6:9, 3:4], "class") + rows cols b c + "integer" "integer" "numeric" "character" +> +Consistent with the data.frame semantics, now requesting a named column reduces to a vector as this happens at the R side: > A[6:9, 3:4]$b [1] 114.5 115.0 117.0 117.5 119.5 120.0 122.0 122.5 > @@ -226,96 +178,78 @@ Sparse ArraysBasic Reading and Writing of Sparse Arrays Simple Examples -Basic reading returns the coordinates and any attributes. The -following examples use the array created by the quickstart_sparse -example. -> A <- tiledb_array(uri = uri, is.sparse = TRUE) -> A[] -$rows -[1] 1 2 2 - -$cols -[1] 1 3 4 - -$a -[1] 1 3 2 - -> -We can also request a data.frame object, either when -opening or by changing this object characteristic on the fly: -> return.data.frame(A) <- TRUE -> A[] - a rows cols -1 1 1 1 -2 3 2 3 -3 2 2 4 -For sparse arrays, the return type is by default ‘extended’ showing -rows and column but this can be overridden. +Basic reading returns the coordinates and any attributes. The following examples use the array created by the quickstart_sparse example. +> A <- tiledb_array(uri = uri, is.sparse = TRUE) +> A[] +$rows +[1] 1 2 2 + +$cols +[1] 1 3 4 + +$a +[1] 1 3 2 + +> +We can also request a data.frame object, either when opening or by changing this object characteristic on the fly: +> return.data.frame(A) <- TRUE +> A[] + a rows cols +1 1 1 1 +2 3 2 3 +3 2 2 4 +For sparse arrays, the return type is by default ‘extended’ showing rows and column but this can be overridden. Assignment works similarly: -> A[4,2] <- 42L -> A[] -> A[] - rows cols a -1 1 1 1 -2 2 3 3 -3 2 4 2 -4 4 2 42 -> +> A[4,2] <- 42L +> A[] +> A[] + rows cols a +1 1 1 1 +2 2 3 3 +3 2 4 2 +4 4 2 42 +> Reads can select rows and or columns: -> A[2,] - rows cols a -1 2 3 3 -2 2 4 2 -> A[,2] - rows cols a -1 4 2 42 -> +> A[2,] + rows cols a +1 2 3 3 +2 2 4 2 +> A[,2] + rows cols a +1 4 2 42 +> Attributes can be selected similarly. Date(time) Attributes -Similar to the dense array case described earlier, the file ex_2.R -illustrates some basic operations on sparse arrays. It also shows date -and datetime types instead of just integer and double precision -floats. -> A <- tiledb_array(uri = uri, return_as = "data.frame") -> A[1577858403:1577858408] - rows cols a b d e -1 1577858403 1 3 103 2020-01-11 2020-01-02 18:24:33.844 -2 1577858404 1 4 104 2020-01-15 2020-01-05 02:28:36.214 -3 1577858405 1 5 105 2020-01-19 2020-01-05 00:44:04.805 -4 1577858406 1 6 106 2020-01-21 2020-01-06 12:58:51.770 -5 1577858407 1 7 107 2020-01-25 2020-01-09 04:29:56.309 -6 1577858408 1 8 108 2020-01-26 2020-01-07 13:55:10.240 -> -The row coordinate is currently a floating point representation of -the underlying time type. We can both select attributes (here we -excluded the “a” column) and select rows by time (as the time stamps get -converted to the required floating point value). -> attrs(A) <- c("b", "d", "e") -> A[as.POSIXct("2020-01-01"):as.POSIXct("2020-01-01 00:00:03")] - rows cols b d e -1 1577858401 1 101 2020-01-05 2020-01-01 03:03:07.548 -2 1577858402 1 102 2020-01-10 2020-01-02 21:02:19.747 -3 1577858403 1 103 2020-01-11 2020-01-02 18:24:33.844 -> -More extended examples are available showing indexing by date(time) -as well as character dimension. +Similar to the dense array case described earlier, the file ex_2.R illustrates some basic operations on sparse arrays. It also shows date and datetime types instead of just integer and double precision floats. +> A <- tiledb_array(uri = uri, return_as = "data.frame") +> A[1577858403:1577858408] + rows cols a b d e +1 1577858403 1 3 103 2020-01-11 2020-01-02 18:24:33.844 +2 1577858404 1 4 104 2020-01-15 2020-01-05 02:28:36.214 +3 1577858405 1 5 105 2020-01-19 2020-01-05 00:44:04.805 +4 1577858406 1 6 106 2020-01-21 2020-01-06 12:58:51.770 +5 1577858407 1 7 107 2020-01-25 2020-01-09 04:29:56.309 +6 1577858408 1 8 108 2020-01-26 2020-01-07 13:55:10.240 +> +The row coordinate is currently a floating point representation of the underlying time type. We can both select attributes (here we excluded the “a” column) and select rows by time (as the time stamps get converted to the required floating point value). +> attrs(A) <- c("b", "d", "e") +> A[as.POSIXct("2020-01-01"):as.POSIXct("2020-01-01 00:00:03")] + rows cols b d e +1 1577858401 1 101 2020-01-05 2020-01-01 03:03:07.548 +2 1577858402 1 102 2020-01-10 2020-01-02 21:02:19.747 +3 1577858403 1 103 2020-01-11 2020-01-02 18:24:33.844 +> +More extended examples are available showing indexing by date(time) as well as character dimension. Additional Information -The TileDB R package is documented via R help functions -(e.g. help("tiledb_array") shows information for -the tiledb_array() function) as well as via a website regrouping all -documentation. Extended API -documentation is available, as is a examples/ -directory. -TileDB itself has extensive installation, -and overall -documentation as well as a support forum. +The TileDB R package is documented via R help functions (e.g. help("tiledb_array") shows information for the tiledb_array() function) as well as via a website regrouping all documentation. Extended API documentation is available, as is a examples/ directory. +TileDB itself has extensive installation, and overall documentation as well as a support forum. @@ -324,11 +258,11 @@ Additional Information diff --git a/docs/articles/introduction_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/introduction_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 0000000000..ca349fd6a5 --- /dev/null +++ b/docs/articles/introduction_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. + +document.addEventListener('DOMContentLoaded', function() { + const codeList = document.getElementsByClassName("sourceCode"); + for (var i = 0; i < codeList.length; i++) { + var linkList = codeList[i].getElementsByTagName('a'); + for (var j = 0; j < linkList.length; j++) { + if (linkList[j].innerHTML === "") { + linkList[j].setAttribute('aria-hidden', 'true'); + } + } + } +}); diff --git a/docs/articles/tiledb-mariadb-examples.html b/docs/articles/tiledb-mariadb-examples.html index 849627c0bf..866cf34a7c 100644 --- a/docs/articles/tiledb-mariadb-examples.html +++ b/docs/articles/tiledb-mariadb-examples.html @@ -12,7 +12,7 @@ - + @@ -26,7 +26,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -68,8 +68,7 @@ - - + TileDB and (R)MariaDB Examples @@ -89,43 +88,26 @@ TileDB and (R)MariaDB Examples Introduction -TileDB provides the -Universal Data Engine that can be accessed in a variety of -ways. The C/C++ library offered by TileDB Embedded is one -approach, and the R -package, as well as the Python package and -other language bindings use it. Another interface is provided by the MariaDB Integration via the -MyTile storage plugin. -This provides TileDB integration with any frontend that interfaces -with MariaDB—such as the RMariaDB package -for R. So this vignette illustrates the use of TileDB via MariaDB using -R and the RMariaDB packages. +TileDB provides the Universal Data Engine that can be accessed in a variety of ways. The C/C++ library offered by TileDB Embedded is one approach, and the R package, as well as the Python package and other language bindings use it. Another interface is provided by the MariaDB Integration via the MyTile storage plugin. +This provides TileDB integration with any frontend that interfaces with MariaDB—such as the RMariaDB package for R. So this vignette illustrates the use of TileDB via MariaDB using R and the RMariaDB packages. Installation or Using Docker -In order to use the MyTile storage plugin, one has to compile both -the storage plugin itself and the MariaDB server with consistent -compiler flags. As the build also requires the TileDB Embedded library -and headers, using a Docker container may be easiest. The Dockerfile -also provides a concrete example of the build setup. -So here we will use the tiledb/tiledb-mariadb-r -container. +In order to use the MyTile storage plugin, one has to compile both the storage plugin itself and the MariaDB server with consistent compiler flags. As the build also requires the TileDB Embedded library and headers, using a Docker container may be easiest. The Dockerfile also provides a concrete example of the build setup. +So here we will use the tiledb/tiledb-mariadb-r container. Launch Container in Background -We launch the container ‘tiledb/tiledb-mariadb-r’ as a daemon, -allowing MariaDB to accept an empty password (using an older MySQL -variable setting), and name the running image ‘tiledb-mariadb-r’: -docker run --name tiledb-mariadb-r -it -d --rm \ - -e MYSQL_ALLOW_EMPTY_PASSWORD=1 tiledb/tiledb-mariadb-r +We launch the container ‘tiledb/tiledb-mariadb-r’ as a daemon, allowing MariaDB to accept an empty password (using an older MySQL variable setting), and name the running image ‘tiledb-mariadb-r’: +docker run --name tiledb-mariadb-r -it -d --rm \ + -e MYSQL_ALLOW_EMPTY_PASSWORD=1 tiledb/tiledb-mariadb-r Access Container Once to Write via TileDB -Using the name given to the running instance, we start an R session -to write data with TileDB: -docker exec -it -u root tiledb-mariadb-r R +Using the name given to the running instance, we start an R session to write data with TileDB: +docker exec -it -u root tiledb-mariadb-r R @@ -134,220 +116,200 @@ Examples Palmer Penguins -With the sessions started as in the previous section, we start an R -session. -> library(tiledb) -> library(palmerpenguins) -> praw <- penguins_raw -> fromDataFrame(praw, "/tmp/penguinsraw") +With the sessions started as in the previous section, we start an R session. +> library(tiledb) +> library(palmerpenguins) +> praw <- penguins_raw +> fromDataFrame(praw, "/tmp/penguinsraw") Access Container Again to Read via RMariaDB -In another shell, we can access the container once more and launch -another R process: -docker exec -it -u root tiledb-mariadb-r R -where we use RMariaDB to access the data via a tibble -object and magrittr pipe -> library(RMariaDB) -> library(dplyr, warn.conflicts=FALSE) -> con <- DBI::dbConnect(RMariaDB::MariaDB(), dbname="test") -> tbl(con, "/tmp/penguinsraw") %>% -+ dplyr::select(contains("Length")) -# Source: lazy query [?? x 2] -# Database: mysql [@localhost:NA/test] - `Culmen Length (mm)` `Flipper Length (mm)` - <dbl> <dbl> - 1 39.1 181 - 2 39.5 186 - 3 40.3 195 - 4 NA NA - 5 36.7 193 - 6 39.3 190 - 7 38.9 181 - 8 39.2 195 - 9 34.1 193 -10 42 190 -# ... with more rows -Note that this R session uses TileDB only via the MyTile plugin which -is activated implicitly via the ‘table location’ (here -/tmp/penguinsraw) of the test database enabling -plugins. -Also note that the query is still ‘lazy’: only column names and the -first ten observations have been retrieved, and the total size is still -unknown as indicated by lazy query [?? x 2]. Adding a -collect() verb materialized the full subset. -> tbl(con, "/tmp/penguinsraw") %>% -+ dplyr::select(contains("Length")) %>% -+ collect() -# A tibble: 344 x 2 - `Culmen Length (mm)` `Flipper Length (mm)` - <dbl> <dbl> - 1 39.1 181 - 2 39.5 186 - 3 40.3 195 - 4 NA NA - 5 36.7 193 - 6 39.3 190 - 7 38.9 181 - 8 39.2 195 - 9 34.1 193 -10 42 190 -# ... with 334 more rows -> -We now see that all 344 rows of this particular result set have been -accessed. +In another shell, we can access the container once more and launch another R process: +docker exec -it -u root tiledb-mariadb-r R +where we use RMariaDB to access the data via a tibble object and magrittr pipe +> library(RMariaDB) +> library(dplyr, warn.conflicts=FALSE) +> con <- DBI::dbConnect(RMariaDB::MariaDB(), dbname="test") +> tbl(con, "/tmp/penguinsraw") %>% ++ dplyr::select(contains("Length")) +# Source: lazy query [?? x 2] +# Database: mysql [@localhost:NA/test] + `Culmen Length (mm)` `Flipper Length (mm)` + <dbl> <dbl> + 1 39.1 181 + 2 39.5 186 + 3 40.3 195 + 4 NA NA + 5 36.7 193 + 6 39.3 190 + 7 38.9 181 + 8 39.2 195 + 9 34.1 193 +10 42 190 +# ... with more rows +Note that this R session uses TileDB only via the MyTile plugin which is activated implicitly via the ‘table location’ (here /tmp/penguinsraw) of the test database enabling plugins. +Also note that the query is still ‘lazy’: only column names and the first ten observations have been retrieved, and the total size is still unknown as indicated by lazy query [?? x 2]. Adding a collect() verb materialized the full subset. +> tbl(con, "/tmp/penguinsraw") %>% ++ dplyr::select(contains("Length")) %>% ++ collect() +# A tibble: 344 x 2 + `Culmen Length (mm)` `Flipper Length (mm)` + <dbl> <dbl> + 1 39.1 181 + 2 39.5 186 + 3 40.3 195 + 4 NA NA + 5 36.7 193 + 6 39.3 190 + 7 38.9 181 + 8 39.2 195 + 9 34.1 193 +10 42 190 +# ... with 334 more rows +> +We now see that all 344 rows of this particular result set have been accessed. Similarly, we can also run summaries on selected column: -> tbl(con, "/tmp/penguinsraw") %>% -+ group_by(Species) %>% -+ summarise(across(starts_with("Flipper"), -+ list(~mean(.x, na.rm=TRUE), ~sd(.x, na.rm=TRUE)))) -# Source: lazy query [?? x 3] -# Database: mysql [@localhost:NA/test] - Species `\`Flipper Length (mm)\`_~me~ `\`Flipper Length (mm)\`_~~ - <chr> <dbl> <dbl> -1 Adelie Penguin (Pyg~ 190. 6.54 -2 Chinstrap penguin (~ 196. 7.13 -3 Gentoo penguin (Pyg~ 217. 6.48 -> +> tbl(con, "/tmp/penguinsraw") %>% ++ group_by(Species) %>% ++ summarise(across(starts_with("Flipper"), ++ list(~mean(.x, na.rm=TRUE), ~sd(.x, na.rm=TRUE)))) +# Source: lazy query [?? x 3] +# Database: mysql [@localhost:NA/test] + Species `\`Flipper Length (mm)\`_~me~ `\`Flipper Length (mm)\`_~~ + <chr> <dbl> <dbl> +1 Adelie Penguin (Pyg~ 190. 6.54 +2 Chinstrap penguin (~ 196. 7.13 +3 Gentoo penguin (Pyg~ 217. 6.48 +> DBI -We can connect directly using the DBI package along with -the RMariaDB package and its MyTile bindings: +We can connect directly using the DBI package along with the RMariaDB package and its MyTile bindings: library(DBI) -con <- dbConnect(RMariaDB::MariaDB(), dbname="test") -res <- dbSendQuery(con, "select * from `/work/penguins` as `q91` limit 10") -df <- dbFetch(res, n = 10) -dbClearResult(res) +con <- dbConnect(RMariaDB::MariaDB(), dbname="test") +res <- dbSendQuery(con, "select * from `/work/penguins` as `q91` limit 10") +df <- dbFetch(res, n = 10) +dbClearResult(res) print(df) -dbDisconnect(con) +dbDisconnect(con) S3 -When using Docker, the container setup needs to be modified to -include the required AWS access environment variables: -docker run --name tiledb-mariadb-r \ - -it -d --rm \ - -v $PWD:/work -w /work \ - -e MYSQL_ALLOW_EMPTY_PASSWORD=1 \ - -e AWS_SECRET_ACCESS_KEY=${AWS_SECRET_ACCESS_KEY} \ - -e AWS_ACCESS_KEY_ID=${AWS_ACCESS_KEY_ID} \ - tiledb/tiledb-mariadb-r -This exports the current working directory (accessed as -$PWD in the shell) as /work inside the -container (via the -v switch), and instructs the container -to start in directory /work (via the -w -switch). -In the following example we also set a TileDB configuration option to -switch AWS regions. -> library(dplyr, warn.conflicts=FALSE) -> # connect as usual -> con <- DBI::dbConnect(RMariaDB::MariaDB(), dbname="test") -> # use connection to update config in order to switch s3 regions -> res1 <- DBI::dbSendQuery(con, "set mytile_tiledb_config=\"vfs.s3.region=us-west-1\";") -> DBI::dbClearResult(res1) -> # run simple query -> tbl(con, "s3://tiledb-public-us-west-1/test-array-4x4") %>% collect() -# A tibble: 16 x 3 - `__dim_0` `__dim_1` `__attr` - <int64> <int64> <dbl> - 1 0 0 0.397 - 2 0 1 0.432 - 3 0 2 0.617 - 4 0 3 0.403 - 5 1 0 0.837 - 6 1 1 0.670 - 7 1 2 0.235 - 8 1 3 0.841 - 9 2 0 0.222 -10 2 1 0.468 -11 2 2 0.970 -12 2 3 0.551 -13 3 0 0.628 -14 3 1 0.0149 -15 3 2 0.0540 -16 3 3 0.445 -> -> DBI::dbDisconnect(con) # close connection +When using Docker, the container setup needs to be modified to include the required AWS access environment variables: +docker run --name tiledb-mariadb-r \ + -it -d --rm \ + -v $PWD:/work -w /work \ + -e MYSQL_ALLOW_EMPTY_PASSWORD=1 \ + -e AWS_SECRET_ACCESS_KEY=${AWS_SECRET_ACCESS_KEY} \ + -e AWS_ACCESS_KEY_ID=${AWS_ACCESS_KEY_ID} \ + tiledb/tiledb-mariadb-r +This exports the current working directory (accessed as $PWD in the shell) as /work inside the container (via the -v switch), and instructs the container to start in directory /work (via the -w switch). +In the following example we also set a TileDB configuration option to switch AWS regions. +> library(dplyr, warn.conflicts=FALSE) +> # connect as usual +> con <- DBI::dbConnect(RMariaDB::MariaDB(), dbname="test") +> # use connection to update config in order to switch s3 regions +> res1 <- DBI::dbSendQuery(con, "set mytile_tiledb_config=\"vfs.s3.region=us-west-1\";") +> DBI::dbClearResult(res1) +> # run simple query +> tbl(con, "s3://tiledb-public-us-west-1/test-array-4x4") %>% collect() +# A tibble: 16 x 3 + `__dim_0` `__dim_1` `__attr` + <int64> <int64> <dbl> + 1 0 0 0.397 + 2 0 1 0.432 + 3 0 2 0.617 + 4 0 3 0.403 + 5 1 0 0.837 + 6 1 1 0.670 + 7 1 2 0.235 + 8 1 3 0.841 + 9 2 0 0.222 +10 2 1 0.468 +11 2 2 0.970 +12 2 3 0.551 +13 3 0 0.628 +14 3 1 0.0149 +15 3 2 0.0540 +16 3 3 0.445 +> +> DBI::dbDisconnect(con) # close connection NYC Taxis -We can write the New York taxi data into TileDB (in the current -directory) after reading it as a csv: -> nyc <- data.table::fread("trip_data_1.csv") -> tiledb::fromDataFrame(nyc, "trip_data_1") -Then we can access it via the path /work/trip_data_1 via -RMariaDB. -> library(dplyr, warn.conflicts=FALSE) -> con <- DBI::dbConnect(RMariaDB::MariaDB(), dbname="test") -> # list column names -> tbl(con, "/work/trip_data_1") %>% colnames() -> tbl(con, "/work/trip_data_1") %>% colnames() - [1] "__tiledb_rows" "dropoff_latitude" "medallion" - [4] "hack_license" "dropoff_longitude" "vendor_id" - [7] "rate_code" "store_and_fwd_flag" "pickup_datetime" -[10] "dropoff_datetime" "trip_time_in_secs" "pickup_latitude" -[13] "passenger_count" "trip_distance" "pickup_longitude" -> # extract one column (here passenger_count) completely and tabulate in R -> tbl(con, "/work/trip_data_1") %>% select(passenger_count) %>% collect() %>% table() -. - 0 1 2 3 4 5 6 9 - 166 10471701 1986196 597485 280992 920006 520066 1 - 208 255 - 1 1 -> # alternatively, run a lazy query -> tbl(con, "/work/trip_data_1") %>% group_by(passenger_count) %>% summarize(nobs = n()) -# Source: lazy query [?? x 2] -# Database: mysql [@localhost:NA/test] - passenger_count nobs - <int> <int64> - 1 0 166 - 2 1 10471701 - 3 2 1986196 - 4 3 597485 - 5 4 280992 - 6 5 920006 - 7 6 520066 - 8 9 1 - 9 208 1 -10 255 1 -> # here the request is actually sent as SQL and the computation is done in the SQL layer -> tbl(con, "/work/trip_data_1") %>% -+ group_by(passenger_count) %>% -+ summarize(nobs = n()) %>% -+ show_query() -<SQL> -SELECT `passenger_count`, COUNT(*) AS `nobs` -FROM `/work/trip_data_1` -GROUP BY `passenger_count` -> # naturally we can also send the query directly to the SQL backend -> sql <- "SELECT passenger_count, count(*) AS n FROM `/work/trip_data_1` GROUP BY passenger_count;" -> DBI::dbGetQuery(con, sql) - passenger_count n -1 0 166 -2 1 10471701 -3 2 1986196 -4 3 597485 -5 4 280992 -6 5 920006 -7 6 520066 -8 9 1 -9 208 1 -10 255 1 -> -> DBI::dbDisconnect(con) # close connection +We can write the New York taxi data into TileDB (in the current directory) after reading it as a csv: +> nyc <- data.table::fread("trip_data_1.csv") +> tiledb::fromDataFrame(nyc, "trip_data_1") +Then we can access it via the path /work/trip_data_1 via RMariaDB. +> library(dplyr, warn.conflicts=FALSE) +> con <- DBI::dbConnect(RMariaDB::MariaDB(), dbname="test") +> # list column names +> tbl(con, "/work/trip_data_1") %>% colnames() +> tbl(con, "/work/trip_data_1") %>% colnames() + [1] "__tiledb_rows" "dropoff_latitude" "medallion" + [4] "hack_license" "dropoff_longitude" "vendor_id" + [7] "rate_code" "store_and_fwd_flag" "pickup_datetime" +[10] "dropoff_datetime" "trip_time_in_secs" "pickup_latitude" +[13] "passenger_count" "trip_distance" "pickup_longitude" +> # extract one column (here passenger_count) completely and tabulate in R +> tbl(con, "/work/trip_data_1") %>% select(passenger_count) %>% collect() %>% table() +. + 0 1 2 3 4 5 6 9 + 166 10471701 1986196 597485 280992 920006 520066 1 + 208 255 + 1 1 +> # alternatively, run a lazy query +> tbl(con, "/work/trip_data_1") %>% group_by(passenger_count) %>% summarize(nobs = n()) +# Source: lazy query [?? x 2] +# Database: mysql [@localhost:NA/test] + passenger_count nobs + <int> <int64> + 1 0 166 + 2 1 10471701 + 3 2 1986196 + 4 3 597485 + 5 4 280992 + 6 5 920006 + 7 6 520066 + 8 9 1 + 9 208 1 +10 255 1 +> # here the request is actually sent as SQL and the computation is done in the SQL layer +> tbl(con, "/work/trip_data_1") %>% ++ group_by(passenger_count) %>% ++ summarize(nobs = n()) %>% ++ show_query() +<SQL> +SELECT `passenger_count`, COUNT(*) AS `nobs` +FROM `/work/trip_data_1` +GROUP BY `passenger_count` +> # naturally we can also send the query directly to the SQL backend +> sql <- "SELECT passenger_count, count(*) AS n FROM `/work/trip_data_1` GROUP BY passenger_count;" +> DBI::dbGetQuery(con, sql) + passenger_count n +1 0 166 +2 1 10471701 +3 2 1986196 +4 3 597485 +5 4 280992 +6 5 920006 +7 6 520066 +8 9 1 +9 208 1 +10 255 1 +> +> DBI::dbDisconnect(con) # close connection Summary -This short vignette demonstrates the use of TileDB-stored data from R -using RMariaDB via the MyTile storage extension to MariaBD. +This short vignette demonstrates the use of TileDB-stored data from R using RMariaDB via the MyTile storage extension to MariaBD. @@ -356,11 +318,11 @@ Summary diff --git a/docs/articles/tiledb-mariadb-examples_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/tiledb-mariadb-examples_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 0000000000..ca349fd6a5 --- /dev/null +++ b/docs/articles/tiledb-mariadb-examples_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. + +document.addEventListener('DOMContentLoaded', function() { + const codeList = document.getElementsByClassName("sourceCode"); + for (var i = 0; i < codeList.length; i++) { + var linkList = codeList[i].getElementsByTagName('a'); + for (var j = 0; j < linkList.length; j++) { + if (linkList[j].innerHTML === "") { + linkList[j].setAttribute('aria-hidden', 'true'); + } + } + } +}); diff --git a/docs/authors.html b/docs/authors.html index 145a22f84f..0eef9fee6c 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -1,5 +1,5 @@ -Authors and Citation • tiledb +Authors and Citation • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -49,11 +49,7 @@ Authors and Citation Authors - . Author, copyright holder. - - - - Dirk Eddelbuettel. Author. + . Author, copyright holder. @@ -66,15 +62,15 @@ Authors Citation Source: DESCRIPTION - TileDB, Inc., Eddelbuettel D (2024). + TileDB, Inc. (2025). tiledb: Modern Database Engine for Complex Data Based on Multi-Dimensional Arrays. -R package version 0.31.0, https://tiledb-inc.github.io/TileDB-R/, https://github.com/TileDB-Inc/TileDB-R. +R package version 0.31.0.1, https://tiledb-inc.github.io/TileDB-R/, https://github.com/TileDB-Inc/TileDB-R. @Manual{, title = {tiledb: Modern Database Engine for Complex Data Based on Multi-Dimensional Arrays}, - author = {{TileDB, Inc.} and Dirk Eddelbuettel}, - year = {2024}, - note = {R package version 0.31.0, https://tiledb-inc.github.io/TileDB-R/}, + author = {{TileDB, Inc.}}, + year = {2025}, + note = {R package version 0.31.0.1, https://tiledb-inc.github.io/TileDB-R/}, url = {https://github.com/TileDB-Inc/TileDB-R}, } @@ -84,11 +80,11 @@ Citation diff --git a/docs/deps/data-deps.txt b/docs/deps/data-deps.txt index 1b877ae225..ca4dfd9c5c 100644 --- a/docs/deps/data-deps.txt +++ b/docs/deps/data-deps.txt @@ -1,4 +1,4 @@ - + diff --git a/docs/index.html b/docs/index.html index cd8955108a..8ebb804b44 100644 --- a/docs/index.html +++ b/docs/index.html @@ -12,7 +12,7 @@ - + @@ -28,7 +28,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -71,7 +71,7 @@ - + The TileDB R package offers an R interface to the modern database by TileDB. @@ -84,19 +84,19 @@ InstallationCRAN and be installed directly via -> install.packages("tiledb") +> install.packages("tiledb") as usual. The most recent released version can be installed from Github using the package remotes. -> if (!requireNamespace("remotes",quietly=TRUE)) install.packages("remotes") -> remotes::install_github("TileDB-Inc/TileDB-R") -... -> library(tiledb) -TileDB R 0.31.0 with TileDB Embedded 2.27.0 on Ubuntu 24.04. -See https://tiledb.com for more information about TileDB. -> help(package=tiledb) +> if (!requireNamespace("remotes",quietly=TRUE)) install.packages("remotes") +> remotes::install_github("TileDB-Inc/TileDB-R") +... +> library(tiledb) +TileDB R 0.31.0 with TileDB Embedded 2.27.0 on Ubuntu 24.04. +See https://tiledb.com for more information about TileDB. +> help(package=tiledb) If the TileDB library is installed in a custom location, you need to pass the explicit path: -> remotes::install_github("TileDB-Inc/TileDB-R", - args="--configure-args='--with-tiledb=/path/to/tiledb'") +> remotes::install_github("TileDB-Inc/TileDB-R", + args="--configure-args='--with-tiledb=/path/to/tiledb'") Note that the TileDB R package is always developed and tested against the latest stable version of TileDB, but should also build against the newest development version. @@ -150,8 +150,7 @@ Citation Developers - Author, copyright holder -Dirk Eddelbuettel Author + Author, copyright holder Isaiah Norton Maintainer @@ -173,11 +172,11 @@ Dev status diff --git a/docs/news/index.html b/docs/news/index.html index 2d9f731da9..ca226604ed 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -1,5 +1,5 @@ -Changelog • tiledb +Changelog • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -53,7 +53,7 @@ tiledb 0.31.0Update unit tests to expect dense current domain Support parentheses in query conditions memory alloc: Accomodate zero buffer size estimate v2 -Apply styler::style_pkg() +Apply styler::style_pkg() Expose include/linking flags for re-using libtiledb in downstream packages Use TileDB Core 2.27.0 @@ -66,12 +66,10 @@ tiledb 0.30.2 tiledb 0.30.1 -This release of the R package builds against TileDB 2.26.1, and has also been tested against earlier releases as well as the development version (#757) - +This release of the R package builds against TileDB 2.26.1, and has also been tested against earlier releases as well as the development version (#757) tiledb 0.30.0 -This release of the R package builds against TileDB 2.26.0, and has also been tested against earlier releases as well as the development version (#745, #749, #750, #754, #755) - +This release of the R package builds against TileDB 2.26.0, and has also been tested against earlier releases as well as the development version (#745, #749, #750, #754, #755) Improvements Error messages displayed when a mismatched external pointer is detected now show both expected and encountered types (#740) NDRectangle objects can now instantiate from more domain data types (#741, #742) @@ -80,8 +78,7 @@ Improvements Documentation -The documentation website now uses favicon symbols for all pages rendered (#739) - +The documentation website now uses favicon symbols for all pages rendered (#739) Build and Test Systems The nighly valgrind matrix now includes release 2.26.0 (#744) @@ -89,17 +86,14 @@ Build and Test Systems Removals -Boolean arguments as.data.frame, as.matrix and as.array to the tiledb_array() accessor, deprecated in release 0.20.0 in July 2023 in favor of the more general return_as="..." form, have been removed. (#751) - +Boolean arguments as.data.frame, as.matrix and as.array to the tiledb_array() accessor, deprecated in release 0.20.0 in July 2023 in favor of the more general return_as="..." form, have been removed. (#751) Deprecation -As BioConductor package still relies on as.data.frame it was temporarily re-admitted as an argument. It is expected to be removed following the upcoming 3.20 release of BioConducto.r (#752) - +As BioConductor package still relies on as.data.frame it was temporarily re-admitted as an argument. It is expected to be removed following the upcoming 3.20 release of BioConducto.r (#752) tiledb 0.29.0 -This release of the R package builds against TileDB 2.25.0, and has also been tested against earlier releases as well as the development version (#728, #736) - +This release of the R package builds against TileDB 2.25.0, and has also been tested against earlier releases as well as the development version (#728, #736) Improvements Three deprecated calls to dump() methods for TileDB Embedded objects now use the preferred streaming alternatives (#727) Two already deprecated functions that are removed in TileDB 2.26.0 are no longer used (#732) @@ -109,20 +103,16 @@ Improvements Build and Test Systems -The nighly valgrind matrix now includes release 2.25.0 (#729) - +The nighly valgrind matrix now includes release 2.25.0 (#729) tiledb 0.28.2 -This release of the R package builds against TileDB 2.24.2, and has also been tested against earlier releases as well as the development version (#725) - +This release of the R package builds against TileDB 2.24.2, and has also been tested against earlier releases as well as the development version (#725) tiledb 0.28.1 -This release of the R package builds against TileDB 2.24.1, and has also been tested against earlier releases as well as the development version (#714, #715, #717, #724) - +This release of the R package builds against TileDB 2.24.1, and has also been tested against earlier releases as well as the development version (#714, #715, #717, #724) Improvements -When creating arrays with fromDataFrame, start and/or end timestamps can now be specified (#719) - +When creating arrays with fromDataFrame, start and/or end timestamps can now be specified (#719) Build and Test Systems The nighly continuous integration matrix now included Core release 2.24.0 and 2.22.0 is dropped (#721) @@ -131,8 +121,7 @@ Build and Test Systems tiledb 0.28.0 -This release of the R package builds against TileDB 2.24.0, and has also been tested against earlier releases as well as the development version (#714, #715, #717) - +This release of the R package builds against TileDB 2.24.0, and has also been tested against earlier releases as well as the development version (#714, #715, #717) Improvements Three internal and unexported helper functions now document more clearly how they can be called explicitly. (#709) Reading and writing of text- and binary files supported by a VFS backend is now supported. (#710) @@ -145,8 +134,7 @@ Build and Test Systems tiledb 0.27.0 -This release of the R package builds against TileDB 2.23.0, and has also been tested against earlier releases as well as the development version (#701, #704) - +This release of the R package builds against TileDB 2.23.0, and has also been tested against earlier releases as well as the development version (#701, #704) Improvements Group elements can now be deleted (#702) Two error messages now show the human-readable type representation instead of the enum counter value (#705) @@ -158,17 +146,14 @@ Build and Test Systems Deprecations -Function libtiledb_array_create_with_key, accessing a deprecated Core function, is now in src/deprecated.cpp and will be removed at later point (#699) - +Function libtiledb_array_create_with_key, accessing a deprecated Core function, is now in src/deprecated.cpp and will be removed at later point (#699) Removals -Functions libtiledb_query_add_range_with_type and libtiledb_query_add_range, deprecated in release 0.17.1 in January 2023, have been now removed (#700). - +Functions libtiledb_query_add_range_with_type and libtiledb_query_add_range, deprecated in release 0.17.1 in January 2023, have been now removed (#700). tiledb 0.26.0 -This release of the R package builds against TileDB 2.22.0, and has also been tested against earlier releases as well as the development version (#679, #686, #693, #696) - +This release of the R package builds against TileDB 2.22.0, and has also been tested against earlier releases as well as the development version (#679, #686, #693, #696) Improvements The display of a filter_list is now labeled correctly as a filter list (@cgiachalis in #681 addressing #678) The Arrow integration has been simplified using nanoarrow returning a single nanoarrow object; an unexported helper function nanoarrow2list() is provided to matching the previous interface (#682, #685) @@ -177,8 +162,7 @@ Improvements Bug Fixes -The column headers now correspond to the column content in the two-column data.frame returns by tiledb_object_walk (#684 closing #683) - +The column headers now correspond to the column content in the two-column data.frame returns by tiledb_object_walk (#684 closing #683) Build and Test Systems The configure and Makevars.in received a minor update correcting small issues (#680) @@ -186,8 +170,7 @@ Build and Test Systems Documentation -A number of minor typographical and grammar errors in the function documentation has been corrected (@cgiachalis in #681) - +A number of minor typographical and grammar errors in the function documentation has been corrected (@cgiachalis in #681) Deprecations Functions tiledb_arrow_array_ptr(), tiledb_arrow_schmea_ptr(), tiledb_arrow_array_del() and tiledb_arrow_schema_del() are deprecated (in favor of using the corresponding nanoarrow functions) and will be removed in a future release (#685) @@ -196,8 +179,7 @@ Deprecations tiledb 0.25.0 -This release of the R package builds against TileDB 2.21.0, and has also been tested against earlier releases as well as the development version (#661, #666, #668, #676, #677) - +This release of the R package builds against TileDB 2.21.0, and has also been tested against earlier releases as well as the development version (#661, #666, #668, #676, #677) Improvements The vendored nanoarrow sources have been update to release 0.4.0, and use of its facilities has been extended (#663) Query conditions can be expressed against non-existing enumeration (i.e., factor) values when TileDB Core 2.21.0 or later is used (#674) @@ -219,8 +201,7 @@ Build and Test Systems tiledb 0.24.0 -This release of the R package builds against TileDB 2.20.0, and has also been tested against earlier releases as well as the development version (#651,#654,#658,#659) - +This release of the R package builds against TileDB 2.20.0, and has also been tested against earlier releases as well as the development version (#651,#654,#658,#659) Improvements Factor level additions now check for possible over in the index type (#645, #646) Aggregate operations can now be performed on dense arrays via a query object with appropriate subarray settings (#650) @@ -233,17 +214,14 @@ Bug Fixes Build and Test Systems -The nightly valgrind run was updated to include release 2.20 (#649) - +The nightly valgrind run was updated to include release 2.20 (#649) Documentation -The DESCRIPTION file now contains a reference to the documentation site in its URL field (#656) - +The DESCRIPTION file now contains a reference to the documentation site in its URL field (#656) tiledb 0.23.0 -This release of the R package builds against TileDB 2.19.0, and has also been tested against earlier releases as well as the development version (#641) - +This release of the R package builds against TileDB 2.19.0, and has also been tested against earlier releases as well as the development version (#641) Improvements A TileDB Array can