diff --git a/.Rbuildignore b/.Rbuildignore index 0c5dd91..acfb233 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -10,3 +10,4 @@ ^pkgdown$ ^CRAN-SUBMISSION$ ^cran-comments.md$ +^LICENSE\.md$ diff --git a/.github/workflows/R-CMD-check-depends-only.yaml b/.github/workflows/R-CMD-check-depends-only.yaml new file mode 100644 index 0000000..e4bffbe --- /dev/null +++ b/.github/workflows/R-CMD-check-depends-only.yaml @@ -0,0 +1,56 @@ +# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples +# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help +on: + push: + branches: [main, rc, dev] + pull_request: + branches: [main, rc, dev] + +name: R-CMD-check-depends-only + +jobs: + R-CMD-check: + runs-on: ${{ matrix.config.os }} + + name: ${{ matrix.config.os }} (${{ matrix.config.r }}) + + strategy: + fail-fast: false + matrix: + config: + - {os: macos-latest, r: 'release'} + - {os: windows-latest, r: 'release'} + - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} + - {os: ubuntu-latest, r: 'release'} + - {os: ubuntu-latest, r: 'oldrel-1'} + + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + R_KEEP_PKG_SOURCE: yes + _R_CHECK_DEPENDS_ONLY_: true + _R_CHECK_FORCE_SUGGESTS_: false + + steps: + - uses: actions/checkout@v3 + + - uses: r-lib/actions/setup-tinytex@v2 + + - uses: r-lib/actions/setup-pandoc@v2 + + - uses: r-lib/actions/setup-r@v2 + with: + r-version: ${{ matrix.config.r }} + http-user-agent: ${{ matrix.config.http-user-agent }} + use-public-rspm: true + extra-repositories: 'https://OHDSI.github.io/drat' + + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + dependencies: '"all"' + extra-packages: any::rcmdcheck + needs: check + + - uses: r-lib/actions/check-r-package@v2 + with: + args: c("--no-manual", "--no-build-vignettes") + upload-snapshots: true diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 98f7eaf..9314018 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -2,9 +2,9 @@ # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help on: push: - branches: [main, rc] + branches: [main, rc, dev] pull_request: - branches: [main, rc] + branches: [main, rc, dev] name: R-CMD-check diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION index e1247f4..d6e7e62 100644 --- a/CRAN-SUBMISSION +++ b/CRAN-SUBMISSION @@ -1,3 +1,3 @@ -Version: 0.1.13 -Date: 2024-05-21 12:28:13 UTC -SHA: 8e49442270867df955cff1d12646dd1ec095f920 +Version: 0.1.14 +Date: 2024-11-28 15:02:25 UTC +SHA: 6b421989f4c43662982bbe2723d109a843f5e982 diff --git a/DESCRIPTION b/DESCRIPTION index 3296503..3dc9380 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: PaRe Type: Package Title: A Way to Perform Code Review or QA on Other Packages -Version: 0.1.13 +Version: 0.1.14 Language: en-US Authors@R: person("Maarten", "van Kessel", email = "m.l.vankessel@erasmusmc.nl", @@ -14,7 +14,7 @@ BugReports: https://github.com/darwin-eu-dev/PaRe/issues License: Apache License (>= 2) Encoding: UTF-8 LazyData: true -RoxygenNote: 7.2.3 +RoxygenNote: 7.3.1 Imports: cli (>= 3.6.0), cyclocomp (>= 1.1.0), @@ -33,7 +33,8 @@ Imports: utils, R6 (>= 2.5.1), git2r (>= 0.31.0), - checkmate (>= 2.1.0) + checkmate (>= 2.1.0), + parallel Suggests: ggplot2, plotly, diff --git a/LICENSE.md b/LICENSE.md new file mode 100644 index 0000000..b62a9b5 --- /dev/null +++ b/LICENSE.md @@ -0,0 +1,194 @@ +Apache License +============== + +_Version 2.0, January 2004_ +_<>_ + +### Terms and Conditions for use, reproduction, and distribution + +#### 1. 