now be opened in ‘keep open’ mode for subsequent use without re-opening (#630) Arrays with factor (or ordered) variables now grow their factor levels in appending writes (#639) @@ -252,8 +230,7 @@ Improvements Bug Fixes -The read buffer is now correctly sized when implementing VFS serialization (#631) - +The read buffer is now correctly sized when implementing VFS serialization (#631) Build and Test Systems Builds from TileDB Core non-release tarballs are now supported via new configure option (#627) @@ -265,16 +242,14 @@ Build and Test Systems tiledb 0.22.0 -This release of the R package builds against TileDB 2.18.0, TileDB 2.18.1, TileDB 2.18.2 and has also been tested against earlier releases as well as the development version (#620,#621,#624) - +This release of the R package builds against TileDB 2.18.0, TileDB 2.18.1, TileDB 2.18.2 and has also been tested against earlier releases as well as the development version (#620,#621,#624) Improvements Use of TileDB Embedded was upgraded to release 2.18.0 (#620), 2.18.1 (#621), and 2.18.2 (#624) Support for Aggregates has been added (#623) Bug Fixes -When using serializing via VFS (as added in #608) the filehandles is now properly released (#619) - +When using serializing via VFS (as added in #608) the filehandles is now properly released (#619) Build and Test Systems Some tests were refactored slightly for greater robustness (#618) @@ -282,29 +257,23 @@ Build and Test Systems Documentation -The README now contains a badge for the r-universe version (in addition to CRAN) (#617) - +The README now contains a badge for the r-universe version (in addition to CRAN) (#617) tiledb 0.21.3 -This release of the R package builds against TileDB 2.17.4, and has also been tested against earlier releases as well as the development version (#611) - +This release of the R package builds against TileDB 2.17.4, and has also been tested against earlier releases as well as the development version (#611) Improvements -Query conditioning parsing now supports factor index columns other than the standard integer type (#614) - +Query conditioning parsing now supports factor index columns other than the standard integer type (#614) Build and Test Systems -The nightly valgrind run was updated to include release 2.18 (#615) - +The nightly valgrind run was updated to include release 2.18 (#615) Documentation -The pkgdown documentation has been updated for release 0.21.2 (#613) and release 0.21.3 (#616) - +The pkgdown documentation has been updated for release 0.21.2 (#613) and release 0.21.3 (#616) tiledb 0.21.2 -This release of the R package builds against TileDB 2.17.4, and has also been tested against earlier releases as well as the development version (#611) - +This release of the R package builds against TileDB 2.17.4, and has also been tested against earlier releases as well as the development version (#611) Improvements Set conditions are supported in query condition expressions (#597) Query conditions expression parsing via parse_query_conditions was extended simmilarly (#598) @@ -326,13 +295,11 @@ Bug Fixes Build and Test Systems -The nightly valgrind run was updated to include release 2.17 (#603) - +The nightly valgrind run was updated to include release 2.17 (#603) tiledb 0.21.1 -This release of the R package builds against TileDB 2.17.1, and has also been tested against earlier releases as well as the development version (#593) - +This release of the R package builds against TileDB 2.17.1, and has also been tested against earlier releases as well as the development version (#593) Improvements Array schema evolution has been extended to support enumerations (#590, #591) Conversion to and from integer64 (and nanotime) now use package RcppInt64 (#592) @@ -340,13 +307,11 @@ Improvements Bug Fixes -An added sorting of factor levels insert has been reverted (#594) - +An added sorting of factor levels insert has been reverted (#594) tiledb 0.21.0 -This release of the R package builds against TileDB 2.17.0, and has also been tested against earlier releases as well as the development version (#583, #587) - +This release of the R package builds against TileDB 2.17.0, and has also been tested against earlier releases as well as the development version (#583, #587) Improvements Use of TileDB Embedded was upgraded to release 2.17.0 (#583,#587) Built-time configuration of TileDB Embedded can now be accessed as a JSON string (#584) @@ -356,16 +321,13 @@ Improvements tiledb 0.20.3 -This release of the R package builds against TileDB 2.16.2, and has also been tested against earlier releases as well as the development version (#582) - +This release of the R package builds against TileDB 2.16.2, and has also been tested against earlier releases as well as the development version (#582) Improvements -Use of TileDB Embedded was upgraded to release 2.16.2 (#581) - +Use of TileDB Embedded was upgraded to release 2.16.2 (#581) tiledb 0.20.2 -This release of the R package builds against TileDB 2.16.1, and has also been tested against earlier releases as well as the development version (#579) - +This release of the R package builds against TileDB 2.16.1, and has also been tested against earlier releases as well as the development version (#579) Improvements The column buffer allocation is now robust to container overflow sanitizer checks (#574) The array schema version is now accessible via a function (#575) @@ -374,13 +336,11 @@ Improvements Build and Test Systems -The minimal version of TileDB Embedded that can be used with the R package is now release 2.7.0 (#578) - +The minimal version of TileDB Embedded that can be used with the R package is now release 2.7.0 (#578) tiledb 0.19.1 -This release of the R package builds against TileDB 2.15.2, and has also been tested against earlier releases as well as the development version (#534, #541). - +This release of the R package builds against TileDB 2.15.2, and has also been tested against earlier releases as well as the development version (#534, #541). Improvements Query conditions can now be expressed for attributes of type UTF-8 (#529) The startup message now displays the operating system and version (#532) @@ -399,11 +359,9 @@ Build and Test Systems tiledb 0.19.0 -This release of the R package builds against TileDB 2.15.0, and has also been tested against earlier releases as well as the development version (#516, #521). - +This release of the R package builds against TileDB 2.15.0, and has also been tested against earlier releases as well as the development version (#516, #521). Breaking Changes -The validity map coding of nullable strings has been corrected: validity map values of one are now interpreted as valid/non-null for full compatibility with other TileDB projects. Previously written arrays with nullable strings can be read by setting the config option r.legacy_validity_mode to true; the option also permits to write to an older installation. A conversion helper script is provided in scripts/legacy_validity_convert.r. (#517) - +The validity map coding of nullable strings has been corrected: validity map values of one are now interpreted as valid/non-null for full compatibility with other TileDB projects. Previously written arrays with nullable strings can be read by setting the config option r.legacy_validity_mode to true; the option also permits to write to an older installation. A conversion helper script is provided in scripts/legacy_validity_convert.r. (#517) Improvements Attributes can now be created, written and read from in (explicit) UTF8 types (and CHAR and ASCII already behaved correctly with respect to utf8 data) (#510) @@ -415,48 +373,34 @@ Improvements Bug Fixes -The access to JSON-formatted performance statistics has been simplified (#514) - +The access to JSON-formatted performance statistics has been simplified (#514) Build and Test Systems The TileDB Embedded version is now used to determine whether a dampener is needed for the deprecation warning (#511) One of the test data sets included with #517 has been regenerated under an older TileDB version in order to test on more systems (#523) Documentation for Metadata accessors no longer states URIs strings are accepted (#527) - -Deprecations - - -Removals - +Deprecations +Removals tiledb 0.18.0 -This release of the R package builds against TileDB 2.14.0, and has also been tested against earlier releases as well as the development version (#502). - +This release of the R package builds against TileDB 2.14.0, and has also been tested against earlier releases as well as the development version (#502). Improvements -Use of TileDB Embedded was upgraded to release 2.14.0 (#505) - - -Bug Fixes - +Use of TileDB Embedded was upgraded to release 2.14.0 (#505) +Bug Fixes Build and Test Systems The nightly valgrind job matrix was updated to releases 2.13 and 2.14 as well as the branch (#504) The nightly valgrind job show the most recent commit sha1 after updating from release branches (#507) A query condition test for utf8 attributes has been added (#507, #508) - -Deprecations - - -Removals - +Deprecations +Removals tiledb 0.17.1 -This release of the R package builds against TileDB 2.13.1, and has also been tested against earlier releases as well as the development version (#502). - +This release of the R package builds against TileDB 2.13.1, and has also been tested against earlier releases as well as the development version (#502). Improvements Support for Subarrays to set ranges has been extended (#496) Deprecated Core API functions for Array access and range setting are longer used (#496) @@ -476,17 +420,14 @@ Build and Test Systems Deprecations -Functions libtiledb_query_add_range{,_with_type} relying on depecreated Core functionality are deprecated, and will be removed with the Core functions. Subarray range setters are available. This is a mostly internal change. - +Functions libtiledb_query_add_range{,_with_type} relying on depecreated Core functionality are deprecated, and will be removed with the Core functions. Subarray range setters are available. This is a mostly internal change. Removals -Functions libtiledb_query_set_coordinates() and libtiledb_coords() which have been deprecated since June 2000 have been removed. (#497) - +Functions libtiledb_query_set_coordinates() and libtiledb_coords() which have been deprecated since June 2000 have been removed. (#497) tiledb 0.17.0 -This release of the R package builds against TileDB 2.13.0, and has also been tested against earlier releases as well as the development version (#492). - +This release of the R package builds against TileDB 2.13.0, and has also been tested against earlier releases as well as the development version (#492). Improvements Support for testing group URIs on being relative has been added (#478) Logging support at the R and C++ level has been added (#479, #487, #489) @@ -509,8 +450,7 @@ Build and Test Systems tiledb 0.16.0 -This release of the R package builds against TileDB 2.12.0, and has also been tested against earlier releases as well as the development version (#476). - +This release of the R package builds against TileDB 2.12.0, and has also been tested against earlier releases as well as the development version (#476). Improvements Several deprecated API entry points of TileDB Embedded are no longer used (#452, #453) Support for DELETE queries has been added (requires TileDB Embedded 2.12.0 or later) (#455, #456) @@ -539,8 +479,7 @@ Build and Test Systems tiledb 0.15.0 -This release of the R package builds against TileDB 2.11.0, and has also been tested against earlier releases as well as the development version (#451). - +This release of the R package builds against TileDB 2.11.0, and has also been tested against earlier releases as well as the development version (#451). Improvements Support for query conditions has been extended to dense arrays (#447) Support for filter lists has extended to both the data.frame helper and the dimension object constructor (#448) @@ -548,17 +487,14 @@ Improvements Bug Fixes -Small enhancements have been made to the test suite (#450) - +Small enhancements have been made to the test suite (#450) Build and Test Systems -A small enhancement was made to the test system (#450) - +A small enhancement was made to the test system (#450) tiledb 0.14.1 -This release of the R package builds against TileDB 2.10.2, and has also been tested against earlier releases as well as the development version. - +This release of the R package builds against TileDB 2.10.2, and has also been tested against earlier releases as well as the development version. Improvements Use of TileDB Embedded was upgraded to release 2.10.2 (#443) following an earlier update to 2.10.1 (#434) List columns are now supported in reading and writing of data frames by extending cell variable numbers beyond one (#438, #440) @@ -572,13 +508,11 @@ Bug Fixes Build and Test Systems -The nightly valgrind check was updated to Ubuntu 22.04 (#435, #439, #442) - +The nightly valgrind check was updated to Ubuntu 22.04 (#435, #439, #442) tiledb 0.14.0 -This release of the R package builds against TileDB 2.10.0, and has also been tested against earlier releases as well as the development version. - +This release of the R package builds against TileDB 2.10.0, and has also been tested against earlier releases as well as the development version. Improvements Use of TileDB Embedded was upgraded to release 2.10.0 (#432) following earlier updates to 2.9.1 (#415), 2.9.2 (#419), 2.9.3 (#422), 2.9.4 (#427) and 2.9.5 (#430) The BOOL data type is now supported (#416) @@ -590,8 +524,7 @@ Improvements Bug Fixes -The attr setter for Attributes was corrected to support NA settings (#425) - +The attr setter for Attributes was corrected to support NA settings (#425) Build and Test Systems Filter compression tests are skipped on systems lacking AVX2 support (#418) @@ -602,8 +535,7 @@ Build and Test Systems tiledb 0.13.0 -This release of the R package builds against TileDB 2.9.0, and has also been tested against earlier releases as well as the development version. - +This release of the R package builds against TileDB 2.9.0, and has also been tested against earlier releases as well as the development version. Improvements Support for groups has been added for TileDB 2.8 or later (#404) The group member name retrieval can now also return the optional group member name (#399) @@ -615,12 +547,10 @@ Improvements Bug Fixes -Tests for filters have been made more robust (#407, #412) - +Tests for filters have been made more robust (#407, #412) Deprecations -The check() function is now deprecated and schema_check() is provided (#409) - +The check() function is now deprecated and schema_check() is provided (#409) Build and Test Systems Nightly valgrind checks were updated to use current versions (#397, #402) @@ -629,8 +559,7 @@ Build and Test Systems tiledb 0.12.0 -This release of the R package builds against TileDB 2.8.0, and has also been tested against earlier releases as well as the development version. - +This release of the R package builds against TileDB 2.8.0, and has also been tested against earlier releases as well as the development version. Improvements A schedule nightly continuous action now checks current and release-candidate branches of TileDB with the R package under valgrind (#387) Support for Groups was added (#388, #392, #395) @@ -651,8 +580,7 @@ Bug Fixes tiledb 0.11.1 -This release of the R package builds against TileDB 2.6.4, but has also been tested against earlier releases, and the development version. - +This release of the R package builds against TileDB 2.6.4, but has also been tested against earlier releases, and the development version. Improvements Use of TileDB Embedded was upgraded to release 2.6.4 (#384) following an earlier upgrade to 2.6.2 (#359) Creations of arrays from data.frame objects now supports a mode= argument with values ‘ingest’, ‘schema_only’, and ‘append’ (#360) @@ -684,13 +612,11 @@ Documentation Deprecations -The tiledb_dense and tiledb_sparse functions which were deprecated in February 2021 have been removed after a twelve-month grace period. - +The tiledb_dense and tiledb_sparse functions which were deprecated in February 2021 have been removed after a twelve-month grace period. tiledb 0.11.0 -This release of the R package builds against TileDB 2.6.1, but has also been tested against previous releases, and the development version. - +This release of the R package builds against TileDB 2.6.1, but has also been tested against previous releases, and the development version. Improvements Use of TileDB Embedded was upgraded to release 2.6.1 (#354) following an earlier upgrade to 2.6.0 (#340) A cell value getter for dimension was added (#341) @@ -709,8 +635,7 @@ Bug Fixes tiledb 0.10.2 -This release of the R package builds against TileDB 2.5.3, but has been tested against previous releases, and the development version. - +This release of the R package builds against TileDB 2.5.3, but has been tested against previous releases, and the development version. Improvements The stopifnot() assertions now use consistent error messages across all functions (#331) A helper function matching TileDB data types to R types is now exported (#336) @@ -723,20 +648,16 @@ Bug Fixes tiledb 0.10.1 -This release of the R package builds against TileDB 2.5.2, but has been tested against previous releases, and the development version. - +This release of the R package builds against TileDB 2.5.2, but has been tested against previous releases, and the development version. Improvements -An accessor for the most-recent error message string has been added (#327) - +An accessor for the most-recent error message string has been added (#327) Bug Fixes -On Linux, if a pre-made TileDB Embedded library is used, lack of AVX2 instructions is now detected and a suitable build is deployed (#328) - +On Linux, if a pre-made TileDB Embedded library is used, lack of AVX2 instructions is now detected and a suitable build is deployed (#328) tiledb 0.10.0 -This release of the R package builds against TileDB 2.5.1, but has been tested against previous releases, and the development version. - +This release of the R package builds against TileDB 2.5.1, but has been tested against previous releases, and the development version. Improvements CI tests were expanded to also test refactored TileDB Embedded readers (#310), and now deactivated as this is now part of release 2.5.0 (#321) The minimal version of TileDB Embedded that can be used with the R package is now release 2.0.0 (#313) @@ -757,8 +678,7 @@ Bug Fixes tiledb 0.9.7 -This release of the R package builds against TileDB 2.4.0, but has been tested against previous releases and the development version. - +This release of the R package builds against TileDB 2.4.0, but has been tested against previous releases and the development version. Improvements Accessors for context and query statistics were added (returning easily parseable JSON strings) (#293). Initial support for schema evolution was added to add or drop attributes (#294). @@ -780,8 +700,7 @@ Bug Fixes tiledb 0.9.6 -This release of the R package builds against TileDB 2.3.4, but has been tested against previous releases and the development version. - +This release of the R package builds against TileDB 2.3.4, but has been tested against previous releases and the development version. Improvements When retrieving results via the [ operator, incomplete queries generate a warning (#283) The interface to query element size of queries was extended (#282) @@ -801,8 +720,7 @@ Bug Fixes tiledb 0.9.5 -This release of the R package builds against TileDB 2.3.3, but has also been tested against previous releases and the development version. - +This release of the R package builds against TileDB 2.3.3, but has also been tested against previous releases and the development version. Improvements A query condition parser was added for use with standard (non-quoted) R expressions (#267) Windows UCRT builds at CRAN are now supported (#268) @@ -824,8 +742,7 @@ Bug Fixes tiledb 0.9.4 -This release of the R package builds against TileDB 2.3.1, but has also been tested against previous releases and the development version. - +This release of the R package builds against TileDB 2.3.1, but has also been tested against previous releases and the development version. Improvements The build defaults to TileDB Embedded 2.3.* (unless another version is found during build, or explicitly selected) (#258, #264) Query condition support is available for TileDB 2.3.0 or later, allowing (possibly multiple) numerical constraints on attributes (#261) @@ -834,13 +751,11 @@ Improvements Bug Fixes -Dense arrays with more than two dimensions can now be written (#260) - +Dense arrays with more than two dimensions can now be written (#260) tiledb 0.9.3 -This release of the R package builds against TileDB 2.2.9, but has also been tested against previous releases as well as the development version. - +This release of the R package builds against TileDB 2.2.9, but has also been tested against previous releases as well as the development version. Improvements Continuous integration at GitHub is now faster as suggested packages are no longer installed (#250) Arrays can now be written incrementally via the higher-level replacement function arr[] <- obj (#251) @@ -855,8 +770,7 @@ Bug Fixes tiledb 0.9.2 -This release of the R package builds against TileDB 2.2.9, but has also been tested against previous releases as well as the development version. - +This release of the R package builds against TileDB 2.2.9, but has also been tested against previous releases as well as the development version. Improvements Matrix objects can now be returned under range selections (#247) Matrix return get turned on and off with setter / getter functions (#248) @@ -870,8 +784,7 @@ Bug Fixes tiledb 0.9.1 -This release of the R package builds against TileDB 2.2.9, but has also been tested against previous releases as well as the development version. - +This release of the R package builds against TileDB 2.2.9, but has also been tested against previous releases as well as the development version. Improvements A new vignette show use of TileDB array via RMariaDB and the MyTile extension to MariaDB (#221) Matrices can now be returned directly from suitable two-dimensional TileDB arrays (#225) @@ -897,8 +810,7 @@ Bug Fixes tiledb 0.9.0 -This release of the R package builds against TileDB 2.2.4, but has also been tested against two previous release series as well as the development version. - +This release of the R package builds against TileDB 2.2.4, but has also been tested against two previous release series as well as the development version. Improvements The older implementations tiledb_dense and tiledb_sparse are now marked as deprecated in favor of tiledb_array. No removal date is set or planned yet, but it is recommended to migrate to new code. (#180) Updated the underlying TileDB library to use TileDB 2.1.2 on macOS and Linux (when no system library is found) (#181) @@ -932,8 +844,7 @@ Improvements tiledb 0.8.2 -This release of the R package builds against TileDB 2.1.1, but has also been tested against previous releases as well as the development version. - +This release of the R package builds against TileDB 2.1.1, but has also been tested against previous releases as well as the development version. Bug Fixes The tiledb_stats_reset() function is now exported, and tiledb_stats_print() has been re-added as a wrapper to tiledb_stats_dump() (#174) Configuration options for compute and input/output concurrency set only the new TileDB 2.1 configuration options; documentation on how to checking values has been expanded. (#175) @@ -943,8 +854,7 @@ Bug Fixes tiledb 0.8.1 -This release of the R package supports TileDB 2.1.0, but has also been tested against the previous release TileDB 2.0.8. - +This release of the R package supports TileDB 2.1.0, but has also been tested against the previous release TileDB 2.0.8. Improvements R-based metadata accessors have been extended to also support tiledb_array arrays (#169) configure now also checks the hardware platform before attempting a download of a prebuilt library (#170) @@ -952,13 +862,11 @@ Improvements Bug Fixes -A typo in the manual page source, copied three more times, has been corrected (#167) - +A typo in the manual page source, copied three more times, has been corrected (#167) tiledb 0.8.0 -This release of the R package supports TileDB 2.0.8, but has also been tested against the previous release TileDB 1.7.7. - +This release of the R package supports TileDB 2.0.8, but has also been tested against the previous release TileDB 1.7.7. Improvements A new function limitTileDBCores() controls resource use, it is being used in tests (#139) The function tiledb_get_context() is now exported (#140) @@ -983,8 +891,7 @@ Bug Fixes tiledb 0.7.1 This release of the R package supports TileDB 1.7.7 and TileDB 2.0.5 - - + Improvements Range selection for tiledb_array objects can get/set matrices defining range (#132) The show methods are now consistently exported and documented (#134) @@ -997,14 +904,12 @@ Improvements Bug Fixes -A character conversion when retrieving array metadata resulting in an out-of-bounds reads has been corrected (#137) - +A character conversion when retrieving array metadata resulting in an out-of-bounds reads has been corrected (#137) tiledb 0.7.0 This release of the R package supports TileDB 1.7.7 and TileDB 2.0.5 - - + Improvements All S4 classes are now consistently documented or aliased (#117) If needed, the build system now builds TileDB and its required component (#118) @@ -1019,8 +924,7 @@ Improvements tiledb 0.6.0 This release of the R package supports TileDB 1.7.7 and TileDB 2.0.0 - - + Improvements Added support for heterogenous domains Added support for string dimensions @@ -1036,40 +940,34 @@ Improvements Changes -Dimension attributes must now be named - +Dimension attributes must now be named tiledb 0.5.0 -This release of the R package builds against the 1.7.5 releases of TileDB. - +This release of the R package builds against the 1.7.5 releases of TileDB. Improvements -Added support for i) multi-range subarrays, ii) incomplete queries, -result size estimation and ‘time travel’ at to time-points has been added #105 - - +Added support for i) multi-range subarrays, ii) incomplete queries,result size estimation and ‘time travel’ at to time-points has been added #105 + Added additional support for metadata #106 tiledb 0.4.0 -This release of the R package builds against the 1.7.* releases of tiledb. - +This release of the R package builds against the 1.7.* releases of tiledb. Improvements -This release contains increased coverage of the underlying API, additional documentation as well as unit tests. - +This release contains increased coverage of the underlying API, additional documentation as well as unit tests. diff --git a/docs/pkgdown.js b/docs/pkgdown.js index 9757bf9ef2..1a99c65f5c 100644 --- a/docs/pkgdown.js +++ b/docs/pkgdown.js @@ -152,3 +152,11 @@ async function searchFuse(query, callback) { }); }); })(window.jQuery || window.$) + +document.addEventListener('keydown', function(event) { + // Check if the pressed key is '/' + if (event.key === '/') { + event.preventDefault(); // Prevent any default action associated with the '/' key + document.getElementById('search-input').focus(); // Set focus to the search input + } +}); diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index f50de19444..8098c90ca7 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,5 +1,5 @@ -pandoc: 3.1.3 -pkgdown: 2.1.0 +pandoc: 2.9.2.1 +pkgdown: 2.1.1 pkgdown_sha: ~ articles: data-ingestion-from-sql: data-ingestion-from-sql.html @@ -7,7 +7,7 @@ articles: installation-options: installation-options.html introduction: introduction.html tiledb-mariadb-examples: tiledb-mariadb-examples.html -last_built: 2024-12-12T15:49Z +last_built: 2025-01-14T19:21Z urls: reference: https://tiledb-inc.github.io/TileDB-R/reference article: https://tiledb-inc.github.io/TileDB-R/articles diff --git a/docs/reference/array_consolidate.html b/docs/reference/array_consolidate.html index ceb1e5aba3..776fadc1b4 100644 --- a/docs/reference/array_consolidate.html +++ b/docs/reference/array_consolidate.html @@ -1,5 +1,5 @@ -Consolidate fragments of a TileDB Array — array_consolidate • tiledbConsolidate fragments of a TileDB Array — array_consolidate • tiledbtiledb - 0.31.0 + 0.31.0.1 @@ -103,11 +103,11 @@ Value diff --git a/docs/reference/array_vacuum.html b/docs/reference/array_vacuum.html index cbffc1efe5..d98a4991fa 100644 --- a/docs/reference/array_vacuum.html +++ b/docs/reference/array_vacuum.html @@ -1,5 +1,5 @@ -After consolidation, remove consolidated fragments of a TileDB Array — array_vacuum • tiledbAfter consolidation, remove consolidated fragments of a TileDB Array — array_vacuum • tiledbtiledb - 0.31.0 + 0.31.0.1 @@ -103,11 +103,11 @@ Details diff --git a/docs/reference/as.data.frame.tiledb_config.html b/docs/reference/as.data.frame.tiledb_config.html index 29000b538a..9fcaca314b 100644 --- a/docs/reference/as.data.frame.tiledb_config.html +++ b/docs/reference/as.data.frame.tiledb_config.html @@ -1,5 +1,5 @@ -Convert a tiledb_config object to a R data.frame — as.data.frame.tiledb_config • tiledb +Convert a tiledb_config object to a R data.frame — as.data.frame.tiledb_config • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -392,11 +392,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/as.vector.tiledb_config.html b/docs/reference/as.vector.tiledb_config.html index 5d069349f0..e7a8e16edc 100644 --- a/docs/reference/as.vector.tiledb_config.html +++ b/docs/reference/as.vector.tiledb_config.html @@ -1,5 +1,5 @@ -Convert a tiledb_config object to a R vector — as.vector.tiledb_config • tiledb +Convert a tiledb_config object to a R vector — as.vector.tiledb_config • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -390,11 +390,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/attrs-set-tiledb_array-method.html b/docs/reference/attrs-set-tiledb_array-method.html index bcbc419dd9..2c64564a6e 100644 --- a/docs/reference/attrs-set-tiledb_array-method.html +++ b/docs/reference/attrs-set-tiledb_array-method.html @@ -1,5 +1,5 @@ -Selects attributes for the given TileDB array — attrs<-,tiledb_array-method • tiledb +Selects attributes for the given TileDB array — attrs<-,tiledb_array-method • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -81,11 +81,11 @@ Value diff --git a/docs/reference/attrs-tiledb_array-ANY-method.html b/docs/reference/attrs-tiledb_array-ANY-method.html index f95ab1fa6e..476d9c86ff 100644 --- a/docs/reference/attrs-tiledb_array-ANY-method.html +++ b/docs/reference/attrs-tiledb_array-ANY-method.html @@ -1,5 +1,5 @@ -Retrieve attributes from tiledb_array object — attrs,tiledb_array,ANY-method • tiledbRetrieve attributes from tiledb_array object — attrs,tiledb_array,ANY-method • tiledbtiledb - 0.31.0 + 0.31.0.1 @@ -82,11 +82,11 @@ Value diff --git a/docs/reference/attrs-tiledb_array_schema-ANY-method.html b/docs/reference/attrs-tiledb_array_schema-ANY-method.html index 7c9859a847..08792afc8c 100644 --- a/docs/reference/attrs-tiledb_array_schema-ANY-method.html +++ b/docs/reference/attrs-tiledb_array_schema-ANY-method.html @@ -1,5 +1,5 @@ -Returns a list of all tiledb_attr objects associated with the tiledb_array_schema — attrs,tiledb_array_schema,ANY-method • tiledb +Returns a list of all tiledb_attr objects associated with the tiledb_array_schema — attrs,tiledb_array_schema,ANY-method • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -62,7 +62,7 @@ Argumentsobject -tiledb_array_schema +A TileDB Schema object idx @@ -75,7 +75,7 @@ Arguments Value - a list of tiledb_attr objects + A list of tiledb_attr objects @@ -108,11 +108,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/attrs-tiledb_array_schema-character-method.html b/docs/reference/attrs-tiledb_array_schema-character-method.html index 20b9e0598b..74a2c867ca 100644 --- a/docs/reference/attrs-tiledb_array_schema-character-method.html +++ b/docs/reference/attrs-tiledb_array_schema-character-method.html @@ -1,5 +1,5 @@ -Returns a tiledb_attr object associated with the tiledb_array_schema with a given name. — attrs,tiledb_array_schema,character-method • tiledb +Returns a tiledb_attr object associated with the tiledb_array_schema with a given name. — attrs,tiledb_array_schema,character-method • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -62,7 +62,7 @@ Argumentsobject -tiledb_array_schema +A TileDB Schema object idx @@ -75,7 +75,7 @@ Arguments Value - a tiledb_attr object + A tiledb_attr object @@ -95,11 +95,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/attrs-tiledb_array_schema-numeric-method.html b/docs/reference/attrs-tiledb_array_schema-numeric-method.html index 948b849bc4..6bb04eb131 100644 --- a/docs/reference/attrs-tiledb_array_schema-numeric-method.html +++ b/docs/reference/attrs-tiledb_array_schema-numeric-method.html @@ -1,5 +1,5 @@ -Returns a tiledb_attr object associated with the tiledb_array_schema with a given index — attrs,tiledb_array_schema,numeric-method • tiledb +Returns a tiledb_attr object associated with the tiledb_array_schema with a given index — attrs,tiledb_array_schema,numeric-method • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -62,7 +62,7 @@ Argumentsobject -tiledb_array_schema +A TileDB Schema object idx @@ -75,7 +75,7 @@ Arguments Value - a tiledb_attr object + A tiledb_attr object @@ -95,11 +95,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/cell_order-tiledb_array_schema-method.html b/docs/reference/cell_order-tiledb_array_schema-method.html index b9b9c8eb06..f4a00f530f 100644 --- a/docs/reference/cell_order-tiledb_array_schema-method.html +++ b/docs/reference/cell_order-tiledb_array_schema-method.html @@ -1,5 +1,5 @@ -Returns the cell layout string associated with the tiledb_array_schema — cell_order,tiledb_array_schema-method • tiledb +Returns the cell layout string associated with the tiledb_array_schema — cell_order,tiledb_array_schema-method • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -62,20 +62,24 @@ Argumentsobject -tiledb object +A TileDB Schema object + + Value + A character string with cell's layout, e.g., "COL_MAJOR". + diff --git a/docs/reference/completedBatched.html b/docs/reference/completedBatched.html index 892f682334..01ef8d0da7 100644 --- a/docs/reference/completedBatched.html +++ b/docs/reference/completedBatched.html @@ -1,5 +1,5 @@ -Check ‘batched’ query for completion — completedBatched • tiledbCheck ‘batched’ query for completion — completedBatched • tiledbtiledb - 0.31.0 + 0.31.0.1 @@ -83,11 +83,11 @@ Value diff --git a/docs/reference/config-tiledb_ctx-method.html b/docs/reference/config-tiledb_ctx-method.html index cc94830b61..9cea2b6080 100644 --- a/docs/reference/config-tiledb_ctx-method.html +++ b/docs/reference/config-tiledb_ctx-method.html @@ -1,5 +1,5 @@ -Retrieve the tiledb_config object from the tiledb_ctx — config,tiledb_ctx-method • tiledb +Retrieve the tiledb_config object from the tiledb_ctx — config,tiledb_ctx-method • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -85,11 +85,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/createBatched.html b/docs/reference/createBatched.html index 014038e547..96531fd689 100644 --- a/docs/reference/createBatched.html +++ b/docs/reference/createBatched.html @@ -1,5 +1,5 @@ -Create a ‘batched’ query object — createBatched • tiledbCreate a ‘batched’ query object — createBatched • tiledbtiledb - 0.31.0 + 0.31.0.1 @@ -88,11 +88,11 @@ Details diff --git a/docs/reference/datatype-tiledb_attr-method.html b/docs/reference/datatype-tiledb_attr-method.html index 9721358d38..e55951f01b 100644 --- a/docs/reference/datatype-tiledb_attr-method.html +++ b/docs/reference/datatype-tiledb_attr-method.html @@ -1,5 +1,5 @@ -Return the tiledb_attr datatype — datatype,tiledb_attr-method • tiledb +Return the tiledb_attr datatype — datatype,tiledb_attr-method • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -87,11 +87,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/datatype-tiledb_dim-method.html b/docs/reference/datatype-tiledb_dim-method.html index b287c4e9cc..5e98247df8 100644 --- a/docs/reference/datatype-tiledb_dim-method.html +++ b/docs/reference/datatype-tiledb_dim-method.html @@ -1,5 +1,5 @@ -Return the tiledb_dim datatype — datatype,tiledb_dim-method • tiledb +Return the tiledb_dim datatype — datatype,tiledb_dim-method • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -62,12 +62,12 @@ Argumentsobject -tiledb_dim object +A tiledb_dim object Value - tiledb datatype string + A character string with tiledb's datatype. @@ -83,11 +83,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/datatype-tiledb_domain-method.html b/docs/reference/datatype-tiledb_domain-method.html index 1d4689c4f3..a67fd407ae 100644 --- a/docs/reference/datatype-tiledb_domain-method.html +++ b/docs/reference/datatype-tiledb_domain-method.html @@ -1,5 +1,5 @@ -Returns the tiledb_domain TileDB type string — datatype,tiledb_domain-method • tiledb +Returns the tiledb_domain TileDB type string — datatype,tiledb_domain-method • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -86,11 +86,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/datetimes_as_int64-set-tiledb_array-method.html b/docs/reference/datetimes_as_int64-set-tiledb_array-method.html index a2fdce73eb..5bda59c128 100644 --- a/docs/reference/datetimes_as_int64-set-tiledb_array-method.html +++ b/docs/reference/datetimes_as_int64-set-tiledb_array-method.html @@ -1,5 +1,5 @@ -Set datetimes_as_int64 toggle — datetimes_as_int64<- • tiledbSet datetimes_as_int64 toggle — datetimes_as_int64<- • tiledbtiledb - 0.31.0 + 0.31.0.1 @@ -93,11 +93,11 @@ Value diff --git a/docs/reference/datetimes_as_int64-tiledb_array-method.html b/docs/reference/datetimes_as_int64-tiledb_array-method.html index 16ba610612..aace3a0b41 100644 --- a/docs/reference/datetimes_as_int64-tiledb_array-method.html +++ b/docs/reference/datetimes_as_int64-tiledb_array-method.html @@ -1,5 +1,5 @@ -Retrieve datetimes_as_int64 toggle — datetimes_as_int64 • tiledbRetrieve datetimes_as_int64 toggle — datetimes_as_int64 • tiledbtiledb - 0.31.0 + 0.31.0.1 @@ -90,11 +90,11 @@ Value diff --git a/docs/reference/describe.html b/docs/reference/describe.html index a5e93448b1..5c3333aaa9 100644 --- a/docs/reference/describe.html +++ b/docs/reference/describe.html @@ -1,5 +1,5 @@ -Describe a TileDB array schema via code to create it — describe • tiledbDescribe a TileDB array schema via code to create it — describe • tiledb Skip to contents @@ -9,7 +9,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -78,11 +78,11 @@ Value diff --git a/docs/reference/dim.tiledb_array_schema.html b/docs/reference/dim.tiledb_array_schema.html index 26fcb447ef..e3465c5b77 100644 --- a/docs/reference/dim.tiledb_array_schema.html +++ b/docs/reference/dim.tiledb_array_schema.html @@ -1,5 +1,5 @@ -Retrieve the dimension (domain extent) of the domain — dim.tiledb_array_schema • tiledb +Retrieve the dimension (domain extent) of the domain — dim.tiledb_array_schema • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -62,7 +62,7 @@ Argumentsx -tiledb_array_schema +A TileDB Schema object @@ -87,11 +87,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/dim.tiledb_dim.html b/docs/reference/dim.tiledb_dim.html index baad9d0a84..b4da1bb552 100644 --- a/docs/reference/dim.tiledb_dim.html +++ b/docs/reference/dim.tiledb_dim.html @@ -1,5 +1,5 @@ -Retrieves the dimension of the tiledb_dim domain — dim.tiledb_dim • tiledb +Retrieves the dimension of the tiledb_dim domain — dim.tiledb_dim • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -62,12 +62,12 @@ Argumentsx -tiledb_dim object +A tiledb_dim object Value - a vector of the tile_dim domain type, of the dim domain dimension (extent) + A vector of the tile_dim domain type, of the dim domain dimension (extent) @@ -83,11 +83,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/dim.tiledb_domain.html b/docs/reference/dim.tiledb_domain.html index 9588671f6d..7f98ae09d3 100644 --- a/docs/reference/dim.tiledb_domain.html +++ b/docs/reference/dim.tiledb_domain.html @@ -1,5 +1,5 @@ -Retrieve the dimension (domain extent) of the domain — dim.tiledb_domain • tiledb +Retrieve the dimension (domain extent) of the domain — dim.tiledb_domain • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -86,11 +86,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/dimensions-tiledb_array_schema-method.html b/docs/reference/dimensions-tiledb_array_schema-method.html index 2435fc863b..227ec18c99 100644 --- a/docs/reference/dimensions-tiledb_array_schema-method.html +++ b/docs/reference/dimensions-tiledb_array_schema-method.html @@ -1,5 +1,5 @@ -Returns a list of tiledb_dim objects associated with the tiledb_array_schema — dimensions,tiledb_array_schema-method • tiledb +Returns a list of tiledb_dim objects associated with the tiledb_array_schema — dimensions,tiledb_array_schema-method • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -62,12 +62,12 @@ Argumentsobject -tiledb_array_schema +A TileDB Schema object Value - a list of tiledb_dim objects + A list of tiledb_dim objects @@ -100,11 +100,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/dimensions-tiledb_domain-method.html b/docs/reference/dimensions-tiledb_domain-method.html index bd6e4bc266..40cdc41eb0 100644 --- a/docs/reference/dimensions-tiledb_domain-method.html +++ b/docs/reference/dimensions-tiledb_domain-method.html @@ -1,5 +1,5 @@ -Returns a list of the tiledb_domain dimension objects — dimensions,tiledb_domain-method • tiledb +Returns a list of the tiledb_domain dimension objects — dimensions,tiledb_domain-method • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -99,11 +99,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/domain-tiledb_array_schema-method.html b/docs/reference/domain-tiledb_array_schema-method.html index 1c8f432bfb..6fcbaf3137 100644 --- a/docs/reference/domain-tiledb_array_schema-method.html +++ b/docs/reference/domain-tiledb_array_schema-method.html @@ -1,5 +1,5 @@ -Returns the tiledb_domain object associated with a given tiledb_array_schema — domain,tiledb_array_schema-method • tiledb +Returns the tiledb_domain object associated with a given tiledb_array_schema — domain,tiledb_array_schema-method • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -62,9 +62,13 @@ Argumentsobject -tiledb_array_schema +A TileDB Schema object + + Value + A tiledb_domain object + Examples @@ -82,11 +86,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/domain-tiledb_dim-method.html b/docs/reference/domain-tiledb_dim-method.html index 057c340931..01b7546a27 100644 --- a/docs/reference/domain-tiledb_dim-method.html +++ b/docs/reference/domain-tiledb_dim-method.html @@ -1,5 +1,5 @@ -Return the tiledb_dim domain — domain,tiledb_dim-method • tiledb +Return the tiledb_dim domain — domain,tiledb_dim-method • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -62,7 +62,7 @@ Argumentsobject -tiledb_dim object +A tiledb_dim object @@ -83,11 +83,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/dot-core_info.html b/docs/reference/dot-core_info.html index 50854e5e86..e36f295511 100644 --- a/docs/reference/dot-core_info.html +++ b/docs/reference/dot-core_info.html @@ -1,5 +1,5 @@ -libtiledb Information — .core_info • tiledb +libtiledb Information — .core_info • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -86,11 +86,11 @@ Checking the Examples .core_info() -#> version libtype -#> "2.27.0" "system" +#> version libtype +#> "2.27.0" "vendored" .core_hash() -#> [1] "17c9b4d820870f7c171fccf2be8fdfea" +#> [1] "712cb7e256376af4fbfecc51290a4241" @@ -99,11 +99,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/dot-pkg_config.html b/docs/reference/dot-pkg_config.html index c13faa4c2c..174a0f304d 100644 --- a/docs/reference/dot-pkg_config.html +++ b/docs/reference/dot-pkg_config.html @@ -1,5 +1,5 @@ -Compiler Arguments for Using libtiledb — .pkg_config • tiledbCompiler Arguments for Using libtiledb — .pkg_config • tiledb Skip to contents @@ -9,7 +9,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -79,9 +79,9 @@ Value Examples .pkg_config() -#> [1] "-I/usr/local/include" +#> [1] "-I/tmp/RtmpiRigbQ/temp_libpath556b1464bc75e/tiledb/include -I/tmp/RtmpiRigbQ/temp_libpath556b1464bc75e/tiledb/tiledb/include" .pkg_config("PKG_CXX_LIBS") -#> [1] "-L/usr/local/lib -ltiledb" +#> [1] "-ltiledb -L/tmp/RtmpiRigbQ/temp_libpath556b1464bc75e/tiledb/lib -L/tmp/RtmpiRigbQ/temp_libpath556b1464bc75e/tiledb/tiledb/lib" @@ -90,11 +90,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/extended-set-tiledb_array-method.html b/docs/reference/extended-set-tiledb_array-method.html index 4618988929..0149ea9749 100644 --- a/docs/reference/extended-set-tiledb_array-method.html +++ b/docs/reference/extended-set-tiledb_array-method.html @@ -1,5 +1,5 @@ -Set data.frame extended return columns toggle — extended<- • tiledbSet data.frame extended return columns toggle — extended<- • tiledbtiledb - 0.31.0 + 0.31.0.1 @@ -87,11 +87,11 @@ Value diff --git a/docs/reference/extended-tiledb_array-method.html b/docs/reference/extended-tiledb_array-method.html index fef6d703a6..29ad827156 100644 --- a/docs/reference/extended-tiledb_array-method.html +++ b/docs/reference/extended-tiledb_array-method.html @@ -1,5 +1,5 @@ -Retrieve data.frame extended returns columns toggle — extended • tiledbRetrieve data.frame extended returns columns toggle — extended • tiledbtiledb - 0.31.0 + 0.31.0.1 @@ -84,11 +84,11 @@ Value diff --git a/docs/reference/fetchBatched.html b/docs/reference/fetchBatched.html index f4ce306d49..4d117316bd 100644 --- a/docs/reference/fetchBatched.html +++ b/docs/reference/fetchBatched.html @@ -1,5 +1,5 @@ -Run a ‘batched’ query — fetchBatched • tiledbRun a ‘batched’ query — fetchBatched • tiledbtiledb - 0.31.0 + 0.31.0.1 @@ -92,11 +92,11 @@ Details diff --git a/docs/reference/filter_list-set-tiledb_attr-method.html b/docs/reference/filter_list-set-tiledb_attr-method.html index aba612335b..a803608564 100644 --- a/docs/reference/filter_list-set-tiledb_attr-method.html +++ b/docs/reference/filter_list-set-tiledb_attr-method.html @@ -1,5 +1,5 @@ -Sets the TileDB Filter List for the TileDB Attribute object — filter_list<-,tiledb_attr-method • tiledb +Sets the TileDB Filter List for the TileDB Attribute object — filter_list<-,tiledb_attr-method • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -79,11 +79,11 @@ Value diff --git a/docs/reference/filter_list-set-tiledb_dim-method.html b/docs/reference/filter_list-set-tiledb_dim-method.html index b11f369606..d7a0418c30 100644 --- a/docs/reference/filter_list-set-tiledb_dim-method.html +++ b/docs/reference/filter_list-set-tiledb_dim-method.html @@ -1,5 +1,5 @@ -Sets the TileDB Filter List for the TileDB Dimension object — filter_list<-,tiledb_dim-method • tiledb +Sets the TileDB Filter List for the TileDB Dimension object — filter_list<-,tiledb_dim-method • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -62,7 +62,7 @@ Argumentsx -TileDB Dimension +A tiledb_dim object value @@ -79,11 +79,11 @@ Value diff --git a/docs/reference/filter_list-tiledb_array_schema-method.html b/docs/reference/filter_list-tiledb_array_schema-method.html index 98baffdf54..59f87c52e5 100644 --- a/docs/reference/filter_list-tiledb_array_schema-method.html +++ b/docs/reference/filter_list-tiledb_array_schema-method.html @@ -1,5 +1,5 @@ -Returns the offsets and coordinate filter_lists associated with the tiledb_array_schema — filter_list,tiledb_array_schema-method • tiledb +Returns the offsets and coordinate filter_lists associated with the tiledb_array_schema — filter_list,tiledb_array_schema-method • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -62,12 +62,12 @@ Argumentsobject -tiledb_array_schema +A TileDB Schema object Value - a list of tiledb_filter_list objects + A list of tiledb_filter_list objects
In the next step we fetch the data—and for simplicity issue just one -select statement returning a single data.frame -(or here a data.table variant). In larger-than-memory -settings the SQL query could easily bucket by symbols, or date range, or -…
select
data.frame
data.table
In the next step we fetch the data—and for simplicity issue just one select statement returning a single data.frame (or here a data.table variant). In larger-than-memory settings the SQL query could easily bucket by symbols, or date range, or …
getDataFromSQL <- function() { con <- dbSetup() @@ -163,12 +133,7 @@ Fetch Data Writing Data to TileDB -Having read the data into memory we can use the TileDB R function -fromDataFrame. It has numerous option to configure, as well -as sensible defaults (to for example enable ZSTD compression). Here we -select the first two columns for symbol and data as dimensions. Symbols, -being text, do not set a domain set. For the date we set two ‘safe’ -outer values for the range. +Having read the data into memory we can use the TileDB R function fromDataFrame. It has numerous option to configure, as well as sensible defaults (to for example enable ZSTD compression). Here we select the first two columns for symbol and data as dimensions. Symbols, being text, do not set a domain set. For the date we set two ‘safe’ outer values for the range. storeDataTDB <- function(dat, uri) { fromDataFrame(dat, uri, @@ -176,16 +141,11 @@ Writing Data to TileDB tile_domain=list(date=c(as.numeric(as.Date("1985-01-01")), as.numeric(as.Date("2030-12-31"))))) } -The mode="append" argument of fromDataFrame -can be used to append to an existing array to support chunked -operation. +The mode="append" argument of fromDataFrame can be used to append to an existing array to support chunked operation. Reading Data Back In -Reading data from TileDB is a very standard operation of opening the -URI, possibly specifying the return type and possibly subsetting by -dimension values, or attributes. Here, for simplicity, we just read -everything. +Reading data from TileDB is a very standard operation of opening the URI, possibly specifying the return type and possibly subsetting by dimension values, or attributes. Here, for simplicity, we just read everything. getDataTDB <- function(uri) { set_allocation_size_preference(1e7) # larger than local default value @@ -206,21 +166,13 @@ Reading Data Back In See Also -The vignette TileDB MariaDB -Examples shows to use MariaDB via the MyTile integration of TileDB -as a direct backend. -The TileDB -R Tutorial at useR! 2021 contained a worked example of writing -much larger data set in chunks. The process is very similar to -the simple example we showed here – and in addition requires a suffient -domain range for the dimension along with a (sequential or parallel) -loop of reading chunks and writing them to TileDB. +The vignette TileDB MariaDB Examples shows to use MariaDB via the MyTile integration of TileDB as a direct backend. +The TileDB R Tutorial at useR! 2021 contained a worked example of writing much larger data set in chunks. The process is very similar to the simple example we showed here – and in addition requires a suffient domain range for the dimension along with a (sequential or parallel) loop of reading chunks and writing them to TileDB. Summary -This vignette provides a commented walk-through of a worked example -of a SQL-to-TileDB data ingestion. +This vignette provides a commented walk-through of a worked example of a SQL-to-TileDB data ingestion. @@ -229,11 +181,11 @@ Summary diff --git a/docs/articles/data-ingestion-from-sql_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/data-ingestion-from-sql_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 0000000000..ca349fd6a5 --- /dev/null +++ b/docs/articles/data-ingestion-from-sql_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. + +document.addEventListener('DOMContentLoaded', function() { + const codeList = document.getElementsByClassName("sourceCode"); + for (var i = 0; i < codeList.length; i++) { + var linkList = codeList[i].getElementsByTagName('a'); + for (var j = 0; j < linkList.length; j++) { + if (linkList[j].innerHTML === "") { + linkList[j].setAttribute('aria-hidden', 'true'); + } + } + } +}); diff --git a/docs/articles/documentation.html b/docs/articles/documentation.html index 48c90de3c6..3ec793d97e 100644 --- a/docs/articles/documentation.html +++ b/docs/articles/documentation.html @@ -12,7 +12,7 @@ - + @@ -26,7 +26,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -68,8 +68,7 @@ - - + TileDB API Documentation @@ -86,15 +85,11 @@ TileDB API Documentation %\VignetteEngine{simplermarkdown::mdweave_to_html} %\VignetteEncoding{UTF-8} --> -This document follows the TileDB API usage -examples. A shorter introductory -vignette is also available. +This document follows the TileDB API usage examples. A shorter introductory vignette is also available. Prelimaries -We will show two initial and basic examples for a dense and sparse -array simply to create array data on disk to refer to later in examples -that follow. +We will show two initial and basic examples for a dense and sparse array simply to create array data on disk to refer to later in examples that follow. library(tiledb) @@ -1304,11 +1299,11 @@ Catching Errors diff --git a/docs/articles/documentation_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/documentation_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 0000000000..ca349fd6a5 --- /dev/null +++ b/docs/articles/documentation_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. + +document.addEventListener('DOMContentLoaded', function() { + const codeList = document.getElementsByClassName("sourceCode"); + for (var i = 0; i < codeList.length; i++) { + var linkList = codeList[i].getElementsByTagName('a'); + for (var j = 0; j < linkList.length; j++) { + if (linkList[j].innerHTML === "") { + linkList[j].setAttribute('aria-hidden', 'true'); + } + } + } +}); diff --git a/docs/articles/index.html b/docs/articles/index.html index e74f7844ec..6eb1a0a5b5 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -1,5 +1,5 @@ -Articles • tiledb +Articles • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -75,11 +75,11 @@ Working with SQL diff --git a/docs/articles/installation-options.html b/docs/articles/installation-options.html index e82d52aade..40b28296d9 100644 --- a/docs/articles/installation-options.html +++ b/docs/articles/installation-options.html @@ -12,7 +12,7 @@ - + @@ -26,7 +26,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -68,8 +68,7 @@ - - + Installation Options for the TileDB R Package @@ -90,53 +89,30 @@ 2022-01-25 Overview -This vignette discusses different options for installing the TileDB R -package. +This vignette discusses different options for installing the TileDB R package. CRAN Binaries -The TileDB R package is released via the Comprehensive R Archive -Network, or CRAN. CRAN generally provides binaries for the two most -widely operating systems, Windows and macOS. So issueing the command +The TileDB R package is released via the Comprehensive R Archive Network, or CRAN. CRAN generally provides binaries for the two most widely operating systems, Windows and macOS. So issueing the command install.packages("tiledb") -will, on those two operating system, default to -type="binary" and install a ready-to-run binary -package. +will, on those two operating system, default to type="binary" and install a ready-to-run binary package. Source -On other operating systems such as Linux, or by explicitly selecting -type="source" on Windows or macOS, an installation from source is attempted when usinginstall.packages(“tiledb”)`. -On Linux or macOS, this invokes the standard R build process which -will rely on configure. If pkg-config is -found, it is used to query the system about a possible TileDB -installation. If one is found, it used. Otherwise, on all three main -operating systems a prebuilt archive with the TileDB Embedded library is -downloaded from GitHub and unpacked. Each build of the R package will -have one matching build of TileDB Embedded associated with it via file -the tools/tiledbVersion.txt specifying a version and -release commit sha1. These two values are used to find the corresponding -binary artifacts from a release at GitHub. -The location of an existing installed version of TileDB Embedded can -also be provided to the configure script which supplies an -argument --with-tiledb=PATH. So on the command-line, one -could say -R CMD INSTALL --configure-args='--with-tiledb=/some/path' tiledb_*.tar.gz -to pass the configure argument on. From within R, the -equivalent command is +On other operating systems such as Linux, or by explicitly selecting type="source" on Windows or macOS, an installation from source is attempted when usinginstall.packages(“tiledb”)`. +On Linux or macOS, this invokes the standard R build process which will rely on configure. If pkg-config is found, it is used to query the system about a possible TileDB installation. If one is found, it used. Otherwise, on all three main operating systems a prebuilt archive with the TileDB Embedded library is downloaded from GitHub and unpacked. Each build of the R package will have one matching build of TileDB Embedded associated with it via file the tools/tiledbVersion.txt specifying a version and release commit sha1. These two values are used to find the corresponding binary artifacts from a release at GitHub. +The location of an existing installed version of TileDB Embedded can also be provided to the configure script which supplies an argument --with-tiledb=PATH. So on the command-line, one could say +R CMD INSTALL --configure-args='--with-tiledb=/some/path' tiledb_*.tar.gz +to pass the configure argument on. From within R, the equivalent command is install.packages("tiledb", repos=NULL, configure.args="--with-tiledb=/some/path") -Lastly, one can also override the default download location -(otherwise inferred via tools/tiledbVersion.txt. The -configure script supports an option ---with-download=URL so the two calls become, -respectively -R CMD INSTALL --configure-args='--with-download=https://some.where.net/file.tgz' tiledb_*.tar.gz +Lastly, one can also override the default download location (otherwise inferred via tools/tiledbVersion.txt. The configure script supports an option --with-download=URL so the two calls become, respectively +R CMD INSTALL --configure-args='--with-download=https://some.where.net/file.tgz' tiledb_*.tar.gz and install.packages("tiledb_0.11.0.tar.gz", repos=NULL, @@ -147,30 +123,23 @@ Source Conda -Using for example the current condaforge/mambaforge -container from the conda-forge project, -we can do -mamba install -y r-tiledb # installs R, tiledb and deps without extra prompt -# ...several lines of installation detail omitted -R -# ... several lines of R startup output omitted -> library(tiledb) -which installs R, the tiledb package and all respective -dependencies. +Using for example the current condaforge/mambaforge container from the conda-forge project, we can do +mamba install -y r-tiledb # installs R, tiledb and deps without extra prompt +# ...several lines of installation detail omitted +R +# ... several lines of R startup output omitted +> library(tiledb) +which installs R, the tiledb package and all respective dependencies. Docker -Builds of the TileDB package could also be provided via Docker -containers. At present, no official TileDB R containers are provided by -TileDB. However, the discussion of installation from source above -describes how to create such containers. +Builds of the TileDB package could also be provided via Docker containers. At present, no official TileDB R containers are provided by TileDB. However, the discussion of installation from source above describes how to create such containers. Summary -This note described several installation options for the TileDB R -package. +This note described several installation options for the TileDB R package. @@ -179,11 +148,11 @@ Summary diff --git a/docs/articles/installation-options_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/installation-options_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 0000000000..ca349fd6a5 --- /dev/null +++ b/docs/articles/installation-options_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. + +document.addEventListener('DOMContentLoaded', function() { + const codeList = document.getElementsByClassName("sourceCode"); + for (var i = 0; i < codeList.length; i++) { + var linkList = codeList[i].getElementsByTagName('a'); + for (var j = 0; j < linkList.length; j++) { + if (linkList[j].innerHTML === "") { + linkList[j].setAttribute('aria-hidden', 'true'); + } + } + } +}); diff --git a/docs/articles/introduction.html b/docs/articles/introduction.html index b87009f33d..bf485522d9 100644 --- a/docs/articles/introduction.html +++ b/docs/articles/introduction.html @@ -12,7 +12,7 @@ - + @@ -26,7 +26,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -68,8 +68,7 @@ - - + First Steps with TileDB @@ -86,29 +85,14 @@ First Steps with TileDB %\VignetteEngine{simplermarkdown::mdweave_to_html} %\VignetteEncoding{UTF-8} --> -This document introduces TileDB via several simple examples. A -corresponding document with more complete API documentation is also available. +This document introduces TileDB via several simple examples. A corresponding document with more complete API documentation is also available. Getting started -Once the TileDB R package is installed, it can be loaded via -library(tiledb). Installation is supported for Windows, -Linux and macOS via the official CRAN -package, on Linux and macOS via the conda package as well as -from source. -Documentation for the TileDB R package is available via the -help() function from within R as well as via the package documentation -and an introductory -notebook. Documentation about TileDB itself is also available. -Several “quickstart” examples that are discussed on the website are -available in the examples -directory. This vignette discusses similar examples. -In the following examples, the URIs describing arrays point to local -file system object. When TileDB has been built with S3 support, and with -proper AWS credentials in the usual environment variables, URIs such as -s3://some/data/bucket can be used where a local file would -be used. See the script ex_S3.R -for an example. +Once the TileDB R package is installed, it can be loaded via library(tiledb). Installation is supported for Windows, Linux and macOS via the official CRAN package, on Linux and macOS via the conda package as well as from source. +Documentation for the TileDB R package is available via the help() function from within R as well as via the package documentation and an introductory notebook. Documentation about TileDB itself is also available. +Several “quickstart” examples that are discussed on the website are available in the examples directory. This vignette discusses similar examples. +In the following examples, the URIs describing arrays point to local file system object. When TileDB has been built with S3 support, and with proper AWS credentials in the usual environment variables, URIs such as s3://some/data/bucket can be used where a local file would be used. See the script ex_S3.R for an example. Dense Arrays @@ -116,104 +100,72 @@ Dense Arrays Preliminaries -These illustrations use the array created by the file ex_1.R -which one can run from within R, or on the command-line. To follow along -with discussion that follows, it helps to run the example once to create -the array after possibly adjusting the array location path from its -default value (using the current directory or, if set as an option, an -override). +These illustrations use the array created by the file ex_1.R which one can run from within R, or on the command-line. To follow along with discussion that follows, it helps to run the example once to create the array after possibly adjusting the array location path from its default value (using the current directory or, if set as an option, an override). Basic Reading of Dense Arrays -The file ex_1.R -in the examples directory is a simple yet complete example extending quickstart_dense.R -by adding a second and third attribute. In this as well as the following -examples we will use tiledb_array() to access the array; -the older variants tiledb_dense() and -tiledb_sparse() remain supported but are deprecated and may -be removed at some point in the future. +The file ex_1.R in the examples directory is a simple yet complete example extending quickstart_dense.R by adding a second and third attribute. In this as well as the following examples we will use tiledb_array() to access the array; the older variants tiledb_dense() and tiledb_sparse() remain supported but are deprecated and may be removed at some point in the future. Read 1-D -The first example extracts rows 1 to 2 and column 2 from an array. It -also limits the selection to just one attribute (via -attrs), asks for the return to be a data.frame -(instead of a simpler list) and for the (row and column, if present as -here) indices to not be printed (via extended=FALSE). -> A <- tiledb_array(uri = uri, attrs = "b", -+ return_as = "data.frame", extended=FALSE)) -> A[1:2,2] -[1] 101.5 104.0 -> -Note that the examples create three two-dimensional attributes. The -attributes can be selected via the attrs argument, or the -attrs() method on the array object. The square-bracket -indexing then selects with in the 2-d attribute object. -If multiple objects are returned (as list or -data.frame), subsetting on the returned object works via -[[var]] or $var. A numeric index also works -(but needs to account for rows and cols). -> A <- tiledb_array(uri = uri, attrs = c("a","b"), -+ return_as = "data.frame") -> A[1:2,2][["a"]] -[1] 2 7 -> A[1:2,2]$a -[1] 2 7 -> +The first example extracts rows 1 to 2 and column 2 from an array. It also limits the selection to just one attribute (via attrs), asks for the return to be a data.frame (instead of a simpler list) and for the (row and column, if present as here) indices to not be printed (via extended=FALSE). +> A <- tiledb_array(uri = uri, attrs = "b", ++ return_as = "data.frame", extended=FALSE)) +> A[1:2,2] +[1] 101.5 104.0 +> +Note that the examples create three two-dimensional attributes. The attributes can be selected via the attrs argument, or the attrs() method on the array object. The square-bracket indexing then selects with in the 2-d attribute object. +If multiple objects are returned (as list or data.frame), subsetting on the returned object works via [[var]] or $var. A numeric index also works (but needs to account for rows and cols). +> A <- tiledb_array(uri = uri, attrs = c("a","b"), ++ return_as = "data.frame") +> A[1:2,2][["a"]] +[1] 2 7 +> A[1:2,2]$a +[1] 2 7 +> Read 2-D -This works analogously. Note that the results are generally returned -as vectors, or as a columns of a data.frame object in case -that option was set. -> A[6:9,3:4] -$a -[1] 28 29 33 34 38 39 43 44 - -$b -[1] 114.5 115.0 117.0 117.5 119.5 120.0 122.0 122.5 - -$c -[1] "fox" "A" "E" "F" "J" "K" "O" "P" -> +This works analogously. Note that the results are generally returned as vectors, or as a columns of a data.frame object in case that option was set. +> A[6:9,3:4] +$a +[1] 28 29 33 34 38 39 43 44 + +$b +[1] 114.5 115.0 117.0 117.5 119.5 120.0 122.0 122.5 + +$c +[1] "fox" "A" "E" "F" "J" "K" "O" "P" +> Read 2-D with attribute selection -We can restrict the selection to a subset of attributes when opening -the array. -> A <- tiledb_dense(uri = uri, attrs = c("b","c"), -+ return_as = "data.frame", extended=FALSE) -> A[6:9,2:4] - b c -1 114.0 brown -2 114.5 fox -3 115.0 A -4 116.5 D -5 117.0 E -6 117.5 F -7 119.0 I -8 119.5 J -9 120.0 K -10 121.5 N -11 122.0 O -12 122.5 P -> -This also illustrated the effect of setting -as.data.frame=TRUE when opening the array. -This scheme can be generalized to variable cells, or cells where -N>1, as we can expand each (atomistic) value over corresponding row -and column indices. -The column types correspond to the attribute typed in the array -schema, subject to the constraint mentioned above on R types. (The char -comes in as a factor variable as is still the R 3.6.* default which is -about to change. We can also override, users can too.) -> A <- tiledb_array("/tmp/tiledb/ex_1/", attrs=c("b","c"), -+ return_as = "data.frame", extended=TRUE) -> sapply(A[6:9, 3:4], "class") - rows cols b c - "integer" "integer" "numeric" "character" -> -Consistent with the data.frame semantics, now -requesting a named column reduces to a vector as this happens -at the R side: +We can restrict the selection to a subset of attributes when opening the array. +> A <- tiledb_dense(uri = uri, attrs = c("b","c"), ++ return_as = "data.frame", extended=FALSE) +> A[6:9,2:4] + b c +1 114.0 brown +2 114.5 fox +3 115.0 A +4 116.5 D +5 117.0 E +6 117.5 F +7 119.0 I +8 119.5 J +9 120.0 K +10 121.5 N +11 122.0 O +12 122.5 P +> +This also illustrated the effect of setting as.data.frame=TRUE when opening the array. +This scheme can be generalized to variable cells, or cells where N>1, as we can expand each (atomistic) value over corresponding row and column indices. +The column types correspond to the attribute typed in the array schema, subject to the constraint mentioned above on R types. (The char comes in as a factor variable as is still the R 3.6.