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However, +in accepting such obligations, You may act only on Your own behalf and on Your +sole responsibility, not on behalf of any other Contributor, and only if You +agree to indemnify, defend, and hold each Contributor harmless for any liability +incurred by, or claims asserted against, such Contributor by reason of your +accepting any such warranty or additional liability. + +_END OF TERMS AND CONDITIONS_ + +### APPENDIX: How to apply the Apache License to your work + +To apply the Apache License to your work, attach the following boilerplate +notice, with the fields enclosed by brackets `[]` replaced with your own +identifying information. (Don't include the brackets!) The text should be +enclosed in the appropriate comment syntax for the file format. We also +recommend that a file or class name and description of purpose be included on +the same “printed page” as the copyright notice for easier identification within +third-party archives. + + Copyright [yyyy] [name of copyright owner] + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. diff --git a/NAMESPACE b/NAMESPACE index c8b7dda..02de003 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -25,6 +25,7 @@ import(checkmate) import(glue) import(lintr) import(pak) +import(parallel) import(rmarkdown) import(rsvg) import(stringr) diff --git a/NEWS.md b/NEWS.md index bcf284e..e343d7d 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,8 @@ +PaRe 0.1.14 +========== +1. Changed tests so R-CMD-Check passes on depends-only environment +2. Added `nThreads` parameter to `makeReport()`, `getDefaultPermittedPackages()` and `getGraphData()` for parallelisation. + PaRe 0.1.13 ========== 1. Fixed issue where pak 0.7.1 broke `getDefaultPermittedPackages()` and `getGraphData()` and updated internal code. diff --git a/R/PaRe-package.R b/R/PaRe-package.R index 02f2588..ce8ffdb 100644 --- a/R/PaRe-package.R +++ b/R/PaRe-package.R @@ -1,3 +1,19 @@ +# Copyright 2024 DARWIN EU® +# +# This file is part of PaRe +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + #' @keywords internal "_PACKAGE" @@ -13,6 +29,7 @@ #' @import rsvg #' @import R6 #' @import checkmate +#' @import parallel #' @importFrom igraph graph_from_data_frame V write_graph all_simple_paths induced_subgraph graph_from_data_frame #' @importFrom cli style_bold col_yellow col_red col_magenta col_green col_blue cli_alert_warning cli_alert_info cli_alert_danger cli_alert #' @importFrom dplyr filter tibble arrange select bind_rows select tally summarise rename relocate mutate group_by diff --git a/R/R6-Code.R b/R/R6-Code.R index 8500c9f..da4710c 100644 --- a/R/R6-Code.R +++ b/R/R6-Code.R @@ -1,3 +1,19 @@ +# Copyright 2024 DARWIN EU® +# +# This file is part of PaRe +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + #' @title #' R6 Code class #' diff --git a/R/R6-File.R b/R/R6-File.R index 42d38c0..89cc230 100644 --- a/R/R6-File.R +++ b/R/R6-File.R @@ -1,3 +1,19 @@ +# Copyright 2024 DARWIN EU® +# +# This file is part of PaRe +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + #' @title #' R6 File class #' diff --git a/R/R6-Function.R b/R/R6-Function.R index 66a2cdc..8031a6e 100644 --- a/R/R6-Function.R +++ b/R/R6-Function.R @@ -1,3 +1,19 @@ +# Copyright 2024 DARWIN EU® +# +# This file is part of PaRe +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + #' @title #' R6 Function class. #' diff --git a/R/R6-Repository.R b/R/R6-Repository.R index 05293f0..af87f9f 100644 --- a/R/R6-Repository.R +++ b/R/R6-Repository.R @@ -1,3 +1,19 @@ +# Copyright 2024 DARWIN EU® +# +# This file is part of PaRe +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + #' @title #' R6 Repository class. #' diff --git a/R/addPareArticle.R b/R/addPareArticle.R index 29c6297..7b677c0 100644 --- a/R/addPareArticle.R +++ b/R/addPareArticle.R @@ -1,3 +1,19 @@ +# Copyright 2024 DARWIN EU® +# +# This file is part of PaRe +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + #' addPareArticle #' #' Writes an Rmd-file to `./vignettes/articles/PaReReport.Rmd`. The relative diff --git a/R/callInvestigators.R b/R/callInvestigators.R index 9d61fee..3dea5af 100644 --- a/R/callInvestigators.R +++ b/R/callInvestigators.R @@ -1,3 +1,19 @@ +# Copyright 2024 DARWIN EU® +# +# This file is part of PaRe +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + #' getMultiLineFun #' #' @param line (\link[base]{numeric})\cr diff --git a/R/checkDependencies.R b/R/checkDependencies.R index f0afd28..5c462db 100644 --- a/R/checkDependencies.R +++ b/R/checkDependencies.R @@ -1,3 +1,19 @@ +# Copyright 2024 DARWIN EU® +# +# This file is part of PaRe +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + #' printMessage #' #' Prints messages dependening of the nrow of the number of rows of the @@ -89,8 +105,8 @@ getVersionDf <- function(dependencies, permittedPackages) { #' Repository object. #' @param dependencyType (`character()`)\cr #' Types of dependencies to be included -#' @param verbose (`logical()`: `TRUE`) -#' TRUE or FALSE. If TRUE, progress will be reported. +#' @param nThreads (`numeric(1)`: 1) +#' Number of threads to use to fetch permitted packages #' #' @return (`data.frame()`)\cr #' Data frame with all the packages that are now permitted. @@ -144,7 +160,7 @@ getVersionDf <- function(dependencies, permittedPackages) { checkDependencies <- function( repo, dependencyType = c("Imports", "Depends"), - verbose = TRUE) { + nThreads = 1) { description <- repo$getDescription() dependencies <- description$get_deps() %>% @@ -157,13 +173,7 @@ checkDependencies <- function( pattern = "[\\s>=<]+" ) - if (isTRUE(verbose)) { - permittedPackages <- getDefaultPermittedPackages() - } else { - suppressMessages( - permittedPackages <- getDefaultPermittedPackages() - ) - } + permittedPackages <- getDefaultPermittedPackages(nThreads) notPermitted <- dependencies %>% dplyr::filter(!.data$package %in% permittedPackages$package) diff --git a/R/countPackageLines.R b/R/countPackageLines.R index 77b279a..ee82234 100644 --- a/R/countPackageLines.R +++ b/R/countPackageLines.R @@ -1,3 +1,19 @@ +# Copyright 2024 DARWIN EU® +# +# This file is part of PaRe +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + #' countPackageLines #' #' Counts the package lines of a \link[PaRe]{Repository} object. diff --git a/R/getDefaultPermittedPackages.R b/R/getDefaultPermittedPackages.R index d3216bf..3355f07 100644 --- a/R/getDefaultPermittedPackages.R +++ b/R/getDefaultPermittedPackages.R @@ -1,7 +1,61 @@ +# Copyright 2024 DARWIN EU® +# +# This file