* default which is about to change. We can also override, users can too.) +> A <- tiledb_array("/tmp/tiledb/ex_1/", attrs=c("b","c"), ++ return_as = "data.frame", extended=TRUE) +> sapply(A[6:9, 3:4], "class") + rows cols b c + "integer" "integer" "numeric" "character" +> +Consistent with the data.frame semantics, now requesting a named column reduces to a vector as this happens at the R side: > A[6:9, 3:4]$b [1] 114.5 115.0 117.0 117.5 119.5 120.0 122.0 122.5 > @@ -226,96 +178,78 @@ Sparse ArraysBasic Reading and Writing of Sparse Arrays Simple Examples -Basic reading returns the coordinates and any attributes. The -following examples use the array created by the quickstart_sparse -example. -> A <- tiledb_array(uri = uri, is.sparse = TRUE) -> A[] -$rows -[1] 1 2 2 - -$cols -[1] 1 3 4 - -$a -[1] 1 3 2 - -> -We can also request a data.frame object, either when -opening or by changing this object characteristic on the fly: -> return.data.frame(A) <- TRUE -> A[] - a rows cols -1 1 1 1 -2 3 2 3 -3 2 2 4 -For sparse arrays, the return type is by default ‘extended’ showing -rows and column but this can be overridden. +Basic reading returns the coordinates and any attributes. The following examples use the array created by the quickstart_sparse example. +> A <- tiledb_array(uri = uri, is.sparse = TRUE) +> A[] +$rows +[1] 1 2 2 + +$cols +[1] 1 3 4 + +$a +[1] 1 3 2 + +> +We can also request a data.frame object, either when opening or by changing this object characteristic on the fly: +> return.data.frame(A) <- TRUE +> A[] + a rows cols +1 1 1 1 +2 3 2 3 +3 2 2 4 +For sparse arrays, the return type is by default ‘extended’ showing rows and column but this can be overridden. Assignment works similarly: -> A[4,2] <- 42L -> A[] -> A[] - rows cols a -1 1 1 1 -2 2 3 3 -3 2 4 2 -4 4 2 42 -> +> A[4,2] <- 42L +> A[] +> A[] + rows cols a +1 1 1 1 +2 2 3 3 +3 2 4 2 +4 4 2 42 +> Reads can select rows and or columns: -> A[2,] - rows cols a -1 2 3 3 -2 2 4 2 -> A[,2] - rows cols a -1 4 2 42 -> +> A[2,] + rows cols a +1 2 3 3 +2 2 4 2 +> A[,2] + rows cols a +1 4 2 42 +> Attributes can be selected similarly. Date(time) Attributes -Similar to the dense array case described earlier, the file ex_2.R -illustrates some basic operations on sparse arrays. It also shows date -and datetime types instead of just integer and double precision -floats. -> A <- tiledb_array(uri = uri, return_as = "data.frame") -> A[1577858403:1577858408] - rows cols a b d e -1 1577858403 1 3 103 2020-01-11 2020-01-02 18:24:33.844 -2 1577858404 1 4 104 2020-01-15 2020-01-05 02:28:36.214 -3 1577858405 1 5 105 2020-01-19 2020-01-05 00:44:04.805 -4 1577858406 1 6 106 2020-01-21 2020-01-06 12:58:51.770 -5 1577858407 1 7 107 2020-01-25 2020-01-09 04:29:56.309 -6 1577858408 1 8 108 2020-01-26 2020-01-07 13:55:10.240 -> -The row coordinate is currently a floating point representation of -the underlying time type. We can both select attributes (here we -excluded the “a” column) and select rows by time (as the time stamps get -converted to the required floating point value). -> attrs(A) <- c("b", "d", "e") -> A[as.POSIXct("2020-01-01"):as.POSIXct("2020-01-01 00:00:03")] - rows cols b d e -1 1577858401 1 101 2020-01-05 2020-01-01 03:03:07.548 -2 1577858402 1 102 2020-01-10 2020-01-02 21:02:19.747 -3 1577858403 1 103 2020-01-11 2020-01-02 18:24:33.844 -> -More extended examples are available showing indexing by date(time) -as well as character dimension. +Similar to the dense array case described earlier, the file ex_2.R illustrates some basic operations on sparse arrays. It also shows date and datetime types instead of just integer and double precision floats. +> A <- tiledb_array(uri = uri, return_as = "data.frame") +> A[1577858403:1577858408] + rows cols a b d e +1 1577858403 1 3 103 2020-01-11 2020-01-02 18:24:33.844 +2 1577858404 1 4 104 2020-01-15 2020-01-05 02:28:36.214 +3 1577858405 1 5 105 2020-01-19 2020-01-05 00:44:04.805 +4 1577858406 1 6 106 2020-01-21 2020-01-06 12:58:51.770 +5 1577858407 1 7 107 2020-01-25 2020-01-09 04:29:56.309 +6 1577858408 1 8 108 2020-01-26 2020-01-07 13:55:10.240 +> +The row coordinate is currently a floating point representation of the underlying time type. We can both select attributes (here we excluded the “a” column) and select rows by time (as the time stamps get converted to the required floating point value). +> attrs(A) <- c("b", "d", "e") +> A[as.POSIXct("2020-01-01"):as.POSIXct("2020-01-01 00:00:03")] + rows cols b d e +1 1577858401 1 101 2020-01-05 2020-01-01 03:03:07.548 +2 1577858402 1 102 2020-01-10 2020-01-02 21:02:19.747 +3 1577858403 1 103 2020-01-11 2020-01-02 18:24:33.844 +> +More extended examples are available showing indexing by date(time) as well as character dimension. Additional Information -The TileDB R package is documented via R help functions -(e.g. help("tiledb_array") shows information for -the tiledb_array() function) as well as via a website regrouping all -documentation. Extended API -documentation is available, as is a examples/ -directory. -TileDB itself has extensive installation, -and overall -documentation as well as a support forum. +The TileDB R package is documented via R help functions (e.g. help("tiledb_array") shows information for the tiledb_array() function) as well as via a website regrouping all documentation. Extended API documentation is available, as is a examples/ directory. +TileDB itself has extensive installation, and overall documentation as well as a support forum. @@ -324,11 +258,11 @@ Additional Information diff --git a/docs/articles/introduction_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/introduction_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 0000000000..ca349fd6a5 --- /dev/null +++ b/docs/articles/introduction_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. + +document.addEventListener('DOMContentLoaded', function() { + const codeList = document.getElementsByClassName("sourceCode"); + for (var i = 0; i < codeList.length; i++) { + var linkList = codeList[i].getElementsByTagName('a'); + for (var j = 0; j < linkList.length; j++) { + if (linkList[j].innerHTML === "") { + linkList[j].setAttribute('aria-hidden', 'true'); + } + } + } +}); diff --git a/docs/articles/tiledb-mariadb-examples.html b/docs/articles/tiledb-mariadb-examples.html index 849627c0bf..866cf34a7c 100644 --- a/docs/articles/tiledb-mariadb-examples.html +++ b/docs/articles/tiledb-mariadb-examples.html @@ -12,7 +12,7 @@ - + @@ -26,7 +26,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -68,8 +68,7 @@ - - + TileDB and (R)MariaDB Examples @@ -89,43 +88,26 @@ TileDB and (R)MariaDB Examples Introduction -TileDB provides the -Universal Data Engine that can be accessed in a variety of -ways. The C/C++ library offered by TileDB Embedded is one -approach, and the R -package, as well as the Python package and -other language bindings use it. Another interface is provided by the MariaDB Integration via the -MyTile storage plugin. -This provides TileDB integration with any frontend that interfaces -with MariaDB—such as the RMariaDB package -for R. So this vignette illustrates the use of TileDB via MariaDB using -R and the RMariaDB packages. +TileDB provides the Universal Data Engine that can be accessed in a variety of ways. The C/C++ library offered by TileDB Embedded is one approach, and the R package, as well as the Python package and other language bindings use it. Another interface is provided by the MariaDB Integration via the MyTile storage plugin. +This provides TileDB integration with any frontend that interfaces with MariaDB—such as the RMariaDB package for R. So this vignette illustrates the use of TileDB via MariaDB using R and the RMariaDB packages. Installation or Using Docker -In order to use the MyTile storage plugin, one has to compile both -the storage plugin itself and the MariaDB server with consistent -compiler flags. As the build also requires the TileDB Embedded library -and headers, using a Docker container may be easiest. The Dockerfile -also provides a concrete example of the build setup. -So here we will use the tiledb/tiledb-mariadb-r -container. +In order to use the MyTile storage plugin, one has to compile both the storage plugin itself and the MariaDB server with consistent compiler flags. As the build also requires the TileDB Embedded library and headers, using a Docker container may be easiest. The Dockerfile also provides a concrete example of the build setup. +So here we will use the tiledb/tiledb-mariadb-r container. Launch Container in Background -We launch the container ‘tiledb/tiledb-mariadb-r’ as a daemon, -allowing MariaDB to accept an empty password (using an older MySQL -variable setting), and name the running image ‘tiledb-mariadb-r’: -docker run --name tiledb-mariadb-r -it -d --rm \ - -e MYSQL_ALLOW_EMPTY_PASSWORD=1 tiledb/tiledb-mariadb-r +We launch the container ‘tiledb/tiledb-mariadb-r’ as a daemon, allowing MariaDB to accept an empty password (using an older MySQL variable setting), and name the running image ‘tiledb-mariadb-r’: +docker run --name tiledb-mariadb-r -it -d --rm \ + -e MYSQL_ALLOW_EMPTY_PASSWORD=1 tiledb/tiledb-mariadb-r Access Container Once to Write via TileDB -Using the name given to the running instance, we start an R session -to write data with TileDB: -docker exec -it -u root tiledb-mariadb-r R +Using the name given to the running instance, we start an R session to write data with TileDB: +docker exec -it -u root tiledb-mariadb-r R @@ -134,220 +116,200 @@ Examples Palmer Penguins -With the sessions started as in the previous section, we start an R -session. -> library(tiledb) -> library(palmerpenguins) -> praw <- penguins_raw -> fromDataFrame(praw, "/tmp/penguinsraw") +With the sessions started as in the previous section, we start an R session. +> library(tiledb) +> library(palmerpenguins) +> praw <- penguins_raw +> fromDataFrame(praw, "/tmp/penguinsraw") Access Container Again to Read via RMariaDB -In another shell, we can access the container once more and launch -another R process: -docker exec -it -u root tiledb-mariadb-r R -where we use RMariaDB to access the data via a tibble -object and magrittr pipe -> library(RMariaDB) -> library(dplyr, warn.conflicts=FALSE) -> con <- DBI::dbConnect(RMariaDB::MariaDB(), dbname="test") -> tbl(con, "/tmp/penguinsraw") %>% -+ dplyr::select(contains("Length")) -# Source: lazy query [?? x 2] -# Database: mysql [@localhost:NA/test] - `Culmen Length (mm)` `Flipper Length (mm)` - <dbl> <dbl> - 1 39.1 181 - 2 39.5 186 - 3 40.3 195 - 4 NA NA - 5 36.7 193 - 6 39.3 190 - 7 38.9 181 - 8 39.2 195 - 9 34.1 193 -10 42 190 -# ... with more rows -Note that this R session uses TileDB only via the MyTile plugin which -is activated implicitly via the ‘table location’ (here -/tmp/penguinsraw) of the test database enabling -plugins. -Also note that the query is still ‘lazy’: only column names and the -first ten observations have been retrieved, and the total size is still -unknown as indicated by lazy query [?? x 2]. Adding a -collect() verb materialized the full subset. -> tbl(con, "/tmp/penguinsraw") %>% -+ dplyr::select(contains("Length")) %>% -+ collect() -# A tibble: 344 x 2 - `Culmen Length (mm)` `Flipper Length (mm)` - <dbl> <dbl> - 1 39.1 181 - 2 39.5 186 - 3 40.3 195 - 4 NA NA - 5 36.7 193 - 6 39.3 190 - 7 38.9 181 - 8 39.2 195 - 9 34.1 193 -10 42 190 -# ... with 334 more rows -> -We now see that all 344 rows of this particular result set have been -accessed. +In another shell, we can access the container once more and launch another R process: +docker exec -it -u root tiledb-mariadb-r R +where we use RMariaDB to access the data via a tibble object and magrittr pipe +> library(RMariaDB) +> library(dplyr, warn.conflicts=FALSE) +> con <- DBI::dbConnect(RMariaDB::MariaDB(), dbname="test") +> tbl(con, "/tmp/penguinsraw") %>% ++ dplyr::select(contains("Length")) +# Source: lazy query [?? x 2] +# Database: mysql [@localhost:NA/test] + `Culmen Length (mm)` `Flipper Length (mm)` + <dbl> <dbl> + 1 39.1 181 + 2 39.5 186 + 3 40.3 195 + 4 NA NA + 5 36.7 193 + 6 39.3 190 + 7 38.9 181 + 8 39.2 195 + 9 34.1 193 +10 42 190 +# ... with more rows +Note that this R session uses TileDB only via the MyTile plugin which is activated implicitly via the ‘table location’ (here /tmp/penguinsraw) of the test database enabling plugins. +Also note that the query is still ‘lazy’: only column names and the first ten observations have been retrieved, and the total size is still unknown as indicated by lazy query [?? x 2]. Adding a collect() verb materialized the full subset. +> tbl(con, "/tmp/penguinsraw") %>% ++ dplyr::select(contains("Length")) %>% ++ collect() +# A tibble: 344 x 2 + `Culmen Length (mm)` `Flipper Length (mm)` + <dbl> <dbl> + 1 39.1 181 + 2 39.5 186 + 3 40.3 195 + 4 NA NA + 5 36.7 193 + 6 39.3 190 + 7 38.9 181 + 8 39.2 195 + 9 34.1 193 +10 42 190 +# ... with 334 more rows +> +We now see that all 344 rows of this particular result set have been accessed. Similarly, we can also run summaries on selected column: -> tbl(con, "/tmp/penguinsraw") %>% -+ group_by(Species) %>% -+ summarise(across(starts_with("Flipper"), -+ list(~mean(.x, na.rm=TRUE), ~sd(.x, na.rm=TRUE)))) -# Source: lazy query [?? x 3] -# Database: mysql [@localhost:NA/test] - Species `\`Flipper Length (mm)\`_~me~ `\`Flipper Length (mm)\`_~~ - <chr> <dbl> <dbl> -1 Adelie Penguin (Pyg~ 190. 6.54 -2 Chinstrap penguin (~ 196. 7.13 -3 Gentoo penguin (Pyg~ 217. 6.48 -> +> tbl(con, "/tmp/penguinsraw") %>% ++ group_by(Species) %>% ++ summarise(across(starts_with("Flipper"), ++ list(~mean(.x, na.rm=TRUE), ~sd(.x, na.rm=TRUE)))) +# Source: lazy query [?? x 3] +# Database: mysql [@localhost:NA/test] + Species `\`Flipper Length (mm)\`_~me~ `\`Flipper Length (mm)\`_~~ + <chr> <dbl> <dbl> +1 Adelie Penguin (Pyg~ 190. 6.54 +2 Chinstrap penguin (~ 196. 7.13 +3 Gentoo penguin (Pyg~ 217. 6.48 +> DBI -We can connect directly using the DBI package along with -the RMariaDB package and its MyTile bindings: +We can connect directly using the DBI package along with the RMariaDB package and its MyTile bindings: library(DBI) -con <- dbConnect(RMariaDB::MariaDB(), dbname="test") -res <- dbSendQuery(con, "select * from `/work/penguins` as `q91` limit 10") -df <- dbFetch(res, n = 10) -dbClearResult(res) +con <- dbConnect(RMariaDB::MariaDB(), dbname="test") +res <- dbSendQuery(con, "select * from `/work/penguins` as `q91` limit 10") +df <- dbFetch(res, n = 10) +dbClearResult(res) print(df) -dbDisconnect(con) +dbDisconnect(con) S3 -When using Docker, the container setup needs to be modified to -include the required AWS access environment variables: -docker run --name tiledb-mariadb-r \ - -it -d --rm \ - -v $PWD:/work -w /work \ - -e MYSQL_ALLOW_EMPTY_PASSWORD=1 \ - -e AWS_SECRET_ACCESS_KEY=${AWS_SECRET_ACCESS_KEY} \ - -e AWS_ACCESS_KEY_ID=${AWS_ACCESS_KEY_ID} \ - tiledb/tiledb-mariadb-r -This exports the current working directory (accessed as -$PWD in the shell) as /work inside the -container (via the -v switch), and instructs the container -to start in directory /work (via the -w -switch). -In the following example we also set a TileDB configuration option to -switch AWS regions. -> library(dplyr, warn.conflicts=FALSE) -> # connect as usual -> con <- DBI::dbConnect(RMariaDB::MariaDB(), dbname="test") -> # use connection to update config in order to switch s3 regions -> res1 <- DBI::dbSendQuery(con, "set mytile_tiledb_config=\"vfs.s3.region=us-west-1\";") -> DBI::dbClearResult(res1) -> # run simple query -> tbl(con, "s3://tiledb-public-us-west-1/test-array-4x4") %>% collect() -# A tibble: 16 x 3 - `__dim_0` `__dim_1` `__attr` - <int64> <int64> <dbl> - 1 0 0 0.397 - 2 0 1 0.432 - 3 0 2 0.617 - 4 0 3 0.403 - 5 1 0 0.837 - 6 1 1 0.670 - 7 1 2 0.235 - 8 1 3 0.841 - 9 2 0 0.222 -10 2 1 0.468 -11 2 2 0.970 -12 2 3 0.551 -13 3 0 0.628 -14 3 1 0.0149 -15 3 2 0.0540 -16 3 3 0.445 -> -> DBI::dbDisconnect(con) # close connection +When using Docker, the container setup needs to be modified to include the required AWS access environment variables: +docker run --name tiledb-mariadb-r \ + -it -d --rm \ + -v $PWD:/work -w /work \ + -e MYSQL_ALLOW_EMPTY_PASSWORD=1 \ + -e AWS_SECRET_ACCESS_KEY=${AWS_SECRET_ACCESS_KEY} \ + -e AWS_ACCESS_KEY_ID=${AWS_ACCESS_KEY_ID} \ + tiledb/tiledb-mariadb-r +This exports the current working directory (accessed as $PWD in the shell) as /work inside the container (via the -v switch), and instructs the container to start in directory /work (via the -w switch). +In the following example we also set a TileDB configuration option to switch AWS regions. +> library(dplyr, warn.conflicts=FALSE) +> # connect as usual +> con <- DBI::dbConnect(RMariaDB::MariaDB(), dbname="test") +> # use connection to update config in order to switch s3 regions +> res1 <- DBI::dbSendQuery(con, "set mytile_tiledb_config=\"vfs.s3.region=us-west-1\";") +> DBI::dbClearResult(res1) +> # run simple query +> tbl(con, "s3://tiledb-public-us-west-1/test-array-4x4") %>% collect() +# A tibble: 16 x 3 + `__dim_0` `__dim_1` `__attr` + <int64> <int64> <dbl> + 1 0 0 0.397 + 2 0 1 0.432 + 3 0 2 0.617 + 4 0 3 0.403 + 5 1 0 0.837 + 6 1 1 0.670 + 7 1 2 0.235 + 8 1 3 0.841 + 9 2 0 0.222 +10 2 1 0.468 +11 2 2 0.970 +12 2 3 0.551 +13 3 0 0.628 +14 3 1 0.0149 +15 3 2 0.0540 +16 3 3 0.445 +> +> DBI::dbDisconnect(con) # close connection NYC Taxis -We can write the New York taxi data into TileDB (in the current -directory) after reading it as a csv: -> nyc <- data.table::fread("trip_data_1.csv") -> tiledb::fromDataFrame(nyc, "trip_data_1") -Then we can access it via the path /work/trip_data_1 via -RMariaDB. -> library(dplyr, warn.conflicts=FALSE) -> con <- DBI::dbConnect(RMariaDB::MariaDB(), dbname="test") -> # list column names -> tbl(con, "/work/trip_data_1") %>% colnames() -> tbl(con, "/work/trip_data_1") %>% colnames() - [1] "__tiledb_rows" "dropoff_latitude" "medallion" - [4] "hack_license" "dropoff_longitude" "vendor_id" - [7] "rate_code" "store_and_fwd_flag" "pickup_datetime" -[10] "dropoff_datetime" "trip_time_in_secs" "pickup_latitude" -[13] "passenger_count" "trip_distance" "pickup_longitude" -> # extract one column (here passenger_count) completely and tabulate in R -> tbl(con, "/work/trip_data_1") %>% select(passenger_count) %>% collect() %>% table() -. - 0 1 2 3 4 5 6 9 - 166 10471701 1986196 597485 280992 920006 520066 1 - 208 255 - 1 1 -> # alternatively, run a lazy query -> tbl(con, "/work/trip_data_1") %>% group_by(passenger_count) %>% summarize(nobs = n()) -# Source: lazy query [?? x 2] -# Database: mysql [@localhost:NA/test] - passenger_count nobs - <int> <int64> - 1 0 166 - 2 1 10471701 - 3 2 1986196 - 4 3 597485 - 5 4 280992 - 6 5 920006 - 7 6 520066 - 8 9 1 - 9 208 1 -10 255 1 -> # here the request is actually sent as SQL and the computation is done in the SQL layer -> tbl(con, "/work/trip_data_1") %>% -+ group_by(passenger_count) %>% -+ summarize(nobs = n()) %>% -+ show_query() -<SQL> -SELECT `passenger_count`, COUNT(*) AS `nobs` -FROM `/work/trip_data_1` -GROUP BY `passenger_count` -> # naturally we can also send the query directly to the SQL backend -> sql <- "SELECT passenger_count, count(*) AS n FROM `/work/trip_data_1` GROUP BY passenger_count;" -> DBI::dbGetQuery(con, sql) - passenger_count n -1 0 166 -2 1 10471701 -3 2 1986196 -4 3 597485 -5 4 280992 -6 5 920006 -7 6 520066 -8 9 1 -9 208 1 -10 255 1 -> -> DBI::dbDisconnect(con) # close connection +We can write the New York taxi data into TileDB (in the current directory) after reading it as a csv: +> nyc <- data.table::fread("trip_data_1.csv") +> tiledb::fromDataFrame(nyc, "trip_data_1") +Then we can access it via the path /work/trip_data_1 via RMariaDB. +> library(dplyr, warn.conflicts=FALSE) +> con <- DBI::dbConnect(RMariaDB::MariaDB(), dbname="test") +> # list column names +> tbl(con, "/work/trip_data_1") %>% colnames() +> tbl(con, "/work/trip_data_1") %>% colnames() + [1] "__tiledb_rows" "dropoff_latitude" "medallion" + [4] "hack_license" "dropoff_longitude" "vendor_id" + [7] "rate_code" "store_and_fwd_flag" "pickup_datetime" +[10] "dropoff_datetime" "trip_time_in_secs" "pickup_latitude" +[13] "passenger_count" "trip_distance" "pickup_longitude" +> # extract one column (here passenger_count) completely and tabulate in R +> tbl(con, "/work/trip_data_1") %>% select(passenger_count) %>% collect() %>% table() +. + 0 1 2 3 4 5 6 9 + 166 10471701 1986196 597485 280992 920006 520066 1 + 208 255 + 1 1 +> # alternatively, run a lazy query +> tbl(con, "/work/trip_data_1") %>% group_by(passenger_count) %>% summarize(nobs = n()) +# Source: lazy query [?? x 2] +# Database: mysql [@localhost:NA/test] + passenger_count nobs + <int> <int64> + 1 0 166 + 2 1 10471701 + 3 2 1986196 + 4 3 597485 + 5 4 280992 + 6 5 920006 + 7 6 520066 + 8 9 1 + 9 208 1 +10 255 1 +> # here the request is actually sent as SQL and the computation is done in the SQL layer +> tbl(con, "/work/trip_data_1") %>% ++ group_by(passenger_count) %>% ++ summarize(nobs = n()) %>% ++ show_query() +<SQL> +SELECT `passenger_count`, COUNT(*) AS `nobs` +FROM `/work/trip_data_1` +GROUP BY `passenger_count` +> # naturally we can also send the query directly to the SQL backend +> sql <- "SELECT passenger_count, count(*) AS n FROM `/work/trip_data_1` GROUP BY passenger_count;" +> DBI::dbGetQuery(con, sql) + passenger_count n +1 0 166 +2 1 10471701 +3 2 1986196 +4 3 597485 +5 4 280992 +6 5 920006 +7 6 520066 +8 9 1 +9 208 1 +10 255 1 +> +> DBI::dbDisconnect(con) # close connection Summary -This short vignette demonstrates the use of TileDB-stored data from R -using RMariaDB via the MyTile storage extension to MariaBD. +This short vignette demonstrates the use of TileDB-stored data from R using RMariaDB via the MyTile storage extension to MariaBD. @@ -356,11 +318,11 @@ Summary diff --git a/docs/articles/tiledb-mariadb-examples_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/tiledb-mariadb-examples_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 0000000000..ca349fd6a5 --- /dev/null +++ b/docs/articles/tiledb-mariadb-examples_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. + +document.addEventListener('DOMContentLoaded', function() { + const codeList = document.getElementsByClassName("sourceCode"); + for (var i = 0; i < codeList.length; i++) { + var linkList = codeList[i].getElementsByTagName('a'); + for (var j = 0; j < linkList.length; j++) { + if (linkList[j].innerHTML === "") { + linkList[j].setAttribute('aria-hidden', 'true'); + } + } + } +}); diff --git a/docs/authors.html b/docs/authors.html index 145a22f84f..0eef9fee6c 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -1,5 +1,5 @@ -Authors and Citation • tiledb +Authors and Citation • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -49,11 +49,7 @@ Authors and Citation Authors - . Author, copyright holder. - - - - Dirk Eddelbuettel. Author. + . Author, copyright holder. @@ -66,15 +62,15 @@ Authors Citation Source: DESCRIPTION - TileDB, Inc., Eddelbuettel D (2024). + TileDB, Inc. (2025). tiledb: Modern Database Engine for Complex Data Based on Multi-Dimensional Arrays. -R package version 0.31.0, https://tiledb-inc.github.io/TileDB-R/, https://github.com/TileDB-Inc/TileDB-R. +R package version 0.31.0.1, https://tiledb-inc.github.io/TileDB-R/, https://github.com/TileDB-Inc/TileDB-R. @Manual{, title = {tiledb: Modern Database Engine for Complex Data Based on Multi-Dimensional Arrays}, - author = {{TileDB, Inc.} and Dirk Eddelbuettel}, - year = {2024}, - note = {R package version 0.31.0, https://tiledb-inc.github.io/TileDB-R/}, + author = {{TileDB, Inc.}}, + year = {2025}, + note = {R package version 0.31.0.1, https://tiledb-inc.github.io/TileDB-R/}, url = {https://github.com/TileDB-Inc/TileDB-R}, } @@ -84,11 +80,11 @@ Citation diff --git a/docs/deps/data-deps.txt b/docs/deps/data-deps.txt index 1b877ae225..ca4dfd9c5c 100644 --- a/docs/deps/data-deps.txt +++ b/docs/deps/data-deps.txt @@ -1,4 +1,4 @@ - + diff --git a/docs/index.html b/docs/index.html index cd8955108a..8ebb804b44 100644 --- a/docs/index.html +++ b/docs/index.html @@ -12,7 +12,7 @@ - + @@ -28,7 +28,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -71,7 +71,7 @@ - + The TileDB R package offers an R interface to the modern database by TileDB. @@ -84,19 +84,19 @@ InstallationCRAN and be installed directly via -> install.packages("tiledb") +> install.packages("tiledb") as usual. The most recent released version can be installed from Github using the package remotes. -> if (!requireNamespace("remotes",quietly=TRUE)) install.packages("remotes") -> remotes::install_github("TileDB-Inc/TileDB-R") -... -> library(tiledb) -TileDB R 0.31.0 with TileDB Embedded 2.27.0 on Ubuntu 24.04. -See https://tiledb.com for more information about TileDB. -> help(package=tiledb) +> if (!requireNamespace("remotes",quietly=TRUE)) install.packages("remotes") +> remotes::install_github("TileDB-Inc/TileDB-R") +... +> library(tiledb) +TileDB R 0.31.0 with TileDB Embedded 2.27.0 on Ubuntu 24.04. +See https://tiledb.com for more information about TileDB. +> help(package=tiledb) If the TileDB library is installed in a custom location, you need to pass the explicit path: -> remotes::install_github("TileDB-Inc/TileDB-R", - args="--configure-args='--with-tiledb=/path/to/tiledb'") +> remotes::install_github("TileDB-Inc/TileDB-R", + args="--configure-args='--with-tiledb=/path/to/tiledb'") Note that the TileDB R package is always developed and tested against the latest stable version of TileDB, but should also build against the newest development version. @@ -150,8 +150,7 @@ Citation Developers - Author, copyright holder -Dirk Eddelbuettel Author + Author, copyright holder Isaiah Norton Maintainer @@ -173,11 +172,11 @@ Dev status diff --git a/docs/news/index.html b/docs/news/index.html index 2d9f731da9..ca226604ed 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -1,5 +1,5 @@ -Changelog • tiledb +Changelog • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -53,7 +53,7 @@ tiledb 0.31.0Update unit tests to expect dense current domain Support parentheses in query conditions memory alloc: Accomodate zero buffer size estimate v2 -Apply styler::style_pkg() +Apply styler::style_pkg() Expose include/linking flags for re-using libtiledb in downstream packages Use TileDB Core 2.27.0 @@ -66,12 +66,10 @@ tiledb 0.30.2 tiledb 0.30.1 -This release of the R package builds against TileDB 2.26.1, and has also been tested against earlier releases as well as the development version (#757) - +This release of the R package builds against TileDB 2.26.1, and has also been tested against earlier releases as well as the development version (#757) tiledb 0.30.0 -This release of the R package builds against TileDB 2.26.0, and has also been tested against earlier releases as well as the development version (#745, #749, #750, #754, #755) - +This release of the R package builds against TileDB 2.26.0, and has also been tested against earlier releases as well as the development version (#745, #749, #750, #754, #755) Improvements Error messages displayed when a mismatched external pointer is detected now show both expected and encountered types (#740) NDRectangle objects can now instantiate from more domain data types (#741, #742) @@ -80,8 +78,7 @@ Improvements Documentation -The documentation website now uses favicon symbols for all pages rendered (#739) - +The documentation website now uses favicon symbols for all pages rendered (#739) Build and Test Systems The nighly valgrind matrix now includes release 2.26.0 (#744) @@ -89,17 +86,14 @@ Build and Test Systems Removals -Boolean arguments as.data.frame, as.matrix and as.array to the tiledb_array() accessor, deprecated in release 0.20.0 in July 2023 in favor of the more general return_as="..." form, have been removed. (#751) - +Boolean arguments as.data.frame, as.matrix and as.array to the tiledb_array() accessor, deprecated in release 0.20.0 in July 2023 in favor of the more general return_as="..." form, have been removed. (#751) Deprecation -As BioConductor package still relies on as.data.frame it was temporarily re-admitted as an argument. It is expected to be removed following the upcoming 3.20 release of BioConducto.r (#752) - +As BioConductor package still relies on as.data.frame it was temporarily re-admitted as an argument. It is expected to be removed following the upcoming 3.20 release of BioConducto.r (#752) tiledb 0.29.0 -This release of the R package builds against TileDB 2.25.0, and has also been tested against earlier releases as well as the development version (#728, #736) - +This release of the R package builds against TileDB 2.25.0, and has also been tested against earlier releases as well as the development version (#728, #736) Improvements Three deprecated calls to dump() methods for TileDB Embedded objects now use the preferred streaming alternatives (#727) Two already deprecated functions that are removed in TileDB 2.26.0 are no longer used (#732) @@ -109,20 +103,16 @@ Improvements Build and Test Systems -The nighly valgrind matrix now includes release 2.25.0 (#729) - +The nighly valgrind matrix now includes release 2.25.0 (#729) tiledb 0.28.2 -This release of the R package builds against TileDB 2.24.2, and has also been tested against earlier releases as well as the development version (#725) - +This release of the R package builds against TileDB 2.24.2, and has also been tested against earlier releases as well as the development version (#725) tiledb 0.28.1 -This release of the R package builds against TileDB 2.24.1, and has also been tested against earlier releases as well as the development version (#714, #715, #717, #724) - +This release of the R package builds against TileDB 2.24.1, and has also been tested against earlier releases as well as the development version (#714, #715, #717, #724) Improvements -When creating arrays with fromDataFrame, start and/or end timestamps can now be specified (#719) - +When creating arrays with fromDataFrame, start and/or end timestamps can now be specified (#719) Build and Test Systems The nighly continuous integration matrix now included Core release 2.24.0 and 2.22.0 is dropped (#721) @@ -131,8 +121,7 @@ Build and Test Systems tiledb 0.28.0 -This release of the R package builds against TileDB 2.24.0, and has also been tested against earlier releases as well as the development version (#714, #715, #717) - +This release of the R package builds against TileDB 2.24.0, and has also been tested against earlier releases as well as the development version (#714, #715, #717) Improvements Three internal and unexported helper functions now document more clearly how they can be called explicitly. (#709) Reading and writing of text- and binary files supported by a VFS backend is now supported. (#710) @@ -145,8 +134,7 @@ Build and Test Systems tiledb 0.27.0 -This release of the R package builds against TileDB 2.23.0, and has also been tested against earlier releases as well as the development version (#701, #704) - +This release of the R package builds against TileDB 2.23.0, and has also been tested against earlier releases as well as the development version (#701, #704) Improvements Group elements can now be deleted (#702) Two error messages now show the human-readable type representation instead of the enum counter value (#705) @@ -158,17 +146,14 @@ Build and Test Systems Deprecations -Function libtiledb_array_create_with_key, accessing a deprecated Core function, is now in src/deprecated.cpp and will be removed at later point (#699) - +Function libtiledb_array_create_with_key, accessing a deprecated Core function, is now in src/deprecated.cpp and will be removed at later point (#699) Removals -Functions libtiledb_query_add_range_with_type and libtiledb_query_add_range, deprecated in release 0.17.1 in January 2023, have been now removed (#700). - +Functions libtiledb_query_add_range_with_type and libtiledb_query_add_range, deprecated in release 0.17.1 in January 2023, have been now removed (#700). tiledb 0.26.0 -This release of the R package builds against TileDB 2.22.0, and has also been tested against earlier releases as well as the development version (#679, #686, #693, #696) - +This release of the R package builds against TileDB 2.22.0, and has also been tested against earlier releases as well as the development version (#679, #686, #693, #696) Improvements The display of a filter_list is now labeled correctly as a filter list (@cgiachalis in #681 addressing #678) The Arrow integration has been simplified using nanoarrow returning a single nanoarrow object; an unexported helper function nanoarrow2list() is provided to matching the previous interface (#682, #685) @@ -177,8 +162,7 @@ Improvements Bug Fixes -The column headers now correspond to the column content in the two-column data.frame returns by tiledb_object_walk (#684 closing #683) - +The column headers now correspond to the column content in the two-column data.frame returns by tiledb_object_walk (#684 closing #683) Build and Test Systems The configure and Makevars.in received a minor update correcting small issues (#680) @@ -186,8 +170,7 @@ Build and Test Systems Documentation -A number of minor typographical and grammar errors in the function documentation has been corrected (@cgiachalis in #681) - +A number of minor typographical and grammar errors in the function documentation has been corrected (@cgiachalis in #681) Deprecations Functions tiledb_arrow_array_ptr(), tiledb_arrow_schmea_ptr(), tiledb_arrow_array_del() and tiledb_arrow_schema_del() are deprecated (in favor of using the corresponding nanoarrow functions) and will be removed in a future release (#685) @@ -196,8 +179,7 @@ Deprecations tiledb 0.25.0 -This release of the R package builds against TileDB 2.21.0, and has also been tested against earlier releases as well as the development version (#661, #666, #668, #676, #677) - +This release of the R package builds against TileDB 2.21.0, and has also been tested against earlier releases as well as the development version (#661, #666, #668, #676, #677) Improvements The vendored nanoarrow sources have been update to release 0.4.0, and use of its facilities has been extended (#663) Query conditions can be expressed against non-existing enumeration (i.e., factor) values when TileDB Core 2.21.0 or later is used (#674) @@ -219,8 +201,7 @@ Build and Test Systems tiledb 0.24.0 -This release of the R package builds against TileDB 2.20.0, and has also been tested against earlier releases as well as the development version (#651,#654,#658,#659) - +This release of the R package builds against TileDB 2.20.0, and has also been tested against earlier releases as well as the development version (#651,#654,#658,#659) Improvements Factor level additions now check for possible over in the index type (#645, #646) Aggregate operations can now be performed on dense arrays via a query object with appropriate subarray settings (#650) @@ -233,17 +214,14 @@ Bug Fixes Build and Test Systems -The nightly valgrind run was updated to include release 2.20 (#649) - +The nightly valgrind run was updated to include release 2.20 (#649) Documentation -The DESCRIPTION file now contains a reference to the documentation site in its URL field (#656) - +The DESCRIPTION file now contains a reference to the documentation site in its URL field (#656) tiledb 0.23.0 -This release of the R package builds against TileDB 2.19.0, and has also been tested against earlier releases as well as the development version (#641) - +This release of the R package builds against TileDB 2.19.0, and has also been tested against earlier releases as well as the development version (#641) Improvements A TileDB Array can now be opened in ‘keep open’ mode for subsequent use without re-opening (#630) Arrays with factor (or ordered) variables now grow their factor levels in appending writes (#639) @@ -252,8 +230,7 @@ Improvements Bug Fixes -The read buffer is now correctly sized when implementing VFS serialization (#631) - +The read buffer is now correctly sized when implementing VFS serialization (#631) Build and Test Systems Builds from TileDB Core non-release tarballs are now supported via new configure option (#627) @@ -265,16 +242,14 @@ Build and Test Systems tiledb 0.22.0 -This release of the R package builds against TileDB 2.18.0, TileDB 2.18.1, TileDB 2.18.2 and has also been tested against earlier releases as well as the development version (#620,#621,#624) - +This release of the R package builds against TileDB 2.18.0, TileDB 2.18.1, TileDB 2.18.2 and has also been tested against earlier releases as well as the development version (#620,#621,#624) Improvements Use of TileDB Embedded was upgraded to release 2.18.0 (#620), 2.18.1 (#621), and 2.18.2 (#624) Support for Aggregates has been added (#623) Bug Fixes -When using serializing via VFS (as added in #608) the filehandles is now properly released (#619) - +When using serializing via VFS (as added in #608) the filehandles is now properly released (#619) Build and Test Systems Some tests were refactored slightly for greater robustness (#618) @@ -282,29 +257,23 @@ Build and Test Systems Documentation -The README now contains a badge for the r-universe version (in addition to CRAN) (#617) - +The README now contains a badge for the r-universe version (in addition to CRAN) (#617) tiledb 0.21.3 -This release of the R package builds against TileDB 2.17.4, and has also been tested against earlier releases as well as the development version (#611) - +This release of the R package builds against TileDB 2.17.4, and has also been tested against earlier releases as well as the development version (#611) Improvements -Query conditioning parsing now supports factor index columns other than the standard integer type (#614) - +Query conditioning parsing now supports factor index columns other than the standard integer type (#614) Build and Test Systems -The nightly valgrind run was updated to include release 2.18 (#615) - +The nightly valgrind run was updated to include release 2.18 (#615) Documentation -The pkgdown documentation has been updated for release 0.21.2 (#613) and release 0.21.3 (#616) - +The pkgdown documentation has been updated for release 0.21.2 (#613) and release 0.21.3 (#616) tiledb 0.21.2 -This release of the R package builds against TileDB 2.17.4, and has also been tested against earlier releases as well as the development version (#611) - +This release of the R package builds against TileDB 2.17.4, and has also been tested against earlier releases as well as the development version (#611) Improvements Set conditions are supported in query condition expressions (#597) Query conditions expression parsing via parse_query_conditions was extended simmilarly (#598) @@ -326,13 +295,11 @@ Bug Fixes Build and Test Systems -The nightly valgrind run was updated to include release 2.17 (#603) - +The nightly valgrind run was updated to include release 2.17 (#603) tiledb 0.21.1 -This release of the R package builds against TileDB 2.17.1, and has also been tested against earlier releases as well as the development version (#593) - +This release of the R package builds against TileDB 2.17.1, and has also been tested against earlier releases as well as the development version (#593) Improvements Array schema evolution has been extended to support enumerations (#590, #591) Conversion to and from integer64 (and nanotime) now use package RcppInt64 (#592) @@ -340,13 +307,11 @@ Improvements Bug Fixes -An added sorting of factor levels insert has been reverted (#594) - +An added sorting of factor levels insert has been reverted (#594) tiledb 0.21.0 -This release of the R package builds against TileDB 2.17.0, and has also been tested against earlier releases as well as the development version (#583, #587) - +This release of the R package builds against TileDB 2.17.0, and has also been tested against earlier releases as well as the development version (#583, #587) Improvements Use of TileDB Embedded was upgraded to release 2.17.0 (#583,#587) Built-time configuration of TileDB Embedded can now be accessed as a JSON string (#584) @@ -356,16 +321,13 @@ Improvements tiledb 0.20.3 -This release of the R package builds against TileDB 2.16.2, and has also been tested against earlier releases as well as the development version (#582) - +This release of the R package builds against TileDB 2.16.2, and has also been tested against earlier releases as well as the development version (#582) Improvements -Use of TileDB Embedded was upgraded to release 2.16.2 (#581) - +Use of TileDB Embedded was upgraded to release 2.16.2 (#581) tiledb 0.20.2 -This release of the R package builds against TileDB 2.16.1, and has also been tested against earlier releases as well as the development version (#579) - +This release of the R package builds against TileDB 2.16.1, and has also been tested against earlier releases as well as the development version (#579) Improvements The column buffer allocation is now robust to container overflow sanitizer checks (#574) The array schema version is now accessible via a function (#575) @@ -374,13 +336,11 @@ Improvements Build and Test Systems -The minimal version of TileDB Embedded that can be used with the R package is now release 2.7.0 (#578) - +The minimal version of TileDB Embedded that can be used with the R package is now release 2.7.0 (#578) tiledb 0.19.1 -This release of the R package builds against TileDB 2.15.2, and has also been tested against earlier releases as well as the development version (#534, #541). - +This release of the R package builds against TileDB 2.15.2, and has also been tested against earlier releases as well as the development version (#534, #541). Improvements Query conditions can now be expressed for attributes of type UTF-8 (#529) The startup message now displays the operating system and version (#532) @@ -399,11 +359,9 @@ Build and Test Systems tiledb 0.19.0 -This release of the R package builds against TileDB 2.15.0, and has also been tested against earlier releases as well as the development version (#516, #521). - +This release of the R package builds against TileDB 2.15.0, and has also been tested against earlier releases as well as the development version (#516, #521). Breaking Changes -The validity map coding of nullable strings has been corrected: validity map values of one are now interpreted as valid/non-null for full compatibility with other TileDB projects. Previously written arrays with nullable strings can be read by setting the config option r.legacy_validity_mode to true; the option also permits to write to an older installation. A conversion helper script is provided in scripts/legacy_validity_convert.r. (#517) - +The validity map coding of nullable strings has been corrected: validity map values of one are now interpreted as valid/non-null for full compatibility with other TileDB projects. Previously written arrays with nullable strings can be read by setting the config option r.legacy_validity_mode to true; the option also permits to write to an older installation. A conversion helper script is provided in scripts/legacy_validity_convert.r. (#517) Improvements Attributes can now be created, written and read from in (explicit) UTF8 types (and CHAR and ASCII already behaved correctly with respect to utf8 data) (#510) @@ -415,48 +373,34 @@ Improvements Bug Fixes -The access to JSON-formatted performance statistics has been simplified (#514) - +The access to JSON-formatted performance statistics has been simplified (#514) Build and Test Systems The TileDB Embedded version is now used to determine whether a dampener is needed for the deprecation warning (#511) One of the test data sets included with #517 has been regenerated under an older TileDB version in order to test on more systems (#523) Documentation for Metadata accessors no longer states URIs strings are accepted (#527) - -Deprecations - - -Removals - +Deprecations +Removals tiledb 0.18.0 -This release of the R package builds against TileDB 2.14.0, and has also been tested against earlier releases as well as the development version (#502). - +This release of the R package builds against TileDB 2.14.0, and has also been tested against earlier releases as well as the development version (#502). Improvements -Use of TileDB Embedded was upgraded to release 2.14.0 (#505) - - -Bug Fixes - +Use of TileDB Embedded was upgraded to release 2.14.0 (#505) +Bug Fixes Build and Test Systems The nightly valgrind job matrix was updated to releases 2.13 and 2.14 as well as the branch (#504) The nightly valgrind job show the most recent commit sha1 after updating from release branches (#507) A query condition test for utf8 attributes has been added (#507, #508) - -Deprecations - - -Removals - +Deprecations +Removals tiledb 0.17.1 -This release of the R package builds against TileDB 2.13.1, and has also been tested against earlier releases as well as the development version (#502). - +This release of the R package builds against TileDB 2.13.1, and has also been tested against earlier releases as well as the development version (#502). Improvements Support for Subarrays to set ranges has been extended (#496) Deprecated Core API functions for Array access and range setting are longer used (#496) @@ -476,17 +420,14 @@ Build and Test Systems Deprecations -Functions libtiledb_query_add_range{,_with_type} relying on depecreated Core functionality are deprecated, and will be removed with the Core functions. Subarray range setters are available. This is a mostly internal change. - +Functions libtiledb_query_add_range{,_with_type} relying on depecreated Core functionality are deprecated, and will be removed with the Core functions. Subarray range setters are available. This is a mostly internal change. Removals -Functions libtiledb_query_set_coordinates() and libtiledb_coords() which have been deprecated since June 2000 have been removed. (#497) - +Functions libtiledb_query_set_coordinates() and libtiledb_coords() which have been deprecated since June 2000 have been removed. (#497) tiledb 0.17.0 -This release of the R package builds against TileDB 2.13.0, and has also been tested against earlier releases as well as the development version (#492). - +This release of the R package builds against TileDB 2.13.0, and has also been tested against earlier releases as well as the development version (#492). Improvements Support for testing group URIs on being relative has been added (#478) Logging support at the R and C++ level has been added (#479, #487, #489) @@ -509,8 +450,7 @@ Build and Test Systems tiledb 0.16.0 -This release of the R package builds against TileDB 2.12.0, and has also been tested against earlier releases as well as the development version (#476). - +This release of the R package builds against TileDB 2.12.0, and has also been tested against earlier releases as well as the development version (#476). Improvements Several deprecated API entry points of TileDB Embedded are no longer used (#452, #453) Support for DELETE queries has been added (requires TileDB Embedded 2.12.0 or later) (#455, #456) @@ -539,8 +479,7 @@ Build and Test Systems tiledb 0.15.0 -This release of the R package builds against TileDB 2.11.0, and has also been tested against earlier releases as well as the development version (#451). - +This release of the R package builds against TileDB 2.11.0, and has also been tested against earlier releases as well as the development version (#451). Improvements Support for query conditions has been extended to dense arrays (#447) Support for filter lists has extended to both the data.frame helper and the dimension object constructor (#448) @@ -548,17 +487,14 @@ Improvements Bug Fixes -Small enhancements have been made to the test suite (#450) - +Small enhancements have been made to the test suite (#450) Build and Test Systems -A small enhancement was made to the test system (#450) - +A small enhancement was made to the test system (#450) tiledb 0.14.1 -This release of the R package builds against TileDB 2.10.2, and has also been tested against earlier releases as well as the development version. - +This release of the R package builds against TileDB 2.10.2, and has also been tested against earlier releases as well as the development version. Improvements Use of TileDB Embedded was upgraded to release 2.10.2 (#443) following an earlier update to 2.10.1 (#434) List columns are now supported in reading and writing of data frames by extending cell variable numbers beyond one (#438, #440) @@ -572,13 +508,11 @@ Bug Fixes Build and Test Systems -The nightly valgrind check was updated to Ubuntu 22.04 (#435, #439, #442) - +The nightly valgrind check was updated to Ubuntu 22.04 (#435, #439, #442) tiledb 0.14.0 -This release of the R package builds against TileDB 2.10.0, and has also been tested against earlier releases as well as the development version. - +This release of the R package builds against TileDB 2.10.0, and has also been tested against earlier releases as well as the development version. Improvements Use of TileDB Embedded was upgraded to release 2.10.0 (#432) following earlier updates to 2.9.1 (#415), 2.9.2 (#419), 2.9.3 (#422), 2.9.4 (#427) and 2.9.5 (#430) The BOOL data type is now supported (#416) @@ -590,8 +524,7 @@ Improvements Bug Fixes -The attr setter for Attributes was corrected to support NA settings (#425) - +The attr setter for Attributes was corrected to support NA settings (#425) Build and Test Systems Filter compression tests are skipped on systems lacking AVX2 support (#418) @@ -602,8 +535,7 @@ Build and Test Systems tiledb 0.13.0 -This release of the R package builds against TileDB 2.9.0, and has also been tested against earlier releases as well as the development version. - +This release of the R package builds against TileDB 2.9.0, and has also been tested against earlier releases as well as the development version. Improvements Support for groups has been added for TileDB 2.8 or later (#404) The group member name retrieval can now also return the optional group member name (#399) @@ -615,12 +547,10 @@ Improvements Bug Fixes -Tests for filters have been made more robust (#407, #412) - +Tests for filters have been made more robust (#407, #412) Deprecations -The check() function is now deprecated and schema_check() is provided (#409) - +The check() function is now deprecated and schema_check() is provided (#409) Build and Test Systems Nightly valgrind checks were updated to use current versions (#397, #402) @@ -629,8 +559,7 @@ Build and Test Systems tiledb 0.12.0 -This release of the R package builds against TileDB 2.8.0, and has also been tested against earlier releases as well as the development version. - +This release of the R package builds against TileDB 2.8.0, and has also been tested against earlier releases as well as the development version. Improvements A schedule nightly continuous action now checks current and release-candidate branches of TileDB with the R package under valgrind (#387) Support for Groups was added (#388, #392, #395) @@ -651,8 +580,7 @@ Bug Fixes tiledb 0.11.1 -This release of the R package builds against TileDB 2.6.4, but has also been tested against earlier releases, and the development version. - +This release of the R package builds against TileDB 2.6.4, but has also been tested against earlier releases, and the development version. Improvements Use of TileDB Embedded was upgraded to release 2.6.4 (#384) following an earlier upgrade to 2.6.2 (#359) Creations of arrays from data.frame objects now supports a mode= argument with values ‘ingest’, ‘schema_only’, and ‘append’ (#360) @@ -684,13 +612,11 @@ Documentation Deprecations -The tiledb_dense and tiledb_sparse functions which were deprecated in February 2021 have been removed after a twelve-month grace period. - +The tiledb_dense and tiledb_sparse functions which were deprecated in February 2021 have been removed after a twelve-month grace period. tiledb 0.11.0 -This release of the R package builds against TileDB 2.6.1, but has also been tested against previous releases, and the development version. - +This release of the R package builds against TileDB 2.6.1, but has also been tested against previous releases, and the development version. Improvements Use of TileDB Embedded was upgraded to release 2.6.1 (#354) following an earlier upgrade to 2.6.0 (#340) A cell value getter for dimension was added (#341) @@ -709,8 +635,7 @@ Bug Fixes tiledb 0.10.2 -This release of the R package builds against TileDB 2.5.3, but has been tested against previous releases, and the development version. - +This release of the R package builds against TileDB 2.5.3, but has been tested against previous releases, and the development version. Improvements The stopifnot() assertions now use consistent error messages across all functions (#331) A helper function matching TileDB data types to R types is now exported (#336) @@ -723,20 +648,16 @@ Bug Fixes tiledb 0.10.1 -This release of the R package builds against TileDB 2.5.2, but has been tested against previous releases, and the development version. - +This release of the R package builds against TileDB 2.5.2, but has been tested against previous releases, and the development version. Improvements -An accessor for the most-recent error message string has been added (#327) - +An accessor for the most-recent error message string has been added (#327) Bug Fixes -On Linux, if a pre-made TileDB Embedded library is used, lack of AVX2 instructions is now detected and a suitable build is deployed (#328) - +On Linux, if a pre-made TileDB Embedded library is used, lack of AVX2 instructions is now detected and a suitable build is deployed (#328) tiledb 0.10.0 -This release of the R package builds against TileDB 2.5.1, but has been tested against previous releases, and the development version. - +This release of the R package builds against TileDB 2.5.1, but has been tested against previous releases, and the development version. Improvements CI tests were expanded to also test refactored TileDB Embedded readers (#310), and now deactivated as this is now part of release 2.5.0 (#321) The minimal version of TileDB Embedded that can be used with the R package is now release 2.0.0 (#313) @@ -757,8 +678,7 @@ Bug Fixes tiledb 0.9.7 -This release of the R package builds against TileDB 2.4.0, but has been tested against previous releases and the development version. - +This release of the R package builds against TileDB 2.4.0, but has been tested against previous releases and the development version. Improvements Accessors for context and query statistics were added (returning easily parseable JSON strings) (#293). Initial support for schema evolution was added to add or drop attributes (#294). @@ -780,8 +700,7 @@ Bug Fixes tiledb 0.9.6 -This release of the R package builds against TileDB 2.3.4, but has been tested against previous releases and the development version. - +This release of the R package builds against TileDB 2.3.4, but has been tested against previous releases and the development version. Improvements When retrieving results via the [ operator, incomplete queries generate a warning (#283) The interface to query element size of queries was extended (#282) @@ -801,8 +720,7 @@ Bug Fixes tiledb 0.9.5 -This release of the R package builds against TileDB 2.3.3, but has also been tested against previous releases and the development version. - +This release of the R package builds against TileDB 2.3.3, but has also been tested against previous releases and the development version. Improvements A query condition parser was added for use with standard (non-quoted) R expressions (#267) Windows UCRT builds at CRAN are now supported (#268) @@ -824,8 +742,7 @@ Bug Fixes tiledb 0.9.4 -This release of the R package builds against TileDB 2.3.1, but has also been tested against previous releases and the development version. - +This release of the R package builds against TileDB 2.3.1, but has also been tested against previous releases and the development version. Improvements The build defaults to TileDB Embedded 2.3.* (unless another version is found during build, or explicitly selected) (#258, #264) Query condition support is available for TileDB 2.3.0 or later, allowing (possibly multiple) numerical constraints on attributes (#261) @@ -834,13 +751,11 @@ Improvements Bug Fixes -Dense arrays with more than two dimensions can now be written (#260) - +Dense arrays with more than two dimensions can now be written (#260) tiledb 0.9.3 -This release of the R package builds against TileDB 2.2.9, but has also been tested against previous releases as well as the development version. - +This release of the R package builds against TileDB 2.2.9, but has also been tested against previous releases as well as the development version. Improvements Continuous integration at GitHub is now faster as suggested packages are no longer installed (#250) Arrays can now be written incrementally via the higher-level replacement function arr[] <- obj (#251) @@ -855,8 +770,7 @@ Bug Fixes tiledb 0.9.2 -This release of the R package builds against TileDB 2.2.9, but has also been tested against previous releases as well as the development version. - +This release of the R package builds against TileDB 2.2.9, but has also been tested against previous releases as well as the development version. Improvements Matrix objects can now be returned under range selections (#247) Matrix return get turned on and off with setter / getter functions (#248) @@ -870,8 +784,7 @@ Bug Fixes tiledb 0.9.1 -This release of the R package builds against TileDB 2.2.9, but has also been tested against previous releases as well as the development version. - +This release of the R package builds against TileDB 2.2.9, but has also been tested against previous releases as well as the development version. Improvements A new vignette show use of TileDB array via RMariaDB and the MyTile extension to MariaDB (#221) Matrices can now be returned directly from suitable two-dimensional TileDB arrays (#225) @@ -897,8 +810,7 @@ Bug Fixes tiledb 0.9.0 -This release of the R package builds against TileDB 2.2.4, but has also been tested against two previous release series as well as the development version. - +This release of the R package builds against TileDB 2.2.4, but has also been tested against two previous release series as well as the development version. Improvements The older implementations tiledb_dense and tiledb_sparse are now marked as deprecated in favor of tiledb_array. No removal date is set or planned yet, but it is recommended to migrate to new code. (#180) Updated the underlying TileDB library to use TileDB 2.1.2 on macOS and Linux (when no system library is found) (#181) @@ -932,8 +844,7 @@ Improvements tiledb 0.8.2 -This release of the R package builds against TileDB 2.1.1, but has also been tested against previous releases as well as the development version. - +This release of the R package builds against TileDB 2.1.1, but has also been tested against previous releases as well as the development version. Bug Fixes The tiledb_stats_reset() function is now exported, and tiledb_stats_print() has been re-added as a wrapper to tiledb_stats_dump() (#174) Configuration options for compute and input/output concurrency set only the new TileDB 2.1 configuration options; documentation on how to checking values has been expanded. (#175) @@ -943,8 +854,7 @@ Bug Fixes tiledb 0.8.1 -This release of the R package supports TileDB 2.1.0, but has also been tested against the previous release TileDB 2.0.8. - +This release of the R package supports TileDB 2.1.0, but has also been tested against the previous release TileDB 2.0.8. Improvements R-based metadata accessors have been extended to also support tiledb_array arrays (#169) configure now also checks the hardware platform before attempting a download of a prebuilt library (#170) @@ -952,13 +862,11 @@ Improvements Bug Fixes -A typo in the manual page source, copied three more times, has been corrected (#167) - +A typo in the manual page source, copied three more times, has been corrected (#167) tiledb 0.8.0 -This release of the R package supports TileDB 2.0.8, but has also been tested against the previous release TileDB 1.7.7. - +This release of the R package supports TileDB 2.0.8, but has also been tested against the previous release TileDB 1.7.7. Improvements A new function limitTileDBCores() controls resource use, it is being used in tests (#139) The function tiledb_get_context() is now exported (#140) @@ -983,8 +891,7 @@ Bug Fixes tiledb 0.7.1 This release of the R package supports TileDB 1.7.7 and TileDB 2.0.5 - - + Improvements Range selection for tiledb_array objects can get/set matrices defining range (#132) The show methods are now consistently exported and documented (#134) @@ -997,14 +904,12 @@ Improvements Bug Fixes -A character conversion when retrieving array metadata resulting in an out-of-bounds reads has been corrected (#137) - +A character conversion when retrieving array metadata resulting in an out-of-bounds reads has been corrected (#137) tiledb 0.7.0 This release of the R package supports TileDB 1.7.7 and TileDB 2.0.5 - - + Improvements All S4 classes are now consistently documented or aliased (#117) If needed, the build system now builds TileDB and its required component (#118) @@ -1019,8 +924,7 @@ Improvements tiledb 0.6.0 This release of the R package supports TileDB 1.7.7 and TileDB 2.0.0 - - + Improvements Added support for heterogenous domains Added support for string dimensions @@ -1036,40 +940,34 @@ Improvements Changes -Dimension attributes must now be named - +Dimension attributes must now be named tiledb 0.5.0 -This release of the R package builds against the 1.7.5 releases of TileDB. - +This release of the R package builds against the 1.7.5 releases of TileDB. Improvements -Added support for i) multi-range subarrays, ii) incomplete queries, -result size estimation and ‘time travel’ at to time-points has been added #105 - - +Added support for i) multi-range subarrays, ii) incomplete queries,result size estimation and ‘time travel’ at to time-points has been added #105 + Added additional support for metadata #106 tiledb 0.4.0 -This release of the R package builds against the 1.7.* releases of tiledb. - +This release of the R package builds against the 1.7.* releases of tiledb. Improvements -This release contains increased coverage of the underlying API, additional documentation as well as unit tests. - +This release contains increased coverage of the underlying API, additional documentation as well as unit tests. diff --git a/docs/pkgdown.js b/docs/pkgdown.js index 9757bf9ef2..1a99c65f5c 100644 --- a/docs/pkgdown.js +++ b/docs/pkgdown.js @@ -152,3 +152,11 @@ async function searchFuse(query, callback) { }); }); })(window.jQuery || window.$) + +document.addEventListener('keydown', function(event) { + // Check if the pressed key is '/' + if (event.key === '/') { + event.preventDefault(); // Prevent any default action associated with the '/' key + document.getElementById('search-input').focus(); // Set focus to the search input + } +}); diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index f50de19444..8098c90ca7 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,5 +1,5 @@ -pandoc: 3.1.3 -pkgdown: 2.1.0 +pandoc: 2.9.2.1 +pkgdown: 2.1.1 pkgdown_sha: ~ articles: data-ingestion-from-sql: data-ingestion-from-sql.html @@ -7,7 +7,7 @@ articles: installation-options: installation-options.html introduction: introduction.html tiledb-mariadb-examples: tiledb-mariadb-examples.html -last_built: 2024-12-12T15:49Z +last_built: 2025-01-14T19:21Z urls: reference: https://tiledb-inc.github.io/TileDB-R/reference article: https://tiledb-inc.github.io/TileDB-R/articles diff --git a/docs/reference/array_consolidate.html b/docs/reference/array_consolidate.html index ceb1e5aba3..776fadc1b4 100644 --- a/docs/reference/array_consolidate.html +++ b/docs/reference/array_consolidate.html @@ -1,5 +1,5 @@ -Consolidate fragments of a TileDB Array — array_consolidate • tiledbConsolidate fragments of a TileDB Array — array_consolidate • tiledbtiledb - 0.31.0 + 0.31.0.1 @@ -103,11 +103,11 @@ Value diff --git a/docs/reference/array_vacuum.html b/docs/reference/array_vacuum.html index cbffc1efe5..d98a4991fa 100644 --- a/docs/reference/array_vacuum.html +++ b/docs/reference/array_vacuum.html @@ -1,5 +1,5 @@ -After consolidation, remove consolidated fragments of a TileDB Array — array_vacuum • tiledbAfter consolidation, remove consolidated fragments of a TileDB Array — array_vacuum • tiledbtiledb - 0.31.0 + 0.31.0.1 @@ -103,11 +103,11 @@ Details diff --git a/docs/reference/as.data.frame.tiledb_config.html b/docs/reference/as.data.frame.tiledb_config.html index 29000b538a..9fcaca314b 100644 --- a/docs/reference/as.data.frame.tiledb_config.html +++ b/docs/reference/as.data.frame.tiledb_config.html @@ -1,5 +1,5 @@ -Convert a tiledb_config object to a R data.frame — as.data.frame.tiledb_config • tiledb +Convert a tiledb_config object to a R data.frame — as.data.frame.tiledb_config • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -392,11 +392,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/as.vector.tiledb_config.html b/docs/reference/as.vector.tiledb_config.html index 5d069349f0..e7a8e16edc 100644 --- a/docs/reference/as.vector.tiledb_config.html +++ b/docs/reference/as.vector.tiledb_config.html @@ -1,5 +1,5 @@ -Convert a tiledb_config object to a R vector — as.vector.tiledb_config • tiledb +Convert a tiledb_config object to a R vector — as.vector.tiledb_config • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -390,11 +390,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/attrs-set-tiledb_array-method.html b/docs/reference/attrs-set-tiledb_array-method.html index bcbc419dd9..2c64564a6e 100644 --- a/docs/reference/attrs-set-tiledb_array-method.html +++ b/docs/reference/attrs-set-tiledb_array-method.html @@ -1,5 +1,5 @@ -Selects attributes for the given TileDB array — attrs<-,tiledb_array-method • tiledb +Selects attributes for the given TileDB array — attrs<-,tiledb_array-method • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -81,11 +81,11 @@ Value diff --git a/docs/reference/attrs-tiledb_array-ANY-method.html b/docs/reference/attrs-tiledb_array-ANY-method.html index f95ab1fa6e..476d9c86ff 100644 --- a/docs/reference/attrs-tiledb_array-ANY-method.html +++ b/docs/reference/attrs-tiledb_array-ANY-method.html @@ -1,5 +1,5 @@ -Retrieve attributes from tiledb_array object — attrs,tiledb_array,ANY-method • tiledbRetrieve attributes from tiledb_array object — attrs,tiledb_array,ANY-method • tiledbtiledb - 0.31.0 + 0.31.0.1 @@ -82,11 +82,11 @@ Value diff --git a/docs/reference/attrs-tiledb_array_schema-ANY-method.html b/docs/reference/attrs-tiledb_array_schema-ANY-method.html index 7c9859a847..08792afc8c 100644 --- a/docs/reference/attrs-tiledb_array_schema-ANY-method.html +++ b/docs/reference/attrs-tiledb_array_schema-ANY-method.html @@ -1,5 +1,5 @@ -Returns a list of all tiledb_attr objects associated with the tiledb_array_schema — attrs,tiledb_array_schema,ANY-method • tiledb +Returns a list of all tiledb_attr objects associated with the tiledb_array_schema — attrs,tiledb_array_schema,ANY-method • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -62,7 +62,7 @@ Argumentsobject -tiledb_array_schema +A TileDB Schema object idx @@ -75,7 +75,7 @@ Arguments Value - a list of tiledb_attr objects + A list of tiledb_attr objects @@ -108,11 +108,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/attrs-tiledb_array_schema-character-method.html b/docs/reference/attrs-tiledb_array_schema-character-method.html index 20b9e0598b..74a2c867ca 100644 --- a/docs/reference/attrs-tiledb_array_schema-character-method.html +++ b/docs/reference/attrs-tiledb_array_schema-character-method.html @@ -1,5 +1,5 @@ -Returns a tiledb_attr object associated with the tiledb_array_schema with a given name. — attrs,tiledb_array_schema,character-method • tiledb +Returns a tiledb_attr object associated with the tiledb_array_schema with a given name. — attrs,tiledb_array_schema,character-method • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -62,7 +62,7 @@ Argumentsobject -tiledb_array_schema +A TileDB Schema object idx @@ -75,7 +75,7 @@ Arguments Value - a tiledb_attr object + A tiledb_attr object @@ -95,11 +95,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/attrs-tiledb_array_schema-numeric-method.html b/docs/reference/attrs-tiledb_array_schema-numeric-method.html index 948b849bc4..6bb04eb131 100644 --- a/docs/reference/attrs-tiledb_array_schema-numeric-method.html +++ b/docs/reference/attrs-tiledb_array_schema-numeric-method.html @@ -1,5 +1,5 @@ -Returns a tiledb_attr object associated with the tiledb_array_schema with a given index — attrs,tiledb_array_schema,numeric-method • tiledb +Returns a tiledb_attr object associated with the tiledb_array_schema with a given index — attrs,tiledb_array_schema,numeric-method • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -62,7 +62,7 @@ Argumentsobject -tiledb_array_schema +A TileDB Schema object idx @@ -75,7 +75,7 @@ Arguments Value - a tiledb_attr object + A tiledb_attr object @@ -95,11 +95,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/cell_order-tiledb_array_schema-method.html b/docs/reference/cell_order-tiledb_array_schema-method.html index b9b9c8eb06..f4a00f530f 100644 --- a/docs/reference/cell_order-tiledb_array_schema-method.html +++ b/docs/reference/cell_order-tiledb_array_schema-method.html @@ -1,5 +1,5 @@ -Returns the cell layout string associated with the tiledb_array_schema — cell_order,tiledb_array_schema-method • tiledb +Returns the cell layout string associated with the tiledb_array_schema — cell_order,tiledb_array_schema-method • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -62,20 +62,24 @@ Argumentsobject -tiledb object +A TileDB Schema object + + Value + A character string with cell's layout, e.g., "COL_MAJOR". + diff --git a/docs/reference/completedBatched.html b/docs/reference/completedBatched.html index 892f682334..01ef8d0da7 100644 --- a/docs/reference/completedBatched.html +++ b/docs/reference/completedBatched.html @@ -1,5 +1,5 @@ -Check ‘batched’ query for completion — completedBatched • tiledbCheck ‘batched’ query for completion — completedBatched • tiledbtiledb - 0.31.0 + 0.31.0.1 @@ -83,11 +83,11 @@ Value diff --git a/docs/reference/config-tiledb_ctx-method.html b/docs/reference/config-tiledb_ctx-method.html index cc94830b61..9cea2b6080 100644 --- a/docs/reference/config-tiledb_ctx-method.html +++ b/docs/reference/config-tiledb_ctx-method.html @@ -1,5 +1,5 @@ -Retrieve the tiledb_config object from the tiledb_ctx — config,tiledb_ctx-method • tiledb +Retrieve the tiledb_config object from the tiledb_ctx — config,tiledb_ctx-method • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -85,11 +85,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/createBatched.html b/docs/reference/createBatched.html index 014038e547..96531fd689 100644 --- a/docs/reference/createBatched.html +++ b/docs/reference/createBatched.html @@ -1,5 +1,5 @@ -Create a ‘batched’ query object — createBatched • tiledbCreate a ‘batched’ query object — createBatched • tiledbtiledb - 0.31.0 + 0.31.0.1 @@ -88,11 +88,11 @@ Details diff --git a/docs/reference/datatype-tiledb_attr-method.html b/docs/reference/datatype-tiledb_attr-method.html index 9721358d38..e55951f01b 100644 --- a/docs/reference/datatype-tiledb_attr-method.html +++ b/docs/reference/datatype-tiledb_attr-method.html @@ -1,5 +1,5 @@ -Return the tiledb_attr datatype — datatype,tiledb_attr-method • tiledb +Return the tiledb_attr datatype — datatype,tiledb_attr-method • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -87,11 +87,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/datatype-tiledb_dim-method.html b/docs/reference/datatype-tiledb_dim-method.html index b287c4e9cc..5e98247df8 100644 --- a/docs/reference/datatype-tiledb_dim-method.html +++ b/docs/reference/datatype-tiledb_dim-method.html @@ -1,5 +1,5 @@ -Return the tiledb_dim datatype — datatype,tiledb_dim-method • tiledb +Return the tiledb_dim datatype — datatype,tiledb_dim-method • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -62,12 +62,12 @@ Argumentsobject -tiledb_dim object +A tiledb_dim object Value - tiledb datatype string + A character string with tiledb's datatype. @@ -83,11 +83,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/datatype-tiledb_domain-method.html b/docs/reference/datatype-tiledb_domain-method.html index 1d4689c4f3..a67fd407ae 100644 --- a/docs/reference/datatype-tiledb_domain-method.html +++ b/docs/reference/datatype-tiledb_domain-method.html @@ -1,5 +1,5 @@ -Returns the tiledb_domain TileDB type string — datatype,tiledb_domain-method • tiledb +Returns the tiledb_domain TileDB type string — datatype,tiledb_domain-method • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -86,11 +86,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/datetimes_as_int64-set-tiledb_array-method.html b/docs/reference/datetimes_as_int64-set-tiledb_array-method.html index a2fdce73eb..5bda59c128 100644 --- a/docs/reference/datetimes_as_int64-set-tiledb_array-method.html +++ b/docs/reference/datetimes_as_int64-set-tiledb_array-method.html @@ -1,5 +1,5 @@ -Set datetimes_as_int64 toggle — datetimes_as_int64<- • tiledbSet datetimes_as_int64 toggle — datetimes_as_int64<- • tiledbtiledb - 0.31.0 + 0.31.0.1 @@ -93,11 +93,11 @@ Value diff --git a/docs/reference/datetimes_as_int64-tiledb_array-method.html b/docs/reference/datetimes_as_int64-tiledb_array-method.html index 16ba610612..aace3a0b41 100644 --- a/docs/reference/datetimes_as_int64-tiledb_array-method.html +++ b/docs/reference/datetimes_as_int64-tiledb_array-method.html @@ -1,5 +1,5 @@ -Retrieve datetimes_as_int64 toggle — datetimes_as_int64 • tiledbRetrieve datetimes_as_int64 toggle — datetimes_as_int64 • tiledbtiledb - 0.31.0 + 0.31.0.1 @@ -90,11 +90,11 @@ Value diff --git a/docs/reference/describe.html b/docs/reference/describe.html index a5e93448b1..5c3333aaa9 100644 --- a/docs/reference/describe.html +++ b/docs/reference/describe.html @@ -1,5 +1,5 @@ -Describe a TileDB array schema via code to create it — describe • tiledbDescribe a TileDB array schema via code to create it — describe • tiledb Skip to contents @@ -9,7 +9,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -78,11 +78,11 @@ Value diff --git a/docs/reference/dim.tiledb_array_schema.html b/docs/reference/dim.tiledb_array_schema.html index 26fcb447ef..e3465c5b77 100644 --- a/docs/reference/dim.tiledb_array_schema.html +++ b/docs/reference/dim.tiledb_array_schema.html @@ -1,5 +1,5 @@ -Retrieve the dimension (domain extent) of the domain — dim.tiledb_array_schema • tiledb +Retrieve the dimension (domain extent) of the domain — dim.tiledb_array_schema • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -62,7 +62,7 @@ Argumentsx -tiledb_array_schema +A TileDB Schema object @@ -87,11 +87,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/dim.tiledb_dim.html b/docs/reference/dim.tiledb_dim.html index baad9d0a84..b4da1bb552 100644 --- a/docs/reference/dim.tiledb_dim.html +++ b/docs/reference/dim.tiledb_dim.html @@ -1,5 +1,5 @@ -Retrieves the dimension of the tiledb_dim domain — dim.tiledb_dim • tiledb +Retrieves the dimension of the tiledb_dim domain — dim.tiledb_dim • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -62,12 +62,12 @@ Argumentsx -tiledb_dim object +A tiledb_dim object Value - a vector of the tile_dim domain type, of the dim domain dimension (extent) + A vector of the tile_dim domain type, of the dim domain dimension (extent) @@ -83,11 +83,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/dim.tiledb_domain.html b/docs/reference/dim.tiledb_domain.html index 9588671f6d..7f98ae09d3 100644 --- a/docs/reference/dim.tiledb_domain.html +++ b/docs/reference/dim.tiledb_domain.html @@ -1,5 +1,5 @@ -Retrieve the dimension (domain extent) of the domain — dim.tiledb_domain • tiledb +Retrieve the dimension (domain extent) of the domain — dim.tiledb_domain • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -86,11 +86,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/dimensions-tiledb_array_schema-method.html b/docs/reference/dimensions-tiledb_array_schema-method.html index 2435fc863b..227ec18c99 100644 --- a/docs/reference/dimensions-tiledb_array_schema-method.html +++ b/docs/reference/dimensions-tiledb_array_schema-method.html @@ -1,5 +1,5 @@ -Returns a list of tiledb_dim objects associated with the tiledb_array_schema — dimensions,tiledb_array_schema-method • tiledb +Returns a list of tiledb_dim objects associated with the tiledb_array_schema — dimensions,tiledb_array_schema-method • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -62,12 +62,12 @@ Argumentsobject -tiledb_array_schema +A TileDB Schema object Value - a list of tiledb_dim objects + A list of tiledb_dim objects @@ -100,11 +100,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/dimensions-tiledb_domain-method.html b/docs/reference/dimensions-tiledb_domain-method.html index bd6e4bc266..40cdc41eb0 100644 --- a/docs/reference/dimensions-tiledb_domain-method.html +++ b/docs/reference/dimensions-tiledb_domain-method.html @@ -1,5 +1,5 @@ -Returns a list of the tiledb_domain dimension objects — dimensions,tiledb_domain-method • tiledb +Returns a list of the tiledb_domain dimension objects — dimensions,tiledb_domain-method • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -99,11 +99,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/domain-tiledb_array_schema-method.html b/docs/reference/domain-tiledb_array_schema-method.html index 1c8f432bfb..6fcbaf3137 100644 --- a/docs/reference/domain-tiledb_array_schema-method.html +++ b/docs/reference/domain-tiledb_array_schema-method.html @@ -1,5 +1,5 @@ -Returns the tiledb_domain object associated with a given tiledb_array_schema — domain,tiledb_array_schema-method • tiledb +Returns the tiledb_domain object associated with a given tiledb_array_schema — domain,tiledb_array_schema-method • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -62,9 +62,13 @@ Argumentsobject -tiledb_array_schema +A TileDB Schema object + + Value + A tiledb_domain object + Examples @@ -82,11 +86,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/domain-tiledb_dim-method.html b/docs/reference/domain-tiledb_dim-method.html index 057c340931..01b7546a27 100644 --- a/docs/reference/domain-tiledb_dim-method.html +++ b/docs/reference/domain-tiledb_dim-method.html @@ -1,5 +1,5 @@ -Return the tiledb_dim domain — domain,tiledb_dim-method • tiledb +Return the tiledb_dim domain — domain,tiledb_dim-method • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -62,7 +62,7 @@ Argumentsobject -tiledb_dim object +A tiledb_dim object @@ -83,11 +83,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/dot-core_info.html b/docs/reference/dot-core_info.html index 50854e5e86..e36f295511 100644 --- a/docs/reference/dot-core_info.html +++ b/docs/reference/dot-core_info.html @@ -1,5 +1,5 @@ -libtiledb Information — .core_info • tiledb +libtiledb Information — .core_info • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -86,11 +86,11 @@ Checking the Examples .core_info() -#> version libtype -#> "2.27.0" "system" +#> version libtype +#> "2.27.0" "vendored" .core_hash() -#> [1] "17c9b4d820870f7c171fccf2be8fdfea" +#> [1] "712cb7e256376af4fbfecc51290a4241" @@ -99,11 +99,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/dot-pkg_config.html b/docs/reference/dot-pkg_config.html index c13faa4c2c..174a0f304d 100644 --- a/docs/reference/dot-pkg_config.html +++ b/docs/reference/dot-pkg_config.html @@ -1,5 +1,5 @@ -Compiler Arguments for Using libtiledb — .pkg_config • tiledbCompiler Arguments for Using libtiledb — .pkg_config • tiledb Skip to contents @@ -9,7 +9,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -79,9 +79,9 @@ Value Examples .pkg_config() -#> [1] "-I/usr/local/include" +#> [1] "-I/tmp/RtmpiRigbQ/temp_libpath556b1464bc75e/tiledb/include -I/tmp/RtmpiRigbQ/temp_libpath556b1464bc75e/tiledb/tiledb/include" .pkg_config("PKG_CXX_LIBS") -#> [1] "-L/usr/local/lib -ltiledb" +#> [1] "-ltiledb -L/tmp/RtmpiRigbQ/temp_libpath556b1464bc75e/tiledb/lib -L/tmp/RtmpiRigbQ/temp_libpath556b1464bc75e/tiledb/tiledb/lib" @@ -90,11 +90,11 @@ Examples - Developed by , Dirk Eddelbuettel, Isaiah Norton. + Developed by , Isaiah Norton. diff --git a/docs/reference/extended-set-tiledb_array-method.html b/docs/reference/extended-set-tiledb_array-method.html index 4618988929..0149ea9749 100644 --- a/docs/reference/extended-set-tiledb_array-method.html +++ b/docs/reference/extended-set-tiledb_array-method.html @@ -1,5 +1,5 @@ -Set data.frame extended return columns toggle — extended<- • tiledbSet data.frame extended return columns toggle — extended<- • tiledbtiledb - 0.31.0 + 0.31.0.1 @@ -87,11 +87,11 @@ Value diff --git a/docs/reference/extended-tiledb_array-method.html b/docs/reference/extended-tiledb_array-method.html index fef6d703a6..29ad827156 100644 --- a/docs/reference/extended-tiledb_array-method.html +++ b/docs/reference/extended-tiledb_array-method.html @@ -1,5 +1,5 @@ -Retrieve data.frame extended returns columns toggle — extended • tiledbRetrieve data.frame extended returns columns toggle — extended • tiledbtiledb - 0.31.0 + 0.31.0.1 @@ -84,11 +84,11 @@ Value diff --git a/docs/reference/fetchBatched.html b/docs/reference/fetchBatched.html index f4ce306d49..4d117316bd 100644 --- a/docs/reference/fetchBatched.html +++ b/docs/reference/fetchBatched.html @@ -1,5 +1,5 @@ -Run a ‘batched’ query — fetchBatched • tiledbRun a ‘batched’ query — fetchBatched • tiledbtiledb - 0.31.0 + 0.31.0.1 @@ -92,11 +92,11 @@ Details diff --git a/docs/reference/filter_list-set-tiledb_attr-method.html b/docs/reference/filter_list-set-tiledb_attr-method.html index aba612335b..a803608564 100644 --- a/docs/reference/filter_list-set-tiledb_attr-method.html +++ b/docs/reference/filter_list-set-tiledb_attr-method.html @@ -1,5 +1,5 @@ -Sets the TileDB Filter List for the TileDB Attribute object — filter_list<-,tiledb_attr-method • tiledb +Sets the TileDB Filter List for the TileDB Attribute object — filter_list<-,tiledb_attr-method • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -79,11 +79,11 @@ Value diff --git a/docs/reference/filter_list-set-tiledb_dim-method.html b/docs/reference/filter_list-set-tiledb_dim-method.html index b11f369606..d7a0418c30 100644 --- a/docs/reference/filter_list-set-tiledb_dim-method.html +++ b/docs/reference/filter_list-set-tiledb_dim-method.html @@ -1,5 +1,5 @@ -Sets the TileDB Filter List for the TileDB Dimension object — filter_list<-,tiledb_dim-method • tiledb +Sets the TileDB Filter List for the TileDB Dimension object — filter_list<-,tiledb_dim-method • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -62,7 +62,7 @@ Argumentsx -TileDB Dimension +A tiledb_dim object value @@ -79,11 +79,11 @@ Value diff --git a/docs/reference/filter_list-tiledb_array_schema-method.html b/docs/reference/filter_list-tiledb_array_schema-method.html index 98baffdf54..59f87c52e5 100644 --- a/docs/reference/filter_list-tiledb_array_schema-method.html +++ b/docs/reference/filter_list-tiledb_array_schema-method.html @@ -1,5 +1,5 @@ -Returns the offsets and coordinate filter_lists associated with the tiledb_array_schema — filter_list,tiledb_array_schema-method • tiledb +Returns the offsets and coordinate filter_lists associated with the tiledb_array_schema — filter_list,tiledb_array_schema-method • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -62,12 +62,12 @@ Argumentsobject -tiledb_array_schema +A TileDB Schema object
Having read the data into memory we can use the TileDB R function -fromDataFrame. It has numerous option to configure, as well -as sensible defaults (to for example enable ZSTD compression). Here we -select the first two columns for symbol and data as dimensions. Symbols, -being text, do not set a domain set. For the date we set two ‘safe’ -outer values for the range.
fromDataFrame
Having read the data into memory we can use the TileDB R function fromDataFrame. It has numerous option to configure, as well as sensible defaults (to for example enable ZSTD compression). Here we select the first two columns for symbol and data as dimensions. Symbols, being text, do not set a domain set. For the date we set two ‘safe’ outer values for the range.
storeDataTDB <- function(dat, uri) { fromDataFrame(dat, uri, @@ -176,16 +141,11 @@ Writing Data to TileDB tile_domain=list(date=c(as.numeric(as.Date("1985-01-01")), as.numeric(as.Date("2030-12-31"))))) }
The mode="append" argument of fromDataFrame -can be used to append to an existing array to support chunked -operation.
mode="append"
The mode="append" argument of fromDataFrame can be used to append to an existing array to support chunked operation.
Reading data from TileDB is a very standard operation of opening the -URI, possibly specifying the return type and possibly subsetting by -dimension values, or attributes. Here, for simplicity, we just read -everything.
Reading data from TileDB is a very standard operation of opening the URI, possibly specifying the return type and possibly subsetting by dimension values, or attributes. Here, for simplicity, we just read everything.
getDataTDB <- function(uri) { set_allocation_size_preference(1e7) # larger than local default value @@ -206,21 +166,13 @@ Reading Data Back In See Also -The vignette TileDB MariaDB -Examples shows to use MariaDB via the MyTile integration of TileDB -as a direct backend. -The TileDB -R Tutorial at useR! 2021 contained a worked example of writing -much larger data set in chunks. The process is very similar to -the simple example we showed here – and in addition requires a suffient -domain range for the dimension along with a (sequential or parallel) -loop of reading chunks and writing them to TileDB. +The vignette TileDB MariaDB Examples shows to use MariaDB via the MyTile integration of TileDB as a direct backend. +The TileDB R Tutorial at useR! 2021 contained a worked example of writing much larger data set in chunks. The process is very similar to the simple example we showed here – and in addition requires a suffient domain range for the dimension along with a (sequential or parallel) loop of reading chunks and writing them to TileDB.
The vignette TileDB MariaDB -Examples shows to use MariaDB via the MyTile integration of TileDB -as a direct backend.
The TileDB -R Tutorial at useR! 2021 contained a worked example of writing -much larger data set in chunks. The process is very similar to -the simple example we showed here – and in addition requires a suffient -domain range for the dimension along with a (sequential or parallel) -loop of reading chunks and writing them to TileDB.
The vignette TileDB MariaDB Examples shows to use MariaDB via the MyTile integration of TileDB as a direct backend.
The TileDB R Tutorial at useR! 2021 contained a worked example of writing much larger data set in chunks. The process is very similar to the simple example we showed here – and in addition requires a suffient domain range for the dimension along with a (sequential or parallel) loop of reading chunks and writing them to TileDB.
This vignette provides a commented walk-through of a worked example -of a SQL-to-TileDB data ingestion.
This vignette provides a commented walk-through of a worked example of a SQL-to-TileDB data ingestion.
This document follows the TileDB API usage -examples. A shorter introductory -vignette is also available.
This document follows the TileDB API usage examples. A shorter introductory vignette is also available.
We will show two initial and basic examples for a dense and sparse -array simply to create array data on disk to refer to later in examples -that follow.
We will show two initial and basic examples for a dense and sparse array simply to create array data on disk to refer to later in examples that follow.
library(tiledb) @@ -1304,11 +1299,11 @@ Catching Errors diff --git a/docs/articles/documentation_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/documentation_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 0000000000..ca349fd6a5 --- /dev/null +++ b/docs/articles/documentation_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. + +document.addEventListener('DOMContentLoaded', function() { + const codeList = document.getElementsByClassName("sourceCode"); + for (var i = 0; i < codeList.length; i++) { + var linkList = codeList[i].getElementsByTagName('a'); + for (var j = 0; j < linkList.length; j++) { + if (linkList[j].innerHTML === "") { + linkList[j].setAttribute('aria-hidden', 'true'); + } + } + } +}); diff --git a/docs/articles/index.html b/docs/articles/index.html index e74f7844ec..6eb1a0a5b5 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -1,5 +1,5 @@ -Articles • tiledb +Articles • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -75,11 +75,11 @@ Working with SQL
This vignette discusses different options for installing the TileDB R -package.
This vignette discusses different options for installing the TileDB R package.
The TileDB R package is released via the Comprehensive R Archive -Network, or CRAN. CRAN generally provides binaries for the two most -widely operating systems, Windows and macOS. So issueing the command
The TileDB R package is released via the Comprehensive R Archive Network, or CRAN. CRAN generally provides binaries for the two most widely operating systems, Windows and macOS. So issueing the command
install.packages("tiledb")
will, on those two operating system, default to -type="binary" and install a ready-to-run binary -package.
type="binary"
will, on those two operating system, default to type="binary" and install a ready-to-run binary package.
On other operating systems such as Linux, or by explicitly selecting -type="source" on Windows or macOS, an installation from source is attempted when usinginstall.packages(“tiledb”)`.
type="source" on Windows or macOS, an installation from source is attempted when using
On Linux or macOS, this invokes the standard R build process which -will rely on configure. If pkg-config is -found, it is used to query the system about a possible TileDB -installation. If one is found, it used. Otherwise, on all three main -operating systems a prebuilt archive with the TileDB Embedded library is -downloaded from GitHub and unpacked. Each build of the R package will -have one matching build of TileDB Embedded associated with it via file -the tools/tiledbVersion.txt specifying a version and -release commit sha1. These two values are used to find the corresponding -binary artifacts from a release at GitHub.
configure
pkg-config
tools/tiledbVersion.txt
The location of an existing installed version of TileDB Embedded can -also be provided to the configure script which supplies an -argument --with-tiledb=PATH. So on the command-line, one -could say
--with-tiledb=PATH
R CMD INSTALL --configure-args='--with-tiledb=/some/path' tiledb_*.tar.gz
to pass the configure argument on. From within R, the -equivalent command is
On other operating systems such as Linux, or by explicitly selecting type="source" on Windows or macOS, an installation from source is attempted when usinginstall.packages(“tiledb”)`.
On Linux or macOS, this invokes the standard R build process which will rely on configure. If pkg-config is found, it is used to query the system about a possible TileDB installation. If one is found, it used. Otherwise, on all three main operating systems a prebuilt archive with the TileDB Embedded library is downloaded from GitHub and unpacked. Each build of the R package will have one matching build of TileDB Embedded associated with it via file the tools/tiledbVersion.txt specifying a version and release commit sha1. These two values are used to find the corresponding binary artifacts from a release at GitHub.
The location of an existing installed version of TileDB Embedded can also be provided to the configure script which supplies an argument --with-tiledb=PATH. So on the command-line, one could say
to pass the configure argument on. From within R, the equivalent command is
install.packages("tiledb", repos=NULL, configure.args="--with-tiledb=/some/path")
Lastly, one can also override the default download location -(otherwise inferred via tools/tiledbVersion.txt. The -configure script supports an option ---with-download=URL so the two calls become, -respectively
--with-download=URL
R CMD INSTALL --configure-args='--with-download=https://some.where.net/file.tgz' tiledb_*.tar.gz
Lastly, one can also override the default download location (otherwise inferred via tools/tiledbVersion.txt. The configure script supports an option --with-download=URL so the two calls become, respectively
and
install.packages("tiledb_0.11.0.tar.gz", repos=NULL, @@ -147,30 +123,23 @@ Source Conda -Using for example the current condaforge/mambaforge -container from the conda-forge project, -we can do -mamba install -y r-tiledb # installs R, tiledb and deps without extra prompt -# ...several lines of installation detail omitted -R -# ... several lines of R startup output omitted -> library(tiledb) -which installs R, the tiledb package and all respective -dependencies. +Using for example the current condaforge/mambaforge container from the conda-forge project, we can do +mamba install -y r-tiledb # installs R, tiledb and deps without extra prompt +# ...several lines of installation detail omitted +R +# ... several lines of R startup output omitted +> library(tiledb) +which installs R, the tiledb package and all respective dependencies. Docker -Builds of the TileDB package could also be provided via Docker -containers. At present, no official TileDB R containers are provided by -TileDB. However, the discussion of installation from source above -describes how to create such containers. +Builds of the TileDB package could also be provided via Docker containers. At present, no official TileDB R containers are provided by TileDB. However, the discussion of installation from source above describes how to create such containers. Summary -This note described several installation options for the TileDB R -package. +This note described several installation options for the TileDB R package. @@ -179,11 +148,11 @@ Summary diff --git a/docs/articles/installation-options_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/installation-options_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 0000000000..ca349fd6a5 --- /dev/null +++ b/docs/articles/installation-options_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. + +document.addEventListener('DOMContentLoaded', function() { + const codeList = document.getElementsByClassName("sourceCode"); + for (var i = 0; i < codeList.length; i++) { + var linkList = codeList[i].getElementsByTagName('a'); + for (var j = 0; j < linkList.length; j++) { + if (linkList[j].innerHTML === "") { + linkList[j].setAttribute('aria-hidden', 'true'); + } + } + } +}); diff --git a/docs/articles/introduction.html b/docs/articles/introduction.html index b87009f33d..bf485522d9 100644 --- a/docs/articles/introduction.html +++ b/docs/articles/introduction.html @@ -12,7 +12,7 @@ - + @@ -26,7 +26,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -68,8 +68,7 @@ - - + First Steps with TileDB @@ -86,29 +85,14 @@ First Steps with TileDB %\VignetteEngine{simplermarkdown::mdweave_to_html} %\VignetteEncoding{UTF-8} --> -This document introduces TileDB via several simple examples. A -corresponding document with more complete API documentation is also available. +This document introduces TileDB via several simple examples. A corresponding document with more complete API documentation is also available. Getting started -Once the TileDB R package is installed, it can be loaded via -library(tiledb). Installation is supported for Windows, -Linux and macOS via the official CRAN -package, on Linux and macOS via the conda package as well as -from source. -Documentation for the TileDB R package is available via the -help() function from within R as well as via the package documentation -and an introductory -notebook. Documentation about TileDB itself is also available. -Several “quickstart” examples that are discussed on the website are -available in the examples -directory. This vignette discusses similar examples. -In the following examples, the URIs describing arrays point to local -file system object. When TileDB has been built with S3 support, and with -proper AWS credentials in the usual environment variables, URIs such as -s3://some/data/bucket can be used where a local file would -be used. See the script ex_S3.R -for an example. +Once the TileDB R package is installed, it can be loaded via library(tiledb). Installation is supported for Windows, Linux and macOS via the official CRAN package, on Linux and macOS via the conda package as well as from source. +Documentation for the TileDB R package is available via the help() function from within R as well as via the package documentation and an introductory notebook. Documentation about TileDB itself is also available. +Several “quickstart” examples that are discussed on the website are available in the examples directory. This vignette discusses similar examples. +In the following examples, the URIs describing arrays point to local file system object. When TileDB has been built with S3 support, and with proper AWS credentials in the usual environment variables, URIs such as s3://some/data/bucket can be used where a local file would be used. See the script ex_S3.R for an example. Dense Arrays @@ -116,104 +100,72 @@ Dense Arrays Preliminaries -These illustrations use the array created by the file ex_1.R -which one can run from within R, or on the command-line. To follow along -with discussion that follows, it helps to run the example once to create -the array after possibly adjusting the array location path from its -default value (using the current directory or, if set as an option, an -override). +These illustrations use the array created by the file ex_1.R which one can run from within R, or on the command-line. To follow along with discussion that follows, it helps to run the example once to create the array after possibly adjusting the array location path from its default value (using the current directory or, if set as an option, an override). Basic Reading of Dense Arrays -The file ex_1.R -in the examples directory is a simple yet complete example extending quickstart_dense.R -by adding a second and third attribute. In this as well as the following -examples we will use tiledb_array() to access the array; -the older variants tiledb_dense() and -tiledb_sparse() remain supported but are deprecated and may -be removed at some point in the future. +The file ex_1.R in the examples directory is a simple yet complete example extending quickstart_dense.R by adding a second and third attribute. In this as well as the following examples we will use tiledb_array() to access the array; the older variants tiledb_dense() and tiledb_sparse() remain supported but are deprecated and may be removed at some point in the future. Read 1-D -The first example extracts rows 1 to 2 and column 2 from an array. It -also limits the selection to just one attribute (via -attrs), asks for the return to be a data.frame -(instead of a simpler list) and for the (row and column, if present as -here) indices to not be printed (via extended=FALSE). -> A <- tiledb_array(uri = uri, attrs = "b", -+ return_as = "data.frame", extended=FALSE)) -> A[1:2,2] -[1] 101.5 104.0 -> -Note that the examples create three two-dimensional attributes. The -attributes can be selected via the attrs argument, or the -attrs() method on the array object. The square-bracket -indexing then selects with in the 2-d attribute object. -If multiple objects are returned (as list or -data.frame), subsetting on the returned object works via -[[var]] or $var. A numeric index also works -(but needs to account for rows and cols). -> A <- tiledb_array(uri = uri, attrs = c("a","b"), -+ return_as = "data.frame") -> A[1:2,2][["a"]] -[1] 2 7 -> A[1:2,2]$a -[1] 2 7 -> +The first example extracts rows 1 to 2 and column 2 from an array. It also limits the selection to just one attribute (via attrs), asks for the return to be a data.frame (instead of a simpler list) and for the (row and column, if present as here) indices to not be printed (via extended=FALSE). +> A <- tiledb_array(uri = uri, attrs = "b", ++ return_as = "data.frame", extended=FALSE)) +> A[1:2,2] +[1] 101.5 104.0 +> +Note that the examples create three two-dimensional attributes. The attributes can be selected via the attrs argument, or the attrs() method on the array object. The square-bracket indexing then selects with in the 2-d attribute object. +If multiple objects are returned (as list or data.frame), subsetting on the returned object works via [[var]] or $var. A numeric index also works (but needs to account for rows and cols). +> A <- tiledb_array(uri = uri, attrs = c("a","b"), ++ return_as = "data.frame") +> A[1:2,2][["a"]] +[1] 2 7 +> A[1:2,2]$a +[1] 2 7 +> Read 2-D -This works analogously. Note that the results are generally returned -as vectors, or as a columns of a data.frame object in case -that option was set. -> A[6:9,3:4] -$a -[1] 28 29 33 34 38 39 43 44 - -$b -[1] 114.5 115.0 117.0 117.5 119.5 120.0 122.0 122.5 - -$c -[1] "fox" "A" "E" "F" "J" "K" "O" "P" -> +This works analogously. Note that the results are generally returned as vectors, or as a columns of a data.frame object in case that option was set. +> A[6:9,3:4] +$a +[1] 28 29 33 34 38 39 43 44 + +$b +[1] 114.5 115.0 117.0 117.5 119.5 120.0 122.0 122.5 + +$c +[1] "fox" "A" "E" "F" "J" "K" "O" "P" +> Read 2-D with attribute selection -We can restrict the selection to a subset of attributes when opening -the array. -> A <- tiledb_dense(uri = uri, attrs = c("b","c"), -+ return_as = "data.frame", extended=FALSE) -> A[6:9,2:4] - b c -1 114.0 brown -2 114.5 fox -3 115.0 A -4 116.5 D -5 117.0 E -6 117.5 F -7 119.0 I -8 119.5 J -9 120.0 K -10 121.5 N -11 122.0 O -12 122.5 P -> -This also illustrated the effect of setting -as.data.frame=TRUE when opening the array. -This scheme can be generalized to variable cells, or cells where -N>1, as we can expand each (atomistic) value over corresponding row -and column indices. -The column types correspond to the attribute typed in the array -schema, subject to the constraint mentioned above on R types. (The char -comes in as a factor variable as is still the R 3.6.* default which is -about to change. We can also override, users can too.) -> A <- tiledb_array("/tmp/tiledb/ex_1/", attrs=c("b","c"), -+ return_as = "data.frame", extended=TRUE) -> sapply(A[6:9, 3:4], "class") - rows cols b c - "integer" "integer" "numeric" "character" -> -Consistent with the data.frame semantics, now -requesting a named column reduces to a vector as this happens -at the R side: +We can restrict the selection to a subset of attributes when opening the array. +> A <- tiledb_dense(uri = uri, attrs = c("b","c"), ++ return_as = "data.frame", extended=FALSE) +> A[6:9,2:4] + b c +1 114.0 brown +2 114.5 fox +3 115.0 A +4 116.5 D +5 117.0 E +6 117.5 F +7 119.0 I +8 119.5 J +9 120.0 K +10 121.5 N +11 122.0 O +12 122.5 P +> +This also illustrated the effect of setting as.data.frame=TRUE when opening the array. +This scheme can be generalized to variable cells, or cells where N>1, as we can expand each (atomistic) value over corresponding row and column indices. +The column types correspond to the attribute typed in the array schema, subject to the constraint mentioned above on R types. (The char comes in as a factor variable as is still the R 3.6.