is part of PaRe +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +getParDeps <- function(pkgs, nThreads) { + deps <- if (nThreads > 1) { + cl <- parallel::makeCluster(nThreads) + on.exit(parallel::stopCluster(cl = cl)) + parallel::clusterEvalQ(cl = cl, expr = {library("pak", character.only = TRUE)}) + + parallel::parLapply(cl = cl, X = pkgs, fun = function(pkg) { + tryCatch({ + res <- pak::pkg_deps(pkg = pkg) + return(res) + }, error = function(e) { + return(NULL) + }, warning = function(w) { + return(res) + }) + }) + } else { + lapply(X = pkgs, function(pkg) { + tryCatch({ + res <- pak::pkg_deps(pkg = pkg) + return(res) + }, error = function(e) { + return(NULL) + }, warning = function(w) { + return(res) + }) + }) + } + + if (any(sapply(deps, is.null))) { + warning(sprintf("Could not fetch dependencies for package: `%s`", pkgs[sapply(deps, is.null)])) + } + return(bind_rows(deps)) +} + #' getDefaultPermittedPackages #' #' Gets permitted packages. An internet connection is required. #' +#' @param nThreads (`numeric(1)`: 1) +#' Number of threads to use to fetch permitted packages +#' #' @export #' #' @return (\link[dplyr]{tibble}) @@ -21,54 +75,39 @@ #' getDefaultPermittedPackages() #' } #' } -getDefaultPermittedPackages <- function() { +getDefaultPermittedPackages <- function(nThreads = 1) { # Custom list - tryCatch( - { - customWhiteList <- lapply(seq_len(nrow(PaRe::whiteList)), function(i) { - pkgs <- utils::read.table( - file = unlist(PaRe::whiteList[i, ]["link"]), - sep = ",", - header = TRUE - ) %>% - dplyr::select(unlist(PaRe::whiteList[i, ]["package"]), unlist(PaRe::whiteList[i, ]["version"])) - }) %>% - dplyr::bind_rows() + customWhiteList <- dplyr::bind_rows(lapply(seq_len(nrow(PaRe::whiteList)), function(i) { + pkgs <- utils::read.table( + file = unlist(PaRe::whiteList[i, ]["link"]), + sep = ",", + header = TRUE + ) %>% + select(unlist(PaRe::whiteList[i, ]["package"]), unlist(PaRe::whiteList[i, ]["version"])) + })) - depList <- invisible(lapply(customWhiteList$package, pak::pkg_deps)) %>% - dplyr::bind_rows() %>% - dplyr::distinct() + depList <- getParDeps(pkgs = customWhiteList$package, nThreads = nThreads) - packages <- c( - "base", "boot", "class", "cluster", "codetools", "compiler", - "datasets", "foreign", "graphics", "grDevices", "grid", "KernSmooth", - "lattice", "MASS", "Matrix", "methods", "mgcv", "nlme", "nnet", - "parallel", "rpart", "spatial", "splines", "stats", "stats4", - "survival", "tcltk", "tools", "utils" - ) + packages <- c( + "base", "boot", "class", "cluster", "codetools", "compiler", + "datasets", "foreign", "graphics", "grDevices", "grid", "KernSmooth", + "lattice", "MASS", "Matrix", "methods", "mgcv", "nlme", "nnet", + "parallel", "rpart", "spatial", "splines", "stats", "stats4", + "survival", "tcltk", "tools", "utils" + ) - basePackages <- data.frame( - package = packages, - version = rep("0.0.0", length(packages)) - ) + basePackages <- data.frame( + package = packages, + version = rep("0.0.0", length(packages)) + ) - permittedPackages <- depList %>% - dplyr::select("package", version) %>% - dplyr::bind_rows(basePackages) + permittedPackages <- depList %>% + dplyr::select("package", version) %>% + dplyr::bind_rows(basePackages) - permittedPackages <- permittedPackages %>% - dplyr::group_by(.data$package) %>% - dplyr::summarise(version = min(as.numeric_version(version))) + permittedPackages <- permittedPackages %>% + group_by(.data$package) %>% + summarise(version = min(as.numeric_version(version))) - permittedPackages - }, - error = function(e) { - message(e) - NULL - }, - warning = function(w) { - message(w) - NULL - } - ) + return(permittedPackages) } diff --git a/R/getDefinedFunctions.R b/R/getDefinedFunctions.R index c6f775b..f50c924 100644 --- a/R/getDefinedFunctions.R +++ b/R/getDefinedFunctions.R @@ -1,3 +1,19 @@ +# Copyright 2024 DARWIN EU® +# +# This file is part of PaRe +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + #' getDefinedFunctions #' #' Gets all the defined functions from a \link[PaRe]{Repository} object. diff --git a/R/getFunctionDiagram.R b/R/getFunctionDiagram.R index 128f6a5..8955898 100644 --- a/R/getFunctionDiagram.R +++ b/R/getFunctionDiagram.R @@ -1,3 +1,19 @@ +# Copyright 2024 DARWIN EU® +# +# This file is part of PaRe +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + #' functionUseGraph #' #' @param repo (\link[PaRe]{Repository}) diff --git a/R/getFunctionUse.R b/R/getFunctionUse.R index 56af2d8..3c3813f 100644 --- a/R/getFunctionUse.R +++ b/R/getFunctionUse.R @@ -1,3 +1,19 @@ +# Copyright 2024 DARWIN EU® +# +# This file is part of PaRe +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + #' funsUsedInLine #' #' Support function for funsUsedInFile. diff --git a/R/getGraphData.R b/R/getGraphData.R index 801e0de..f3611f7 100644 --- a/R/getGraphData.R +++ b/R/getGraphData.R @@ -1,3 +1,19 @@ +# Copyright 2024 DARWIN EU® +# +# This file is part of PaRe +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + #' getGraphData #' #' Get the dependency interactions as a graph representation. @@ -14,6 +30,8 @@ #' \item "enhances" #' \item "linkingto" #' } +#' @param nThreads (`numeric(1)`: 1) +#' Number of threads to use to fetch permitted packages #' #' @return (\link[tidygraph]{as_tbl_graph}) #' @@ -52,7 +70,7 @@ #' getGraphData(repo = repo, packageTypes = c("Imports")) #' } #' } -getGraphData <- function(repo, packageTypes = c("Imports")) { +getGraphData <- function(repo, packageTypes = c("Imports"), nThreads = 1) { deps <- repo$getDescription()$get_deps() %>% dplyr::filter(tolower(.data$type) %in% tolower(packageTypes)) %>% dplyr::pull(.data$package) @@ -61,9 +79,7 @@ getGraphData <- function(repo, packageTypes = c("Imports")) { deps[deps %in% basename(remoteRef)] <- remoteRef[basename(remoteRef) %in% deps] # Get all dependencies using pak - data <- invisible(lapply(deps, pak::pkg_deps)) %>% - dplyr::bind_rows() %>% - dplyr::distinct() + data <- getParDeps(pkgs = deps, nThreads = nThreads) # Add current package data <- data %>% diff --git a/R/lint.R b/R/lint.R index 5f17a57..5a693f7 100644 --- a/R/lint.R +++ b/R/lint.R @@ -1,3 +1,19 @@ +# Copyright 2024 DARWIN EU® +# +# This file is part of PaRe +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + #' lintRepo #' #' Get all the lintr messages of the \link[PaRe]{Repository} object. diff --git a/R/makeReport.R b/R/makeReport.R index 632b67d..9ab2297 100644 --- a/R/makeReport.R +++ b/R/makeReport.R @@ -1,3 +1,19 @@ +# Copyright 2024 DARWIN EU® +# +# This file is part of PaRe +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + #' makeReport #' #' Uses rmarkdown's render function to render a html-report of the given package. @@ -10,6 +26,8 @@ #' Path to html-file. #' @param showCode (\link[base]{logical}: FALSE)\cr #' Logical to show code or not in the report. +#' @param nThreads (`numeric(1)`: 1) +#' Number of threads to use to fetch permitted packages #' #' @return (`NULL`) #' @@ -48,7 +66,7 @@ #' makeReport(repo = repo, outputFile = tempfile()) #' } #' } -makeReport <- function(repo, outputFile, showCode = FALSE) { +makeReport <- function(repo, outputFile, showCode = FALSE, nThreads = 1) { if (checkInstalled()) { outputFile <- normalizePath(outputFile, mustWork = FALSE) writeLines("", con = outputFile) @@ -60,7 +78,7 @@ makeReport <- function(repo, outputFile, showCode = FALSE) { rmarkdown::render( input = system.file(package = "PaRe", "rmd", "report.Rmd"), output_file = outputFile, - params = list(pkgName = pkgName, repo = repo, showCode = showCode) + params = list(pkgName = pkgName, repo = repo, showCode = showCode, nThreads = nThreads) ) } } diff --git a/R/pkgDiagram.R b/R/pkgDiagram.R index d4b730e..b201485 100644 --- a/R/pkgDiagram.R +++ b/R/pkgDiagram.R @@ -1,3 +1,19 @@ +# Copyright 2024 DARWIN EU® +# +# This file is part of PaRe +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + #' makeGraph #' #' Makes the graph diff --git a/R/utils-pipe.R b/R/utils-pipe.R index fd0b1d1..de1fbff 100644 --- a/R/utils-pipe.R +++ b/R/utils-pipe.R @@ -1,3 +1,19 @@ +# Copyright 2024 DARWIN EU® +# +# This file is part of PaRe +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + #' Pipe operator #' #' See \code{magrittr::\link[magrittr:pipe]{\%>\%}} for details. diff --git a/README.Rmd b/README.Rmd index 385d643..0231bac 100644 --- a/README.Rmd +++ b/README.Rmd @@ -15,8 +15,11 @@ knitr::opts_chunk$set( # PaRe + +[![Lifecycle:experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental) ![R-CMD-check](https://github.com/darwin-eu-dev/PaRe/actions/workflows/R-CMD-check.yaml/badge.svg) -![CRAN](https://www.r-pkg.org/badges/version/PaRe) +[![CRAN](https://www.r-pkg.org/badges/version/PaRe)](https://CRAN.R-project.org/package=PaRe) + PaRe (**Pa**ckage **Re**viewer) is the successor of the DependencyReviewer package. PaRe reviews other packages during code review and has the following features: diff --git a/README.md b/README.md index f196737..98d9eda 100644 --- a/README.md +++ b/README.md @@ -5,9 +5,11 @@ +[![Lifecycle:experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental) ![R-CMD-check](https://github.com/darwin-eu-dev/PaRe/actions/workflows/R-CMD-check.yaml/badge.svg) -[![codecov.io](https://codecov.io/gh/darwin-eu-dev/PaRe/coverage.svg?branch=main)](https://app.codecov.io/gh/darwin-eu-dev/PaRe?branch=main) -![CRAN](https://www.r-pkg.org/badges/version/PaRe) +[![CRAN](https://www.r-pkg.org/badges/version/PaRe)](https://CRAN.R-project.org/package=PaRe) + + PaRe (**Pa**ckage **Re**viewer) is the successor of the DependencyReviewer package. PaRe reviews other packages during code diff --git a/docs/404.html b/docs/404.html index 81b6d62..c01a57c 100644 --- a/docs/404.html +++ b/docs/404.html @@ -39,7 +39,7 @@ PaRe - 0.1.12 + 0.1.14 diff --git a/docs/LICENSE.html b/docs/LICENSE.html new file mode 100644 index 0000000..85acc01 --- /dev/null +++ b/docs/LICENSE.html @@ -0,0 +1,177 @@ + +Apache License • PaRe + + +
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Developed by Maarten van Kessel.