* default which is about to change. We can also override, users can too.) +> A <- tiledb_array("/tmp/tiledb/ex_1/", attrs=c("b","c"), ++ return_as = "data.frame", extended=TRUE) +> sapply(A[6:9, 3:4], "class") + rows cols b c + "integer" "integer" "numeric" "character" +> +Consistent with the data.frame semantics, now requesting a named column reduces to a vector as this happens at the R side: > A[6:9, 3:4]$b [1] 114.5 115.0 117.0 117.5 119.5 120.0 122.0 122.5 > @@ -226,96 +178,78 @@ Sparse ArraysBasic Reading and Writing of Sparse Arrays Simple Examples -Basic reading returns the coordinates and any attributes. The -following examples use the array created by the quickstart_sparse -example. -> A <- tiledb_array(uri = uri, is.sparse = TRUE) -> A[] -$rows -[1] 1 2 2 - -$cols -[1] 1 3 4 - -$a -[1] 1 3 2 - -> -We can also request a data.frame object, either when -opening or by changing this object characteristic on the fly: -> return.data.frame(A) <- TRUE -> A[] - a rows cols -1 1 1 1 -2 3 2 3 -3 2 2 4 -For sparse arrays, the return type is by default ‘extended’ showing -rows and column but this can be overridden. +Basic reading returns the coordinates and any attributes. The following examples use the array created by the quickstart_sparse example. +> A <- tiledb_array(uri = uri, is.sparse = TRUE) +> A[] +$rows +[1] 1 2 2 + +$cols +[1] 1 3 4 + +$a +[1] 1 3 2 + +> +We can also request a data.frame object, either when opening or by changing this object characteristic on the fly: +> return.data.frame(A) <- TRUE +> A[] + a rows cols +1 1 1 1 +2 3 2 3 +3 2 2 4 +For sparse arrays, the return type is by default ‘extended’ showing rows and column but this can be overridden. Assignment works similarly: -> A[4,2] <- 42L -> A[] -> A[] - rows cols a -1 1 1 1 -2 2 3 3 -3 2 4 2 -4 4 2 42 -> +> A[4,2] <- 42L +> A[] +> A[] + rows cols a +1 1 1 1 +2 2 3 3 +3 2 4 2 +4 4 2 42 +> Reads can select rows and or columns: -> A[2,] - rows cols a -1 2 3 3 -2 2 4 2 -> A[,2] - rows cols a -1 4 2 42 -> +> A[2,] + rows cols a +1 2 3 3 +2 2 4 2 +> A[,2] + rows cols a +1 4 2 42 +> Attributes can be selected similarly. Date(time) Attributes -Similar to the dense array case described earlier, the file ex_2.R -illustrates some basic operations on sparse arrays. It also shows date -and datetime types instead of just integer and double precision -floats. -> A <- tiledb_array(uri = uri, return_as = "data.frame") -> A[1577858403:1577858408] - rows cols a b d e -1 1577858403 1 3 103 2020-01-11 2020-01-02 18:24:33.844 -2 1577858404 1 4 104 2020-01-15 2020-01-05 02:28:36.214 -3 1577858405 1 5 105 2020-01-19 2020-01-05 00:44:04.805 -4 1577858406 1 6 106 2020-01-21 2020-01-06 12:58:51.770 -5 1577858407 1 7 107 2020-01-25 2020-01-09 04:29:56.309 -6 1577858408 1 8 108 2020-01-26 2020-01-07 13:55:10.240 -> -The row coordinate is currently a floating point representation of -the underlying time type. We can both select attributes (here we -excluded the “a” column) and select rows by time (as the time stamps get -converted to the required floating point value). -> attrs(A) <- c("b", "d", "e") -> A[as.POSIXct("2020-01-01"):as.POSIXct("2020-01-01 00:00:03")] - rows cols b d e -1 1577858401 1 101 2020-01-05 2020-01-01 03:03:07.548 -2 1577858402 1 102 2020-01-10 2020-01-02 21:02:19.747 -3 1577858403 1 103 2020-01-11 2020-01-02 18:24:33.844 -> -More extended examples are available showing indexing by date(time) -as well as character dimension. +Similar to the dense array case described earlier, the file ex_2.R illustrates some basic operations on sparse arrays. It also shows date and datetime types instead of just integer and double precision floats. +> A <- tiledb_array(uri = uri, return_as = "data.frame") +> A[1577858403:1577858408] + rows cols a b d e +1 1577858403 1 3 103 2020-01-11 2020-01-02 18:24:33.844 +2 1577858404 1 4 104 2020-01-15 2020-01-05 02:28:36.214 +3 1577858405 1 5 105 2020-01-19 2020-01-05 00:44:04.805 +4 1577858406 1 6 106 2020-01-21 2020-01-06 12:58:51.770 +5 1577858407 1 7 107 2020-01-25 2020-01-09 04:29:56.309 +6 1577858408 1 8 108 2020-01-26 2020-01-07 13:55:10.240 +> +The row coordinate is currently a floating point representation of the underlying time type. We can both select attributes (here we excluded the “a” column) and select rows by time (as the time stamps get converted to the required floating point value). +> attrs(A) <- c("b", "d", "e") +> A[as.POSIXct("2020-01-01"):as.POSIXct("2020-01-01 00:00:03")] + rows cols b d e +1 1577858401 1 101 2020-01-05 2020-01-01 03:03:07.548 +2 1577858402 1 102 2020-01-10 2020-01-02 21:02:19.747 +3 1577858403 1 103 2020-01-11 2020-01-02 18:24:33.844 +> +More extended examples are available showing indexing by date(time) as well as character dimension. Additional Information -The TileDB R package is documented via R help functions -(e.g. help("tiledb_array") shows information for -the tiledb_array() function) as well as via a website regrouping all -documentation. Extended API -documentation is available, as is a examples/ -directory. -TileDB itself has extensive installation, -and overall -documentation as well as a support forum. +The TileDB R package is documented via R help functions (e.g. help("tiledb_array") shows information for the tiledb_array() function) as well as via a website regrouping all documentation. Extended API documentation is available, as is a examples/ directory. +TileDB itself has extensive installation, and overall documentation as well as a support forum. @@ -324,11 +258,11 @@ Additional Information diff --git a/docs/articles/introduction_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/introduction_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 0000000000..ca349fd6a5 --- /dev/null +++ b/docs/articles/introduction_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. + +document.addEventListener('DOMContentLoaded', function() { + const codeList = document.getElementsByClassName("sourceCode"); + for (var i = 0; i < codeList.length; i++) { + var linkList = codeList[i].getElementsByTagName('a'); + for (var j = 0; j < linkList.length; j++) { + if (linkList[j].innerHTML === "") { + linkList[j].setAttribute('aria-hidden', 'true'); + } + } + } +}); diff --git a/docs/articles/tiledb-mariadb-examples.html b/docs/articles/tiledb-mariadb-examples.html index 849627c0bf..866cf34a7c 100644 --- a/docs/articles/tiledb-mariadb-examples.html +++ b/docs/articles/tiledb-mariadb-examples.html @@ -12,7 +12,7 @@ - + @@ -26,7 +26,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -68,8 +68,7 @@ - - + TileDB and (R)MariaDB Examples @@ -89,43 +88,26 @@ TileDB and (R)MariaDB Examples Introduction -TileDB provides the -Universal Data Engine that can be accessed in a variety of -ways. The C/C++ library offered by TileDB Embedded is one -approach, and the R -package, as well as the Python package and -other language bindings use it. Another interface is provided by the MariaDB Integration via the -MyTile storage plugin. -This provides TileDB integration with any frontend that interfaces -with MariaDB—such as the RMariaDB package -for R. So this vignette illustrates the use of TileDB via MariaDB using -R and the RMariaDB packages. +TileDB provides the Universal Data Engine that can be accessed in a variety of ways. The C/C++ library offered by TileDB Embedded is one approach, and the R package, as well as the Python package and other language bindings use it. Another interface is provided by the MariaDB Integration via the MyTile storage plugin. +This provides TileDB integration with any frontend that interfaces with MariaDB—such as the RMariaDB package for R. So this vignette illustrates the use of TileDB via MariaDB using R and the RMariaDB packages. Installation or Using Docker -In order to use the MyTile storage plugin, one has to compile both -the storage plugin itself and the MariaDB server with consistent -compiler flags. As the build also requires the TileDB Embedded library -and headers, using a Docker container may be easiest. The Dockerfile -also provides a concrete example of the build setup. -So here we will use the tiledb/tiledb-mariadb-r -container. +In order to use the MyTile storage plugin, one has to compile both the storage plugin itself and the MariaDB server with consistent compiler flags. As the build also requires the TileDB Embedded library and headers, using a Docker container may be easiest. The Dockerfile also provides a concrete example of the build setup. +So here we will use the tiledb/tiledb-mariadb-r container. Launch Container in Background -We launch the container ‘tiledb/tiledb-mariadb-r’ as a daemon, -allowing MariaDB to accept an empty password (using an older MySQL -variable setting), and name the running image ‘tiledb-mariadb-r’: -docker run --name tiledb-mariadb-r -it -d --rm \ - -e MYSQL_ALLOW_EMPTY_PASSWORD=1 tiledb/tiledb-mariadb-r +We launch the container ‘tiledb/tiledb-mariadb-r’ as a daemon, allowing MariaDB to accept an empty password (using an older MySQL variable setting), and name the running image ‘tiledb-mariadb-r’: +docker run --name tiledb-mariadb-r -it -d --rm \ + -e MYSQL_ALLOW_EMPTY_PASSWORD=1 tiledb/tiledb-mariadb-r Access Container Once to Write via TileDB -Using the name given to the running instance, we start an R session -to write data with TileDB: -docker exec -it -u root tiledb-mariadb-r R +Using the name given to the running instance, we start an R session to write data with TileDB: +docker exec -it -u root tiledb-mariadb-r R @@ -134,220 +116,200 @@ Examples Palmer Penguins -With the sessions started as in the previous section, we start an R -session. -> library(tiledb) -> library(palmerpenguins) -> praw <- penguins_raw -> fromDataFrame(praw, "/tmp/penguinsraw") +With the sessions started as in the previous section, we start an R session. +> library(tiledb) +> library(palmerpenguins) +> praw <- penguins_raw +> fromDataFrame(praw, "/tmp/penguinsraw") Access Container Again to Read via RMariaDB -In another shell, we can access the container once more and launch -another R process: -docker exec -it -u root tiledb-mariadb-r R -where we use RMariaDB to access the data via a tibble -object and magrittr pipe -> library(RMariaDB) -> library(dplyr, warn.conflicts=FALSE) -> con <- DBI::dbConnect(RMariaDB::MariaDB(), dbname="test") -> tbl(con, "/tmp/penguinsraw") %>% -+ dplyr::select(contains("Length")) -# Source: lazy query [?? x 2] -# Database: mysql [@localhost:NA/test] - `Culmen Length (mm)` `Flipper Length (mm)` - <dbl> <dbl> - 1 39.1 181 - 2 39.5 186 - 3 40.3 195 - 4 NA NA - 5 36.7 193 - 6 39.3 190 - 7 38.9 181 - 8 39.2 195 - 9 34.1 193 -10 42 190 -# ... with more rows -Note that this R session uses TileDB only via the MyTile plugin which -is activated implicitly via the ‘table location’ (here -/tmp/penguinsraw) of the test database enabling -plugins. -Also note that the query is still ‘lazy’: only column names and the -first ten observations have been retrieved, and the total size is still -unknown as indicated by lazy query [?? x 2]. Adding a -collect() verb materialized the full subset. -> tbl(con, "/tmp/penguinsraw") %>% -+ dplyr::select(contains("Length")) %>% -+ collect() -# A tibble: 344 x 2 - `Culmen Length (mm)` `Flipper Length (mm)` - <dbl> <dbl> - 1 39.1 181 - 2 39.5 186 - 3 40.3 195 - 4 NA NA - 5 36.7 193 - 6 39.3 190 - 7 38.9 181 - 8 39.2 195 - 9 34.1 193 -10 42 190 -# ... with 334 more rows -> -We now see that all 344 rows of this particular result set have been -accessed. +In another shell, we can access the container once more and launch another R process: +docker exec -it -u root tiledb-mariadb-r R +where we use RMariaDB to access the data via a tibble object and magrittr pipe +> library(RMariaDB) +> library(dplyr, warn.conflicts=FALSE) +> con <- DBI::dbConnect(RMariaDB::MariaDB(), dbname="test") +> tbl(con, "/tmp/penguinsraw") %>% ++ dplyr::select(contains("Length")) +# Source: lazy query [?? x 2] +# Database: mysql [@localhost:NA/test] + `Culmen Length (mm)` `Flipper Length (mm)` + <dbl> <dbl> + 1 39.1 181 + 2 39.5 186 + 3 40.3 195 + 4 NA NA + 5 36.7 193 + 6 39.3 190 + 7 38.9 181 + 8 39.2 195 + 9 34.1 193 +10 42 190 +# ... with more rows +Note that this R session uses TileDB only via the MyTile plugin which is activated implicitly via the ‘table location’ (here /tmp/penguinsraw) of the test database enabling plugins. +Also note that the query is still ‘lazy’: only column names and the first ten observations have been retrieved, and the total size is still unknown as indicated by lazy query [?? x 2]. Adding a collect() verb materialized the full subset. +> tbl(con, "/tmp/penguinsraw") %>% ++ dplyr::select(contains("Length")) %>% ++ collect() +# A tibble: 344 x 2 + `Culmen Length (mm)` `Flipper Length (mm)` + <dbl> <dbl> + 1 39.1 181 + 2 39.5 186 + 3 40.3 195 + 4 NA NA + 5 36.7 193 + 6 39.3 190 + 7 38.9 181 + 8 39.2 195 + 9 34.1 193 +10 42 190 +# ... with 334 more rows +> +We now see that all 344 rows of this particular result set have been accessed. Similarly, we can also run summaries on selected column: -> tbl(con, "/tmp/penguinsraw") %>% -+ group_by(Species) %>% -+ summarise(across(starts_with("Flipper"), -+ list(~mean(.x, na.rm=TRUE), ~sd(.x, na.rm=TRUE)))) -# Source: lazy query [?? x 3] -# Database: mysql [@localhost:NA/test] - Species `\`Flipper Length (mm)\`_~me~ `\`Flipper Length (mm)\`_~~ - <chr> <dbl> <dbl> -1 Adelie Penguin (Pyg~ 190. 6.54 -2 Chinstrap penguin (~ 196. 7.13 -3 Gentoo penguin (Pyg~ 217. 6.48 -> +> tbl(con, "/tmp/penguinsraw") %>% ++ group_by(Species) %>% ++ summarise(across(starts_with("Flipper"), ++ list(~mean(.x, na.rm=TRUE), ~sd(.x, na.rm=TRUE)))) +# Source: lazy query [?? x 3] +# Database: mysql [@localhost:NA/test] + Species `\`Flipper Length (mm)\`_~me~ `\`Flipper Length (mm)\`_~~ + <chr> <dbl> <dbl> +1 Adelie Penguin (Pyg~ 190. 6.54 +2 Chinstrap penguin (~ 196. 7.13 +3 Gentoo penguin (Pyg~ 217. 6.48 +> DBI -We can connect directly using the DBI package along with -the RMariaDB package and its MyTile bindings: +We can connect directly using the DBI package along with the RMariaDB package and its MyTile bindings: library(DBI) -con <- dbConnect(RMariaDB::MariaDB(), dbname="test") -res <- dbSendQuery(con, "select * from `/work/penguins` as `q91` limit 10") -df <- dbFetch(res, n = 10) -dbClearResult(res) +con <- dbConnect(RMariaDB::MariaDB(), dbname="test") +res <- dbSendQuery(con, "select * from `/work/penguins` as `q91` limit 10") +df <- dbFetch(res, n = 10) +dbClearResult(res) print(df) -dbDisconnect(con) +dbDisconnect(con) S3 -When using Docker, the container setup needs to be modified to -include the required AWS access environment variables: -docker run --name tiledb-mariadb-r \ - -it -d --rm \ - -v $PWD:/work -w /work \ - -e MYSQL_ALLOW_EMPTY_PASSWORD=1 \ - -e AWS_SECRET_ACCESS_KEY=${AWS_SECRET_ACCESS_KEY} \ - -e AWS_ACCESS_KEY_ID=${AWS_ACCESS_KEY_ID} \ - tiledb/tiledb-mariadb-r -This exports the current working directory (accessed as -$PWD in the shell) as /work inside the -container (via the -v switch), and instructs the container -to start in directory /work (via the -w -switch). -In the following example we also set a TileDB configuration option to -switch AWS regions. -> library(dplyr, warn.conflicts=FALSE) -> # connect as usual -> con <- DBI::dbConnect(RMariaDB::MariaDB(), dbname="test") -> # use connection to update config in order to switch s3 regions -> res1 <- DBI::dbSendQuery(con, "set mytile_tiledb_config=\"vfs.s3.region=us-west-1\";") -> DBI::dbClearResult(res1) -> # run simple query -> tbl(con, "s3://tiledb-public-us-west-1/test-array-4x4") %>% collect() -# A tibble: 16 x 3 - `__dim_0` `__dim_1` `__attr` - <int64> <int64> <dbl> - 1 0 0 0.397 - 2 0 1 0.432 - 3 0 2 0.617 - 4 0 3 0.403 - 5 1 0 0.837 - 6 1 1 0.670 - 7 1 2 0.235 - 8 1 3 0.841 - 9 2 0 0.222 -10 2 1 0.468 -11 2 2 0.970 -12 2 3 0.551 -13 3 0 0.628 -14 3 1 0.0149 -15 3 2 0.0540 -16 3 3 0.445 -> -> DBI::dbDisconnect(con) # close connection +When using Docker, the container setup needs to be modified to include the required AWS access environment variables: +docker run --name tiledb-mariadb-r \ + -it -d --rm \ + -v $PWD:/work -w /work \ + -e MYSQL_ALLOW_EMPTY_PASSWORD=1 \ + -e AWS_SECRET_ACCESS_KEY=${AWS_SECRET_ACCESS_KEY} \ + -e AWS_ACCESS_KEY_ID=${AWS_ACCESS_KEY_ID} \ + tiledb/tiledb-mariadb-r +This exports the current working directory (accessed as $PWD in the shell) as /work inside the container (via the -v switch), and instructs the container to start in directory /work (via the -w switch). +In the following example we also set a TileDB configuration option to switch AWS regions. +> library(dplyr, warn.conflicts=FALSE) +> # connect as usual +> con <- DBI::dbConnect(RMariaDB::MariaDB(), dbname="test") +> # use connection to update config in order to switch s3 regions +> res1 <- DBI::dbSendQuery(con, "set mytile_tiledb_config=\"vfs.s3.region=us-west-1\";") +> DBI::dbClearResult(res1) +> # run simple query +> tbl(con, "s3://tiledb-public-us-west-1/test-array-4x4") %>% collect() +# A tibble: 16 x 3 + `__dim_0` `__dim_1` `__attr` + <int64> <int64> <dbl> + 1 0 0 0.397 + 2 0 1 0.432 + 3 0 2 0.617 + 4 0 3 0.403 + 5 1 0 0.837 + 6 1 1 0.670 + 7 1 2 0.235 + 8 1 3 0.841 + 9 2 0 0.222 +10 2 1 0.468 +11 2 2 0.970 +12 2 3 0.551 +13 3 0 0.628 +14 3 1 0.0149 +15 3 2 0.0540 +16 3 3 0.445 +> +> DBI::dbDisconnect(con) # close connection NYC Taxis -We can write the New York taxi data into TileDB (in the current -directory) after reading it as a csv: -> nyc <- data.table::fread("trip_data_1.csv") -> tiledb::fromDataFrame(nyc, "trip_data_1") -Then we can access it via the path /work/trip_data_1 via -RMariaDB. -> library(dplyr, warn.conflicts=FALSE) -> con <- DBI::dbConnect(RMariaDB::MariaDB(), dbname="test") -> # list column names -> tbl(con, "/work/trip_data_1") %>% colnames() -> tbl(con, "/work/trip_data_1") %>% colnames() - [1] "__tiledb_rows" "dropoff_latitude" "medallion" - [4] "hack_license" "dropoff_longitude" "vendor_id" - [7] "rate_code" "store_and_fwd_flag" "pickup_datetime" -[10] "dropoff_datetime" "trip_time_in_secs" "pickup_latitude" -[13] "passenger_count" "trip_distance" "pickup_longitude" -> # extract one column (here passenger_count) completely and tabulate in R -> tbl(con, "/work/trip_data_1") %>% select(passenger_count) %>% collect() %>% table() -. - 0 1 2 3 4 5 6 9 - 166 10471701 1986196 597485 280992 920006 520066 1 - 208 255 - 1 1 -> # alternatively, run a lazy query -> tbl(con, "/work/trip_data_1") %>% group_by(passenger_count) %>% summarize(nobs = n()) -# Source: lazy query [?? x 2] -# Database: mysql [@localhost:NA/test] - passenger_count nobs - <int> <int64> - 1 0 166 - 2 1 10471701 - 3 2 1986196 - 4 3 597485 - 5 4 280992 - 6 5 920006 - 7 6 520066 - 8 9 1 - 9 208 1 -10 255 1 -> # here the request is actually sent as SQL and the computation is done in the SQL layer -> tbl(con, "/work/trip_data_1") %>% -+ group_by(passenger_count) %>% -+ summarize(nobs = n()) %>% -+ show_query() -<SQL> -SELECT `passenger_count`, COUNT(*) AS `nobs` -FROM `/work/trip_data_1` -GROUP BY `passenger_count` -> # naturally we can also send the query directly to the SQL backend -> sql <- "SELECT passenger_count, count(*) AS n FROM `/work/trip_data_1` GROUP BY passenger_count;" -> DBI::dbGetQuery(con, sql) - passenger_count n -1 0 166 -2 1 10471701 -3 2 1986196 -4 3 597485 -5 4 280992 -6 5 920006 -7 6 520066 -8 9 1 -9 208 1 -10 255 1 -> -> DBI::dbDisconnect(con) # close connection +We can write the New York taxi data into TileDB (in the current directory) after reading it as a csv: +> nyc <- data.table::fread("trip_data_1.csv") +> tiledb::fromDataFrame(nyc, "trip_data_1") +Then we can access it via the path /work/trip_data_1 via RMariaDB. +> library(dplyr, warn.conflicts=FALSE) +> con <- DBI::dbConnect(RMariaDB::MariaDB(), dbname="test") +> # list column names +> tbl(con, "/work/trip_data_1") %>% colnames() +> tbl(con, "/work/trip_data_1") %>% colnames() + [1] "__tiledb_rows" "dropoff_latitude" "medallion" + [4] "hack_license" "dropoff_longitude" "vendor_id" + [7] "rate_code" "store_and_fwd_flag" "pickup_datetime" +[10] "dropoff_datetime" "trip_time_in_secs" "pickup_latitude" +[13] "passenger_count" "trip_distance" "pickup_longitude" +> # extract one column (here passenger_count) completely and tabulate in R +> tbl(con, "/work/trip_data_1") %>% select(passenger_count) %>% collect() %>% table() +. + 0 1 2 3 4 5 6 9 + 166 10471701 1986196 597485 280992 920006 520066 1 + 208 255 + 1 1 +> # alternatively, run a lazy query +> tbl(con, "/work/trip_data_1") %>% group_by(passenger_count) %>% summarize(nobs = n()) +# Source: lazy query [?? x 2] +# Database: mysql [@localhost:NA/test] + passenger_count nobs + <int> <int64> + 1 0 166 + 2 1 10471701 + 3 2 1986196 + 4 3 597485 + 5 4 280992 + 6 5 920006 + 7 6 520066 + 8 9 1 + 9 208 1 +10 255 1 +> # here the request is actually sent as SQL and the computation is done in the SQL layer +> tbl(con, "/work/trip_data_1") %>% ++ group_by(passenger_count) %>% ++ summarize(nobs = n()) %>% ++ show_query() +<SQL> +SELECT `passenger_count`, COUNT(*) AS `nobs` +FROM `/work/trip_data_1` +GROUP BY `passenger_count` +> # naturally we can also send the query directly to the SQL backend +> sql <- "SELECT passenger_count, count(*) AS n FROM `/work/trip_data_1` GROUP BY passenger_count;" +> DBI::dbGetQuery(con, sql) + passenger_count n +1 0 166 +2 1 10471701 +3 2 1986196 +4 3 597485 +5 4 280992 +6 5 920006 +7 6 520066 +8 9 1 +9 208 1 +10 255 1 +> +> DBI::dbDisconnect(con) # close connection Summary -This short vignette demonstrates the use of TileDB-stored data from R -using RMariaDB via the MyTile storage extension to MariaBD. +This short vignette demonstrates the use of TileDB-stored data from R using RMariaDB via the MyTile storage extension to MariaBD. @@ -356,11 +318,11 @@ Summary diff --git a/docs/articles/tiledb-mariadb-examples_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/tiledb-mariadb-examples_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 0000000000..ca349fd6a5 --- /dev/null +++ b/docs/articles/tiledb-mariadb-examples_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. + +document.addEventListener('DOMContentLoaded', function() { + const codeList = document.getElementsByClassName("sourceCode"); + for (var i = 0; i < codeList.length; i++) { + var linkList = codeList[i].getElementsByTagName('a'); + for (var j = 0; j < linkList.length; j++) { + if (linkList[j].innerHTML === "") { + linkList[j].setAttribute('aria-hidden', 'true'); + } + } + } +}); diff --git a/docs/authors.html b/docs/authors.html index 145a22f84f..0eef9fee6c 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -1,5 +1,5 @@ -Authors and Citation • tiledb +Authors and Citation • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -49,11 +49,7 @@ Authors and Citation Authors - . Author, copyright holder. - - - - Dirk Eddelbuettel. Author. + . Author, copyright holder. @@ -66,15 +62,15 @@ Authors Citation Source: DESCRIPTION - TileDB, Inc., Eddelbuettel D (2024). + TileDB, Inc. (2025). tiledb: Modern Database Engine for Complex Data Based on Multi-Dimensional Arrays. -R package version 0.31.0, https://tiledb-inc.github.io/TileDB-R/, https://github.com/TileDB-Inc/TileDB-R. +R package version 0.31.0.1, https://tiledb-inc.github.io/TileDB-R/, https://github.com/TileDB-Inc/TileDB-R. @Manual{, title = {tiledb: Modern Database Engine for Complex Data Based on Multi-Dimensional Arrays}, - author = {{TileDB, Inc.} and Dirk Eddelbuettel}, - year = {2024}, - note = {R package version 0.31.0, https://tiledb-inc.github.io/TileDB-R/}, + author = {{TileDB, Inc.}}, + year = {2025}, + note = {R package version 0.31.0.1, https://tiledb-inc.github.io/TileDB-R/}, url = {https://github.com/TileDB-Inc/TileDB-R}, } @@ -84,11 +80,11 @@ Citation diff --git a/docs/deps/data-deps.txt b/docs/deps/data-deps.txt index 1b877ae225..ca4dfd9c5c 100644 --- a/docs/deps/data-deps.txt +++ b/docs/deps/data-deps.txt @@ -1,4 +1,4 @@ - + diff --git a/docs/index.html b/docs/index.html index cd8955108a..8ebb804b44 100644 --- a/docs/index.html +++ b/docs/index.html @@ -12,7 +12,7 @@ - + @@ -28,7 +28,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -71,7 +71,7 @@ - + The TileDB R package offers an R interface to the modern database by TileDB. @@ -84,19 +84,19 @@ InstallationCRAN and be installed directly via -> install.packages("tiledb") +> install.packages("tiledb") as usual. The most recent released version can be installed from Github using the package remotes. -> if (!requireNamespace("remotes",quietly=TRUE)) install.packages("remotes") -> remotes::install_github("TileDB-Inc/TileDB-R") -... -> library(tiledb) -TileDB R 0.31.0 with TileDB Embedded 2.27.0 on Ubuntu 24.04. -See https://tiledb.com for more information about TileDB. -> help(package=tiledb) +> if (!requireNamespace("remotes",quietly=TRUE)) install.packages("remotes") +> remotes::install_github("TileDB-Inc/TileDB-R") +... +> library(tiledb) +TileDB R 0.31.0 with TileDB Embedded 2.27.0 on Ubuntu 24.04. +See https://tiledb.com for more information about TileDB. +> help(package=tiledb) If the TileDB library is installed in a custom location, you need to pass the explicit path: -> remotes::install_github("TileDB-Inc/TileDB-R", - args="--configure-args='--with-tiledb=/path/to/tiledb'") +> remotes::install_github("TileDB-Inc/TileDB-R", + args="--configure-args='--with-tiledb=/path/to/tiledb'") Note that the TileDB R package is always developed and tested against the latest stable version of TileDB, but should also build against the newest development version. @@ -150,8 +150,7 @@ Citation Developers - Author, copyright holder -Dirk Eddelbuettel Author + Author, copyright holder Isaiah Norton Maintainer @@ -173,11 +172,11 @@ Dev status diff --git a/docs/news/index.html b/docs/news/index.html index 2d9f731da9..ca226604ed 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -1,5 +1,5 @@ -Changelog • tiledb +Changelog • tiledb Skip to contents @@ -7,7 +7,7 @@ tiledb - 0.31.0 + 0.31.0.1 @@ -53,7 +53,7 @@ tiledb 0.31.0Update unit tests to expect dense current domain Support parentheses in query conditions memory alloc: Accomodate zero buffer size estimate v2 -Apply styler::style_pkg() +Apply styler::style_pkg() Expose include/linking flags for re-using libtiledb in downstream packages Use TileDB Core 2.27.0 @@ -66,12 +66,10 @@ tiledb 0.30.2 tiledb 0.30.1 -This release of the R package builds against TileDB 2.26.1, and has also been tested against earlier releases as well as the development version (#757) - +This release of the R package builds against TileDB 2.26.1, and has also been tested against earlier releases as well as the development version (#757) tiledb 0.30.0 -This release of the R package builds against TileDB 2.26.0, and has also been tested against earlier releases as well as the development version (#745, #749, #750, #754, #755) - +This release of the R package builds against TileDB 2.26.0, and has also been tested against earlier releases as well as the development version (#745, #749, #750, #754, #755) Improvements Error messages displayed when a mismatched external pointer is detected now show both expected and encountered types (#740) NDRectangle objects can now instantiate from more domain data types (#741, #742) @@ -80,8 +78,7 @@ Improvements Documentation -The documentation website now uses favicon symbols for all pages rendered (#739) - +The documentation website now uses favicon symbols for all pages rendered (#739) Build and Test Systems The nighly valgrind matrix now includes release 2.26.0 (#744) @@ -89,17 +86,14 @@ Build and Test Systems Removals -Boolean arguments as.data.frame, as.matrix and as.array to the tiledb_array() accessor, deprecated in release 0.20.0 in July 2023 in favor of the more general return_as="..." form, have been removed. (#751) - +Boolean arguments as.data.frame, as.matrix and as.array to the tiledb_array() accessor, deprecated in release 0.20.0 in July 2023 in favor of the more general return_as="..." form, have been removed. (#751) Deprecation -As BioConductor package still relies on as.data.frame it was temporarily re-admitted as an argument. It is expected to be removed following the upcoming 3.20 release of BioConducto.r (#752) - +As BioConductor package still relies on as.data.frame it was temporarily re-admitted as an argument. It is expected to be removed following the upcoming 3.20 release of BioConducto.r (#752)
Using for example the current condaforge/mambaforge -container from the conda-forge project, -we can do
condaforge/mambaforge
mamba install -y r-tiledb # installs R, tiledb and deps without extra prompt -# ...several lines of installation detail omitted -R -# ... several lines of R startup output omitted -> library(tiledb)
which installs R, the tiledb package and all respective -dependencies.
Using for example the current condaforge/mambaforge container from the conda-forge project, we can do
mamba install -y r-tiledb # installs R, tiledb and deps without extra prompt +# ...several lines of installation detail omitted +R +# ... several lines of R startup output omitted +> library(tiledb)
which installs R, the tiledb package and all respective dependencies.
Builds of the TileDB package could also be provided via Docker -containers. At present, no official TileDB R containers are provided by -TileDB. However, the discussion of installation from source above -describes how to create such containers.
Builds of the TileDB package could also be provided via Docker containers. At present, no official TileDB R containers are provided by TileDB. However, the discussion of installation from source above describes how to create such containers.
This note described several installation options for the TileDB R -package.
This note described several installation options for the TileDB R package.
This document introduces TileDB via several simple examples. A -corresponding document with more complete API documentation is also available.
This document introduces TileDB via several simple examples. A corresponding document with more complete API documentation is also available.
Once the TileDB R package is installed, it can be loaded via -library(tiledb). Installation is supported for Windows, -Linux and macOS via the official CRAN -package, on Linux and macOS via the conda package as well as -from source.
library(tiledb)
Documentation for the TileDB R package is available via the -help() function from within R as well as via the package documentation -and an introductory -notebook. Documentation about TileDB itself is also available.
help()
Several “quickstart” examples that are discussed on the website are -available in the examples -directory. This vignette discusses similar examples.
In the following examples, the URIs describing arrays point to local -file system object. When TileDB has been built with S3 support, and with -proper AWS credentials in the usual environment variables, URIs such as -s3://some/data/bucket can be used where a local file would -be used. See the script ex_S3.R -for an example.
s3://some/data/bucket
Once the TileDB R package is installed, it can be loaded via library(tiledb). Installation is supported for Windows, Linux and macOS via the official CRAN package, on Linux and macOS via the conda package as well as from source.
Documentation for the TileDB R package is available via the help() function from within R as well as via the package documentation and an introductory notebook. Documentation about TileDB itself is also available.
Several “quickstart” examples that are discussed on the website are available in the examples directory. This vignette discusses similar examples.
In the following examples, the URIs describing arrays point to local file system object. When TileDB has been built with S3 support, and with proper AWS credentials in the usual environment variables, URIs such as s3://some/data/bucket can be used where a local file would be used. See the script ex_S3.R for an example.
These illustrations use the array created by the file ex_1.R -which one can run from within R, or on the command-line. To follow along -with discussion that follows, it helps to run the example once to create -the array after possibly adjusting the array location path from its -default value (using the current directory or, if set as an option, an -override).
These illustrations use the array created by the file ex_1.R which one can run from within R, or on the command-line. To follow along with discussion that follows, it helps to run the example once to create the array after possibly adjusting the array location path from its default value (using the current directory or, if set as an option, an override).
The file ex_1.R -in the examples directory is a simple yet complete example extending quickstart_dense.R -by adding a second and third attribute. In this as well as the following -examples we will use tiledb_array() to access the array; -the older variants tiledb_dense() and -tiledb_sparse() remain supported but are deprecated and may -be removed at some point in the future.
tiledb_array()
tiledb_dense()
tiledb_sparse()
The file ex_1.R in the examples directory is a simple yet complete example extending quickstart_dense.R by adding a second and third attribute. In this as well as the following examples we will use tiledb_array() to access the array; the older variants tiledb_dense() and tiledb_sparse() remain supported but are deprecated and may be removed at some point in the future.
Read 1-D
The first example extracts rows 1 to 2 and column 2 from an array. It -also limits the selection to just one attribute (via -attrs), asks for the return to be a data.frame -(instead of a simpler list) and for the (row and column, if present as -here) indices to not be printed (via extended=FALSE).
attrs
extended=FALSE
> A <- tiledb_array(uri = uri, attrs = "b", -+ return_as = "data.frame", extended=FALSE)) -> A[1:2,2] -[1] 101.5 104.0 ->
Note that the examples create three two-dimensional attributes. The -attributes can be selected via the attrs argument, or the -attrs() method on the array object. The square-bracket -indexing then selects with in the 2-d attribute object.
attrs()
If multiple objects are returned (as list or -data.frame), subsetting on the returned object works via -[[var]] or $var. A numeric index also works -(but needs to account for rows and cols).
list
[[var]]
$var
rows
cols
> A <- tiledb_array(uri = uri, attrs = c("a","b"), -+ return_as = "data.frame") -> A[1:2,2][["a"]] -[1] 2 7 -> A[1:2,2]$a -[1] 2 7 ->
The first example extracts rows 1 to 2 and column 2 from an array. It also limits the selection to just one attribute (via attrs), asks for the return to be a data.frame (instead of a simpler list) and for the (row and column, if present as here) indices to not be printed (via extended=FALSE).
> A <- tiledb_array(uri = uri, attrs = "b", ++ return_as = "data.frame", extended=FALSE)) +> A[1:2,2] +[1] 101.5 104.0 +>
Note that the examples create three two-dimensional attributes. The attributes can be selected via the attrs argument, or the attrs() method on the array object. The square-bracket indexing then selects with in the 2-d attribute object.
If multiple objects are returned (as list or data.frame), subsetting on the returned object works via [[var]] or $var. A numeric index also works (but needs to account for rows and cols).
> A <- tiledb_array(uri = uri, attrs = c("a","b"), ++ return_as = "data.frame") +> A[1:2,2][["a"]] +[1] 2 7 +> A[1:2,2]$a +[1] 2 7 +>
Read 2-D
This works analogously. Note that the results are generally returned -as vectors, or as a columns of a data.frame object in case -that option was set.
> A[6:9,3:4] -$a -[1] 28 29 33 34 38 39 43 44 - -$b -[1] 114.5 115.0 117.0 117.5 119.5 120.0 122.0 122.5 - -$c -[1] "fox" "A" "E" "F" "J" "K" "O" "P" ->
This works analogously. Note that the results are generally returned as vectors, or as a columns of a data.frame object in case that option was set.
> A[6:9,3:4] +$a +[1] 28 29 33 34 38 39 43 44 + +$b +[1] 114.5 115.0 117.0 117.5 119.5 120.0 122.0 122.5 + +$c +[1] "fox" "A" "E" "F" "J" "K" "O" "P" +>
We can restrict the selection to a subset of attributes when opening -the array.
> A <- tiledb_dense(uri = uri, attrs = c("b","c"), -+ return_as = "data.frame", extended=FALSE) -> A[6:9,2:4] - b c -1 114.0 brown -2 114.5 fox -3 115.0 A -4 116.5 D -5 117.0 E -6 117.5 F -7 119.0 I -8 119.5 J -9 120.0 K -10 121.5 N -11 122.0 O -12 122.5 P ->
This also illustrated the effect of setting -as.data.frame=TRUE when opening the array.
as.data.frame=TRUE
This scheme can be generalized to variable cells, or cells where -N>1, as we can expand each (atomistic) value over corresponding row -and column indices.
The column types correspond to the attribute typed in the array -schema, subject to the constraint mentioned above on R types. (The char -comes in as a factor variable as is still the R 3.6.* default which is -about to change. We can also override, users can too.)
> A <- tiledb_array("/tmp/tiledb/ex_1/", attrs=c("b","c"), -+ return_as = "data.frame", extended=TRUE) -> sapply(A[6:9, 3:4], "class") - rows cols b c - "integer" "integer" "numeric" "character" ->
Consistent with the data.frame semantics, now -requesting a named column reduces to a vector as this happens -at the R side:
We can restrict the selection to a subset of attributes when opening the array.
> A <- tiledb_dense(uri = uri, attrs = c("b","c"), ++ return_as = "data.frame", extended=FALSE) +> A[6:9,2:4] + b c +1 114.0 brown +2 114.5 fox +3 115.0 A +4 116.5 D +5 117.0 E +6 117.5 F +7 119.0 I +8 119.5 J +9 120.0 K +10 121.5 N +11 122.0 O +12 122.5 P +>
This also illustrated the effect of setting as.data.frame=TRUE when opening the array.
This scheme can be generalized to variable cells, or cells where N>1, as we can expand each (atomistic) value over corresponding row and column indices.
The column types correspond to the attribute typed in the array schema, subject to the constraint mentioned above on R types. (The char comes in as a factor variable as is still the R 3.6.* default which is about to change. We can also override, users can too.)
> A <- tiledb_array("/tmp/tiledb/ex_1/", attrs=c("b","c"), ++ return_as = "data.frame", extended=TRUE) +> sapply(A[6:9, 3:4], "class") + rows cols b c + "integer" "integer" "numeric" "character" +>
Consistent with the data.frame semantics, now requesting a named column reduces to a vector as this happens at the R side:
> A[6:9, 3:4]$b [1] 114.5 115.0 117.0 117.5 119.5 120.0 122.0 122.5 >
Simple Examples
Basic reading returns the coordinates and any attributes. The -following examples use the array created by the quickstart_sparse -example.
> A <- tiledb_array(uri = uri, is.sparse = TRUE) -> A[] -$rows -[1] 1 2 2 - -$cols -[1] 1 3 4 - -$a -[1] 1 3 2 - ->
We can also request a data.frame object, either when -opening or by changing this object characteristic on the fly:
> return.data.frame(A) <- TRUE -> A[] - a rows cols -1 1 1 1 -2 3 2 3 -3 2 2 4
For sparse arrays, the return type is by default ‘extended’ showing -rows and column but this can be overridden.
Basic reading returns the coordinates and any attributes. The following examples use the array created by the quickstart_sparse example.
> A <- tiledb_array(uri = uri, is.sparse = TRUE) +> A[] +$rows +[1] 1 2 2 + +$cols +[1] 1 3 4 + +$a +[1] 1 3 2 + +>
We can also request a data.frame object, either when opening or by changing this object characteristic on the fly:
> return.data.frame(A) <- TRUE +> A[] + a rows cols +1 1 1 1 +2 3 2 3 +3 2 2 4
For sparse arrays, the return type is by default ‘extended’ showing rows and column but this can be overridden.
Assignment works similarly:
> A[4,2] <- 42L -> A[] -> A[] - rows cols a -1 1 1 1 -2 2 3 3 -3 2 4 2 -4 4 2 42 ->
> A[4,2] <- 42L +> A[] +> A[] + rows cols a +1 1 1 1 +2 2 3 3 +3 2 4 2 +4 4 2 42 +>
Reads can select rows and or columns:
> A[2,] - rows cols a -1 2 3 3 -2 2 4 2 -> A[,2] - rows cols a -1 4 2 42 ->
> A[2,] + rows cols a +1 2 3 3 +2 2 4 2 +> A[,2] + rows cols a +1 4 2 42 +>
Attributes can be selected similarly.
Similar to the dense array case described earlier, the file ex_2.R -illustrates some basic operations on sparse arrays. It also shows date -and datetime types instead of just integer and double precision -floats.
> A <- tiledb_array(uri = uri, return_as = "data.frame") -> A[1577858403:1577858408] - rows cols a b d e -1 1577858403 1 3 103 2020-01-11 2020-01-02 18:24:33.844 -2 1577858404 1 4 104 2020-01-15 2020-01-05 02:28:36.214 -3 1577858405 1 5 105 2020-01-19 2020-01-05 00:44:04.805 -4 1577858406 1 6 106 2020-01-21 2020-01-06 12:58:51.770 -5 1577858407 1 7 107 2020-01-25 2020-01-09 04:29:56.309 -6 1577858408 1 8 108 2020-01-26 2020-01-07 13:55:10.240 ->
The row coordinate is currently a floating point representation of -the underlying time type. We can both select attributes (here we -excluded the “a” column) and select rows by time (as the time stamps get -converted to the required floating point value).
> attrs(A) <- c("b", "d", "e") -> A[as.POSIXct("2020-01-01"):as.POSIXct("2020-01-01 00:00:03")] - rows cols b d e -1 1577858401 1 101 2020-01-05 2020-01-01 03:03:07.548 -2 1577858402 1 102 2020-01-10 2020-01-02 21:02:19.747 -3 1577858403 1 103 2020-01-11 2020-01-02 18:24:33.844 ->
More extended examples are available showing indexing by date(time) -as well as character dimension.
Similar to the dense array case described earlier, the file ex_2.R illustrates some basic operations on sparse arrays. It also shows date and datetime types instead of just integer and double precision floats.
> A <- tiledb_array(uri = uri, return_as = "data.frame") +> A[1577858403:1577858408] + rows cols a b d e +1 1577858403 1 3 103 2020-01-11 2020-01-02 18:24:33.844 +2 1577858404 1 4 104 2020-01-15 2020-01-05 02:28:36.214 +3 1577858405 1 5 105 2020-01-19 2020-01-05 00:44:04.805 +4 1577858406 1 6 106 2020-01-21 2020-01-06 12:58:51.770 +5 1577858407 1 7 107 2020-01-25 2020-01-09 04:29:56.309 +6 1577858408 1 8 108 2020-01-26 2020-01-07 13:55:10.240 +>
The row coordinate is currently a floating point representation of the underlying time type. We can both select attributes (here we excluded the “a” column) and select rows by time (as the time stamps get converted to the required floating point value).
> attrs(A) <- c("b", "d", "e") +> A[as.POSIXct("2020-01-01"):as.POSIXct("2020-01-01 00:00:03")] + rows cols b d e +1 1577858401 1 101 2020-01-05 2020-01-01 03:03:07.548 +2 1577858402 1 102 2020-01-10 2020-01-02 21:02:19.747 +3 1577858403 1 103 2020-01-11 2020-01-02 18:24:33.844 +>
More extended examples are available showing indexing by date(time) as well as character dimension.
The TileDB R package is documented via R help functions -(e.g. help("tiledb_array") shows information for -the tiledb_array() function) as well as via a website regrouping all -documentation. Extended API -documentation is available, as is a examples/ -directory.
help("tiledb_array")
TileDB itself has extensive installation, -and overall -documentation as well as a support forum.
The TileDB R package is documented via R help functions (e.g. help("tiledb_array") shows information for the tiledb_array() function) as well as via a website regrouping all documentation. Extended API documentation is available, as is a examples/ directory.
TileDB itself has extensive installation, and overall documentation as well as a support forum.
TileDB provides the -Universal Data Engine that can be accessed in a variety of -ways. The C/C++ library offered by TileDB Embedded is one -approach, and the R -package, as well as the Python package and -other language bindings use it. Another interface is provided by the MariaDB Integration via the -MyTile storage plugin.
This provides TileDB integration with any frontend that interfaces -with MariaDB—such as the RMariaDB package -for R. So this vignette illustrates the use of TileDB via MariaDB using -R and the RMariaDB packages.
TileDB provides the Universal Data Engine that can be accessed in a variety of ways. The C/C++ library offered by TileDB Embedded is one approach, and the R package, as well as the Python package and other language bindings use it. Another interface is provided by the MariaDB Integration via the MyTile storage plugin.
This provides TileDB integration with any frontend that interfaces with MariaDB—such as the RMariaDB package for R. So this vignette illustrates the use of TileDB via MariaDB using R and the RMariaDB packages.
In order to use the MyTile storage plugin, one has to compile both -the storage plugin itself and the MariaDB server with consistent -compiler flags. As the build also requires the TileDB Embedded library -and headers, using a Docker container may be easiest. The Dockerfile -also provides a concrete example of the build setup.
So here we will use the tiledb/tiledb-mariadb-r -container.
tiledb/tiledb-mariadb-r
In order to use the MyTile storage plugin, one has to compile both the storage plugin itself and the MariaDB server with consistent compiler flags. As the build also requires the TileDB Embedded library and headers, using a Docker container may be easiest. The Dockerfile also provides a concrete example of the build setup.
So here we will use the tiledb/tiledb-mariadb-r container.
We launch the container ‘tiledb/tiledb-mariadb-r’ as a daemon, -allowing MariaDB to accept an empty password (using an older MySQL -variable setting), and name the running image ‘tiledb-mariadb-r’:
docker run --name tiledb-mariadb-r -it -d --rm \ - -e MYSQL_ALLOW_EMPTY_PASSWORD=1 tiledb/tiledb-mariadb-r
We launch the container ‘tiledb/tiledb-mariadb-r’ as a daemon, allowing MariaDB to accept an empty password (using an older MySQL variable setting), and name the running image ‘tiledb-mariadb-r’:
docker run --name tiledb-mariadb-r -it -d --rm \ + -e MYSQL_ALLOW_EMPTY_PASSWORD=1 tiledb/tiledb-mariadb-r
Using the name given to the running instance, we start an R session -to write data with TileDB:
docker exec -it -u root tiledb-mariadb-r R
Using the name given to the running instance, we start an R session to write data with TileDB:
With the sessions started as in the previous section, we start an R -session.
> library(tiledb) -> library(palmerpenguins) -> praw <- penguins_raw -> fromDataFrame(praw, "/tmp/penguinsraw")
With the sessions started as in the previous section, we start an R session.
> library(tiledb) +> library(palmerpenguins) +> praw <- penguins_raw +> fromDataFrame(praw, "/tmp/penguinsraw")
In another shell, we can access the container once more and launch -another R process:
where we use RMariaDB to access the data via a tibble -object and magrittr pipe
tibble
magrittr
> library(RMariaDB) -> library(dplyr, warn.conflicts=FALSE) -> con <- DBI::dbConnect(RMariaDB::MariaDB(), dbname="test") -> tbl(con, "/tmp/penguinsraw") %>% -+ dplyr::select(contains("Length")) -# Source: lazy query [?? x 2] -# Database: mysql [@localhost:NA/test] - `Culmen Length (mm)` `Flipper Length (mm)` - <dbl> <dbl> - 1 39.1 181 - 2 39.5 186 - 3 40.3 195 - 4 NA NA - 5 36.7 193 - 6 39.3 190 - 7 38.9 181 - 8 39.2 195 - 9 34.1 193 -10 42 190 -# ... with more rows
Note that this R session uses TileDB only via the MyTile plugin which -is activated implicitly via the ‘table location’ (here -/tmp/penguinsraw) of the test database enabling -plugins.
/tmp/penguinsraw
Also note that the query is still ‘lazy’: only column names and the -first ten observations have been retrieved, and the total size is still -unknown as indicated by lazy query [?? x 2]. Adding a -collect() verb materialized the full subset.
lazy query [?? x 2]
collect()
> tbl(con, "/tmp/penguinsraw") %>% -+ dplyr::select(contains("Length")) %>% -+ collect() -# A tibble: 344 x 2 - `Culmen Length (mm)` `Flipper Length (mm)` - <dbl> <dbl> - 1 39.1 181 - 2 39.5 186 - 3 40.3 195 - 4 NA NA - 5 36.7 193 - 6 39.3 190 - 7 38.9 181 - 8 39.2 195 - 9 34.1 193 -10 42 190 -# ... with 334 more rows ->
We now see that all 344 rows of this particular result set have been -accessed.
In another shell, we can access the container once more and launch another R process:
where we use RMariaDB to access the data via a tibble object and magrittr pipe
> library(RMariaDB) +> library(dplyr, warn.conflicts=FALSE) +> con <- DBI::dbConnect(RMariaDB::MariaDB(), dbname="test") +> tbl(con, "/tmp/penguinsraw") %>% ++ dplyr::select(contains("Length")) +# Source: lazy query [?? x 2] +# Database: mysql [@localhost:NA/test] + `Culmen Length (mm)` `Flipper Length (mm)` + <dbl> <dbl> + 1 39.1 181 + 2 39.5 186 + 3 40.3 195 + 4 NA NA + 5 36.7 193 + 6 39.3 190 + 7 38.9 181 + 8 39.2 195 + 9 34.1 193 +10 42 190 +# ... with more rows
Note that this R session uses TileDB only via the MyTile plugin which is activated implicitly via the ‘table location’ (here /tmp/penguinsraw) of the test database enabling plugins.
Also note that the query is still ‘lazy’: only column names and the first ten observations have been retrieved, and the total size is still unknown as indicated by lazy query [?? x 2]. Adding a collect() verb materialized the full subset.
> tbl(con, "/tmp/penguinsraw") %>% ++ dplyr::select(contains("Length")) %>% ++ collect() +# A tibble: 344 x 2 + `Culmen Length (mm)` `Flipper Length (mm)` + <dbl> <dbl> + 1 39.1 181 + 2 39.5 186 + 3 40.3 195 + 4 NA NA + 5 36.7 193 + 6 39.3 190 + 7 38.9 181 + 8 39.2 195 + 9 34.1 193 +10 42 190 +# ... with 334 more rows +>
We now see that all 344 rows of this particular result set have been accessed.
Similarly, we can also run summaries on selected column:
> tbl(con, "/tmp/penguinsraw") %>% -+ group_by(Species) %>% -+ summarise(across(starts_with("Flipper"), -+ list(~mean(.x, na.rm=TRUE), ~sd(.x, na.rm=TRUE)))) -# Source: lazy query [?? x 3] -# Database: mysql [@localhost:NA/test] - Species `\`Flipper Length (mm)\`_~me~ `\`Flipper Length (mm)\`_~~ - <chr> <dbl> <dbl> -1 Adelie Penguin (Pyg~ 190. 6.54 -2 Chinstrap penguin (~ 196. 7.13 -3 Gentoo penguin (Pyg~ 217. 6.48 ->
> tbl(con, "/tmp/penguinsraw") %>% ++ group_by(Species) %>% ++ summarise(across(starts_with("Flipper"), ++ list(~mean(.x, na.rm=TRUE), ~sd(.x, na.rm=TRUE)))) +# Source: lazy query [?? x 3] +# Database: mysql [@localhost:NA/test] + Species `\`Flipper Length (mm)\`_~me~ `\`Flipper Length (mm)\`_~~ + <chr> <dbl> <dbl> +1 Adelie Penguin (Pyg~ 190. 6.54 +2 Chinstrap penguin (~ 196. 7.13 +3 Gentoo penguin (Pyg~ 217. 6.48 +>
We can connect directly using the DBI package along with -the RMariaDB package and its MyTile bindings:
DBI
RMariaDB
We can connect directly using the DBI package along with the RMariaDB package and its MyTile bindings:
library(DBI) -con <- dbConnect(RMariaDB::MariaDB(), dbname="test") -res <- dbSendQuery(con, "select * from `/work/penguins` as `q91` limit 10") -df <- dbFetch(res, n = 10) -dbClearResult(res) +con <- dbConnect(RMariaDB::MariaDB(), dbname="test") +res <- dbSendQuery(con, "select * from `/work/penguins` as `q91` limit 10") +df <- dbFetch(res, n = 10) +dbClearResult(res) print(df) -dbDisconnect(con)
When using Docker, the container setup needs to be modified to -include the required AWS access environment variables:
docker run --name tiledb-mariadb-r \ - -it -d --rm \ - -v $PWD:/work -w /work \ - -e MYSQL_ALLOW_EMPTY_PASSWORD=1 \ - -e AWS_SECRET_ACCESS_KEY=${AWS_SECRET_ACCESS_KEY} \ - -e AWS_ACCESS_KEY_ID=${AWS_ACCESS_KEY_ID} \ - tiledb/tiledb-mariadb-r
This exports the current working directory (accessed as -$PWD in the shell) as /work inside the -container (via the -v switch), and instructs the container -to start in directory /work (via the -w -switch).
$PWD
/work
-v
-w
In the following example we also set a TileDB configuration option to -switch AWS regions.
> library(dplyr, warn.conflicts=FALSE) -> # connect as usual -> con <- DBI::dbConnect(RMariaDB::MariaDB(), dbname="test") -> # use connection to update config in order to switch s3 regions -> res1 <- DBI::dbSendQuery(con, "set mytile_tiledb_config=\"vfs.s3.region=us-west-1\";") -> DBI::dbClearResult(res1) -> # run simple query -> tbl(con, "s3://tiledb-public-us-west-1/test-array-4x4") %>% collect() -# A tibble: 16 x 3 - `__dim_0` `__dim_1` `__attr` - <int64> <int64> <dbl> - 1 0 0 0.397 - 2 0 1 0.432 - 3 0 2 0.617 - 4 0 3 0.403 - 5 1 0 0.837 - 6 1 1 0.670 - 7 1 2 0.235 - 8 1 3 0.841 - 9 2 0 0.222 -10 2 1 0.468 -11 2 2 0.970 -12 2 3 0.551 -13 3 0 0.628 -14 3 1 0.0149 -15 3 2 0.0540 -16 3 3 0.445 -> -> DBI::dbDisconnect(con) # close connection
When using Docker, the container setup needs to be modified to include the required AWS access environment variables:
docker run --name tiledb-mariadb-r \ + -it -d --rm \ + -v $PWD:/work -w /work \ + -e MYSQL_ALLOW_EMPTY_PASSWORD=1 \ + -e AWS_SECRET_ACCESS_KEY=${AWS_SECRET_ACCESS_KEY} \ + -e AWS_ACCESS_KEY_ID=${AWS_ACCESS_KEY_ID} \ + tiledb/tiledb-mariadb-r
This exports the current working directory (accessed as $PWD in the shell) as /work inside the container (via the -v switch), and instructs the container to start in directory /work (via the -w switch).
In the following example we also set a TileDB configuration option to switch AWS regions.
> library(dplyr, warn.conflicts=FALSE) +> # connect as usual +> con <- DBI::dbConnect(RMariaDB::MariaDB(), dbname="test") +> # use connection to update config in order to switch s3 regions +> res1 <- DBI::dbSendQuery(con, "set mytile_tiledb_config=\"vfs.s3.region=us-west-1\";") +> DBI::dbClearResult(res1) +> # run simple query +> tbl(con, "s3://tiledb-public-us-west-1/test-array-4x4") %>% collect() +# A tibble: 16 x 3 + `__dim_0` `__dim_1` `__attr` + <int64> <int64> <dbl> + 1 0 0 0.397 + 2 0 1 0.432 + 3 0 2 0.617 + 4 0 3 0.403 + 5 1 0 0.837 + 6 1 1 0.670 + 7 1 2 0.235 + 8 1 3 0.841 + 9 2 0 0.222 +10 2 1 0.468 +11 2 2 0.970 +12 2 3 0.551 +13 3 0 0.628 +14 3 1 0.0149 +15 3 2 0.0540 +16 3 3 0.445 +> +> DBI::dbDisconnect(con) # close connection
We can write the New York taxi data into TileDB (in the current -directory) after reading it as a csv:
> nyc <- data.table::fread("trip_data_1.csv") -> tiledb::fromDataFrame(nyc, "trip_data_1")
Then we can access it via the path /work/trip_data_1 via -RMariaDB.
/work/trip_data_1
> library(dplyr, warn.conflicts=FALSE) -> con <- DBI::dbConnect(RMariaDB::MariaDB(), dbname="test") -> # list column names -> tbl(con, "/work/trip_data_1") %>% colnames() -> tbl(con, "/work/trip_data_1") %>% colnames() - [1] "__tiledb_rows" "dropoff_latitude" "medallion" - [4] "hack_license" "dropoff_longitude" "vendor_id" - [7] "rate_code" "store_and_fwd_flag" "pickup_datetime" -[10] "dropoff_datetime" "trip_time_in_secs" "pickup_latitude" -[13] "passenger_count" "trip_distance" "pickup_longitude" -> # extract one column (here passenger_count) completely and tabulate in R -> tbl(con, "/work/trip_data_1") %>% select(passenger_count) %>% collect() %>% table() -. - 0 1 2 3 4 5 6 9 - 166 10471701 1986196 597485 280992 920006 520066 1 - 208 255 - 1 1 -> # alternatively, run a lazy query -> tbl(con, "/work/trip_data_1") %>% group_by(passenger_count) %>% summarize(nobs = n()) -# Source: lazy query [?? x 2] -# Database: mysql [@localhost:NA/test] - passenger_count nobs - <int> <int64> - 1 0 166 - 2 1 10471701 - 3 2 1986196 - 4 3 597485 - 5 4 280992 - 6 5 920006 - 7 6 520066 - 8 9 1 - 9 208 1 -10 255 1 -> # here the request is actually sent as SQL and the computation is done in the SQL layer -> tbl(con, "/work/trip_data_1") %>% -+ group_by(passenger_count) %>% -+ summarize(nobs = n()) %>% -+ show_query() -<SQL> -SELECT `passenger_count`, COUNT(*) AS `nobs` -FROM `/work/trip_data_1` -GROUP BY `passenger_count` -> # naturally we can also send the query directly to the SQL backend -> sql <- "SELECT passenger_count, count(*) AS n FROM `/work/trip_data_1` GROUP BY passenger_count;" -> DBI::dbGetQuery(con, sql) - passenger_count n -1 0 166 -2 1 10471701 -3 2 1986196 -4 3 597485 -5 4 280992 -6 5 920006 -7 6 520066 -8 9 1 -9 208 1 -10 255 1 -> -> DBI::dbDisconnect(con) # close connection
We can write the New York taxi data into TileDB (in the current directory) after reading it as a csv:
> nyc <- data.table::fread("trip_data_1.csv") +> tiledb::fromDataFrame(nyc, "trip_data_1")
Then we can access it via the path /work/trip_data_1 via RMariaDB.
> library(dplyr, warn.conflicts=FALSE) +> con <- DBI::dbConnect(RMariaDB::MariaDB(), dbname="test") +> # list column names +> tbl(con, "/work/trip_data_1") %>% colnames() +> tbl(con, "/work/trip_data_1") %>% colnames() + [1] "__tiledb_rows" "dropoff_latitude" "medallion" + [4] "hack_license" "dropoff_longitude" "vendor_id" + [7] "rate_code" "store_and_fwd_flag" "pickup_datetime" +[10] "dropoff_datetime" "trip_time_in_secs" "pickup_latitude" +[13] "passenger_count" "trip_distance" "pickup_longitude" +> # extract one column (here passenger_count) completely and tabulate in R +> tbl(con, "/work/trip_data_1") %>% select(passenger_count) %>% collect() %>% table() +. + 0 1 2 3 4 5 6 9 + 166 10471701 1986196 597485 280992 920006 520066 1 + 208 255 + 1 1 +> # alternatively, run a lazy query +> tbl(con, "/work/trip_data_1") %>% group_by(passenger_count) %>% summarize(nobs = n()) +# Source: lazy query [?? x 2] +# Database: mysql [@localhost:NA/test] + passenger_count nobs + <int> <int64> + 1 0 166 + 2 1 10471701 + 3 2 1986196 + 4 3 597485 + 5 4 280992 + 6 5 920006 + 7 6 520066 + 8 9 1 + 9 208 1 +10 255 1 +> # here the request is actually sent as SQL and the computation is done in the SQL layer +> tbl(con, "/work/trip_data_1") %>% ++ group_by(passenger_count) %>% ++ summarize(nobs = n()) %>% ++ show_query() +<SQL> +SELECT `passenger_count`, COUNT(*) AS `nobs` +FROM `/work/trip_data_1` +GROUP BY `passenger_count` +> # naturally we can also send the query directly to the SQL backend +> sql <- "SELECT passenger_count, count(*) AS n FROM `/work/trip_data_1` GROUP BY passenger_count;" +> DBI::dbGetQuery(con, sql) + passenger_count n +1 0 166 +2 1 10471701 +3 2 1986196 +4 3 597485 +5 4 280992 +6 5 920006 +7 6 520066 +8 9 1 +9 208 1 +10 255 1 +> +> DBI::dbDisconnect(con) # close connection
This short vignette demonstrates the use of TileDB-stored data from R -using RMariaDB via the MyTile storage extension to MariaBD.
This short vignette demonstrates the use of TileDB-stored data from R using RMariaDB via the MyTile storage extension to MariaBD.
. Author, copyright holder. -
Dirk Eddelbuettel. Author. +
. Author, copyright holder.
Source: DESCRIPTION
DESCRIPTION
TileDB, Inc., Eddelbuettel D (2024). +
TileDB, Inc. (2025). tiledb: Modern Database Engine for Complex Data Based on Multi-Dimensional Arrays. -R package version 0.31.0, https://tiledb-inc.github.io/TileDB-R/, https://github.com/TileDB-Inc/TileDB-R. +R package version 0.31.0.1, https://tiledb-inc.github.io/TileDB-R/, https://github.com/TileDB-Inc/TileDB-R.
@Manual{, title = {tiledb: Modern Database Engine for Complex Data Based on Multi-Dimensional Arrays}, - author = {{TileDB, Inc.} and Dirk Eddelbuettel}, - year = {2024}, - note = {R package version 0.31.0, https://tiledb-inc.github.io/TileDB-R/}, + author = {{TileDB, Inc.}}, + year = {2025}, + note = {R package version 0.31.0.1, https://tiledb-inc.github.io/TileDB-R/}, url = {https://github.com/TileDB-Inc/TileDB-R}, }
The TileDB R package offers an R interface to the modern database by TileDB.
> install.packages("tiledb")
as usual.
The most recent released version can be installed from Github using the package remotes.
> if (!requireNamespace("remotes",quietly=TRUE)) install.packages("remotes") -> remotes::install_github("TileDB-Inc/TileDB-R") -... -> library(tiledb) -TileDB R 0.31.0 with TileDB Embedded 2.27.0 on Ubuntu 24.04. -See https://tiledb.com for more information about TileDB. -> help(package=tiledb)
> if (!requireNamespace("remotes",quietly=TRUE)) install.packages("remotes") +> remotes::install_github("TileDB-Inc/TileDB-R") +... +> library(tiledb) +TileDB R 0.31.0 with TileDB Embedded 2.27.0 on Ubuntu 24.04. +See https://tiledb.com for more information about TileDB. +> help(package=tiledb)
If the TileDB library is installed in a custom location, you need to pass the explicit path:
> remotes::install_github("TileDB-Inc/TileDB-R", - args="--configure-args='--with-tiledb=/path/to/tiledb'")
> remotes::install_github("TileDB-Inc/TileDB-R", + args="--configure-args='--with-tiledb=/path/to/tiledb'")
Note that the TileDB R package is always developed and tested against the latest stable version of TileDB, but should also build against the newest development version.
styler::style_pkg()
libtiledb
Error messages displayed when a mismatched external pointer is detected now show both expected and encountered types (#740)
NDRectangle objects can now instantiate from more domain data types (#741, #742)
NDRectangle
The nighly valgrind matrix now includes release 2.26.0 (#744)
as.data.frame
as.matrix
as.array
return_as="..."
Three deprecated calls to dump() methods for TileDB Embedded objects now use the preferred streaming alternatives (#727)
dump()
Two already deprecated functions that are removed in TileDB 2.26.0 are no longer used (#732)
The nighly continuous integration matrix now included Core release 2.24.0 and 2.22.0 is dropped (#721)
Three internal and unexported helper functions now document more clearly how they can be called explicitly. (#709)
Reading and writing of text- and binary files supported by a VFS backend is now supported. (#710)
Group elements can now be deleted (#702)
Two error messages now show the human-readable type representation instead of the enum counter value (#705)
libtiledb_array_create_with_key
src/deprecated.cpp
libtiledb_query_add_range_with_type
libtiledb_query_add_range
The display of a filter_list is now labeled correctly as a filter list (@cgiachalis in #681 addressing #678)
filter_list
The Arrow integration has been simplified using nanoarrow returning a single nanoarrow object; an unexported helper function nanoarrow2list() is provided to matching the previous interface (#682, #685)
nanoarrow
nanoarrow2list()
tiledb_object_walk
The configure and Makevars.in received a minor update correcting small issues (#680)
Makevars.in
Functions tiledb_arrow_array_ptr(), tiledb_arrow_schmea_ptr(), tiledb_arrow_array_del() and tiledb_arrow_schema_del() are deprecated (in favor of using the corresponding nanoarrow functions) and will be removed in a future release (#685)
tiledb_arrow_array_ptr()
tiledb_arrow_schmea_ptr()
tiledb_arrow_array_del()
tiledb_arrow_schema_del()
The vendored nanoarrow sources have been update to release 0.4.0, and use of its facilities has been extended (#663)
Query conditions can be expressed against non-existing enumeration (i.e., factor) values when TileDB Core 2.21.0 or later is used (#674)
factor
Factor level additions now check for possible over in the index type (#645, #646)
Aggregate operations can now be performed on dense arrays via a query object with appropriate subarray settings (#650)
A TileDB Array can now be opened in ‘keep open’ mode for subsequent use without re-opening (#630)
Arrays with factor (or ordered) variables now grow their factor levels in appending writes (#639)
Builds from TileDB Core non-release tarballs are now supported via new configure option (#627)
Use of TileDB Embedded was upgraded to release 2.18.0 (#620), 2.18.1 (#621), and 2.18.2 (#624)
Support for Aggregates has been added (#623)
Some tests were refactored slightly for greater robustness (#618)
integer
Set conditions are supported in query condition expressions (#597)
Query conditions expression parsing via parse_query_conditions was extended simmilarly (#598)
parse_query_conditions
Array schema evolution has been extended to support enumerations (#590, #591)
Conversion to and from integer64 (and nanotime) now use package RcppInt64 (#592)
integer64
nanotime
Use of TileDB Embedded was upgraded to release 2.17.0 (#583,#587)
Built-time configuration of TileDB Embedded can now be accessed as a JSON string (#584)
The column buffer allocation is now robust to container overflow sanitizer checks (#574)
The array schema version is now accessible via a function (#575)
Query conditions can now be expressed for attributes of type UTF-8 (#529)
The startup message now displays the operating system and version (#532)
r.legacy_validity_mode
true
scripts/legacy_validity_convert.r
Attributes can now be created, written and read from in (explicit) UTF8 types (and CHAR and ASCII already behaved correctly with respect to utf8 data) (#510)
The TileDB Embedded version is now used to determine whether a dampener is needed for the deprecation warning (#511)
One of the test data sets included with #517 has been regenerated under an older TileDB version in order to test on more systems (#523)
Documentation for Metadata accessors no longer states URIs strings are accepted (#527)
The nightly valgrind job matrix was updated to releases 2.13 and 2.14 as well as the branch (#504)
The nightly valgrind job show the most recent commit sha1 after updating from release branches (#507)
A query condition test for utf8 attributes has been added (#507, #508)
Support for Subarrays to set ranges has been extended (#496)
Deprecated Core API functions for Array access and range setting are longer used (#496)
libtiledb_query_add_range{,_with_type}
libtiledb_query_set_coordinates()
libtiledb_coords()
Support for testing group URIs on being relative has been added (#478)
Logging support at the R and C++ level has been added (#479, #487, #489)
Several deprecated API entry points of TileDB Embedded are no longer used (#452, #453)
Support for DELETE queries has been added (requires TileDB Embedded 2.12.0 or later) (#455, #456)
Support for query conditions has been extended to dense arrays (#447)
Support for filter lists has extended to both the data.frame helper and the dimension object constructor (#448)
Use of TileDB Embedded was upgraded to release 2.10.2 (#443) following an earlier update to 2.10.1 (#434)
List columns are now supported in reading and writing of data frames by extending cell variable numbers beyond one (#438, #440)
valgrind
Use of TileDB Embedded was upgraded to release 2.10.0 (#432) following earlier updates to 2.9.1 (#415), 2.9.2 (#419), 2.9.3 (#422), 2.9.4 (#427) and 2.9.5 (#430)
The BOOL data type is now supported (#416)
attr
Filter compression tests are skipped on systems lacking AVX2 support (#418)
Support for groups has been added for TileDB 2.8 or later (#404)
The group member name retrieval can now also return the optional group member name (#399)
check()
schema_check()
Nightly valgrind checks were updated to use current versions (#397, #402)
A schedule nightly continuous action now checks current and release-candidate branches of TileDB with the R package under valgrind (#387)
Support for Groups was added (#388, #392, #395)
Use of TileDB Embedded was upgraded to release 2.6.4 (#384) following an earlier upgrade to 2.6.2 (#359)
Creations of arrays from data.frame objects now supports a mode= argument with values ‘ingest’, ‘schema_only’, and ‘append’ (#360)
mode=
tiledb_dense
tiledb_sparse
Use of TileDB Embedded was upgraded to release 2.6.1 (#354) following an earlier upgrade to 2.6.0 (#340)
A cell value getter for dimension was added (#341)
The stopifnot() assertions now use consistent error messages across all functions (#331)
stopifnot()
A helper function matching TileDB data types to R types is now exported (#336)
CI tests were expanded to also test refactored TileDB Embedded readers (#310), and now deactivated as this is now part of release 2.5.0 (#321)
The minimal version of TileDB Embedded that can be used with the R package is now release 2.0.0 (#313)
Accessors for context and query statistics were added (returning easily parseable JSON strings) (#293).
Initial support for schema evolution was added to add or drop attributes (#294).
When retrieving results via the [ operator, incomplete queries generate a warning (#283)
[
The interface to query element size of queries was extended (#282)
A query condition parser was added for use with standard (non-quoted) R expressions (#267)
Windows UCRT builds at CRAN are now supported (#268)
The build defaults to TileDB Embedded 2.3.* (unless another version is found during build, or explicitly selected) (#258, #264)
Query condition support is available for TileDB 2.3.0 or later, allowing (possibly multiple) numerical constraints on attributes (#261)
Continuous integration at GitHub is now faster as suggested packages are no longer installed (#250)
Arrays can now be written incrementally via the higher-level replacement function arr[] <- obj (#251)
arr[] <- obj
Matrix objects can now be returned under range selections (#247)
Matrix return get turned on and off with setter / getter functions (#248)
A new vignette show use of TileDB array via RMariaDB and the MyTile extension to MariaDB (#221)
Matrices can now be returned directly from suitable two-dimensional TileDB arrays (#225)
The older implementations tiledb_dense and tiledb_sparse are now marked as deprecated in favor of tiledb_array. No removal date is set or planned yet, but it is recommended to migrate to new code. (#180)
tiledb_array
Updated the underlying TileDB library to use TileDB 2.1.2 on macOS and Linux (when no system library is found) (#181)
The tiledb_stats_reset() function is now exported, and tiledb_stats_print() has been re-added as a wrapper to tiledb_stats_dump() (#174)
tiledb_stats_reset()
tiledb_stats_print()
tiledb_stats_dump()
Configuration options for compute and input/output concurrency set only the new TileDB 2.1 configuration options; documentation on how to checking values has been expanded. (#175)
R-based metadata accessors have been extended to also support tiledb_array arrays (#169)
configure now also checks the hardware platform before attempting a download of a prebuilt library (#170)
A new function limitTileDBCores() controls resource use, it is being used in tests (#139)
limitTileDBCores()
The function tiledb_get_context() is now exported (#140)
tiledb_get_context()
Range selection for tiledb_array objects can get/set matrices defining range (#132)
The show methods are now consistently exported and documented (#134)
show
All S4 classes are now consistently documented or aliased (#117)
If needed, the build system now builds TileDB and its required component (#118)
Added support for heterogenous domains
Added support for string dimensions
Developed by , Dirk Eddelbuettel, Isaiah Norton.
Developed by , Isaiah Norton.
tiledb_array_schema
A TileDB Schema object
a list of tiledb_attr objects
A list of tiledb_attr objects
tiledb_attr
a tiledb_attr object
A tiledb_attr object
tiledb object
A character string with cell's layout, e.g., "COL_MAJOR".
"COL_MAJOR"
tiledb_dim object
A tiledb_dim object
tiledb_dim
tiledb datatype string
A character string with tiledb's datatype.
a vector of the tile_dim domain type, of the dim domain dimension (extent)
A vector of the tile_dim domain type, of the dim domain dimension (extent)
a list of tiledb_dim objects
A list of tiledb_dim objects
A tiledb_domain object
tiledb_domain
.core_info() -#> version libtype -#> "2.27.0" "system" +#> version libtype +#> "2.27.0" "vendored" .core_hash() -#> [1] "17c9b4d820870f7c171fccf2be8fdfea" +#> [1] "712cb7e256376af4fbfecc51290a4241"
.pkg_config() -#> [1] "-I/usr/local/include" +#> [1] "-I/tmp/RtmpiRigbQ/temp_libpath556b1464bc75e/tiledb/include -I/tmp/RtmpiRigbQ/temp_libpath556b1464bc75e/tiledb/tiledb/include" .pkg_config("PKG_CXX_LIBS") -#> [1] "-L/usr/local/lib -ltiledb" +#> [1] "-ltiledb -L/tmp/RtmpiRigbQ/temp_libpath556b1464bc75e/tiledb/lib -L/tmp/RtmpiRigbQ/temp_libpath556b1464bc75e/tiledb/tiledb/lib"
TileDB Dimension
a list of tiledb_filter_list objects
A list of tiledb_filter_list objects
tiledb_filter_list
TileDB_Dimension
A TileDB_filter_list object
A tiledb_filter_list object
A schema for a TileDB Array
TRUE if tiledb_array_schema is sparse
TRUE if tiledb_array_schema object is sparse
TRUE