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Site built with pkgdown 2.0.7.

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+ + + + + + + + diff --git a/docs/articles/ComparingBranches.html b/docs/articles/ComparingBranches.html index a974753..0638b30 100644 --- a/docs/articles/ComparingBranches.html +++ b/docs/articles/ComparingBranches.html @@ -40,7 +40,7 @@ PaRe - 0.1.12 + 0.1.14 @@ -94,15 +94,16 @@ - -
+ + +

Comparing branches

Maarten van Kessel

-

2023-08-11

+

2024-11-28

Source: vignettes/articles/ComparingBranches.Rmd @@ -122,21 +123,21 @@

git package= "https://github.com/darwin-eu/CDMConnector.git", local_path = pathToRepo )

-
## cloning into 'C:\Users\MVANKE~1\AppData\Local\Temp\RtmpKgSdK4/CDMConnector'...
-## Receiving objects:   1% (34/3319),   63 kb
-## Receiving objects:  11% (366/3319),  120 kb
-## Receiving objects:  21% (697/3319),  176 kb
-## Receiving objects:  31% (1029/3319),  288 kb
-## Receiving objects:  41% (1361/3319),  400 kb
-## Receiving objects:  51% (1693/3319),  456 kb
-## Receiving objects:  61% (2025/3319), 7292 kb
-## Receiving objects:  71% (2357/3319), 12223 kb
-## Receiving objects:  81% (2689/3319), 12279 kb
-## Receiving objects:  91% (3021/3319), 12335 kb
-## Receiving objects: 100% (3319/3319), 19820 kb, done.
-
## Local:    main C:/Users/mvankessel/AppData/Local/Temp/RtmpKgSdK4/CDMConnector
+
## cloning into 'C:\Users\MVANKE~1\AppData\Local\Temp\RtmpE9RQLo/CDMConnector'...
+## Receiving objects:   1% (86/8529),  124 kb
+## Receiving objects:  11% (939/8529), 1436 kb
+## Receiving objects:  21% (1792/8529), 4350 kb
+## Receiving objects:  31% (2644/8529), 6896 kb
+## Receiving objects:  41% (3497/8529), 7064 kb
+## Receiving objects:  51% (4350/8529), 8713 kb
+## Receiving objects:  61% (5203/8529), 10370 kb
+## Receiving objects:  71% (6056/8529), 13115 kb
+## Receiving objects:  81% (6909/8529), 16268 kb
+## Receiving objects:  91% (7762/8529), 16381 kb
+## Receiving objects: 100% (8529/8529), 29661 kb, done.

+
## Local:    main C:/Users/mvankessel/AppData/Local/Temp/RtmpE9RQLo/CDMConnector
 ## Remote:   main @ origin (https://github.com/darwin-eu/CDMConnector.git)
-## Head:     [764154b] 2023-06-13: bugfix

+## Head:     [af064fc] 2024-11-13: V1.6 cran release (#514)

Objects @@ -163,7 +164,7 @@

Repository properties 
 repo$getPath()
-
## [1] "C:\\Users\\mvankessel\\AppData\\Local\\Temp\\RtmpKgSdK4\\CDMConnector"
+
## [1] "C:\\Users\\mvankessel\\AppData\\Local\\Temp\\RtmpE9RQLo\\CDMConnector"
 repo$getName()
## [1] "CDMConnector"
@@ -171,7 +172,7 @@

Repository propertiesrepo$getDescription()

## Package: CDMConnector
 ## Title: Connect to an OMOP Common Data Model
-## Version: 1.0.0
+## Version: 1.6.0
 ## Authors@R (parsed):
 ##     * Adam Black <black@ohdsi.org> [aut, cre] (<https://orcid.org/0000-0001-5576-8701>)
 ##     * Artem Gorbachev <artem.gorbachev@odysseusinc.com> [aut]
@@ -192,27 +193,28 @@ 
Repository properties##     checkmate,
 ##     cli,
 ##     DBI (>= 0.3.0),
-##     dbplyr,
+##     dbplyr (>= 2.5.0),
 ##     dplyr,
 ##     fs,
 ##     generics,
 ##     glue,
 ##     jsonlite,
 ##     lifecycle,
-##     magrittr,
 ##     methods,
-##     pillar,
+##     omopgenerics (>= 0.1.2),
 ##     purrr,
 ##     readr,
 ##     rlang,
+##     stringi,
 ##     stringr,
 ##     tidyr,
 ##     tidyselect,
 ##     waldo,
 ##     withr
 ## Suggests:
-##     arrow,
 ##     bigrquery,
+##     CirceR,
+##     clock,
 ##     covr,
 ##     DatabaseConnector,
 ##     duckdb,
@@ -220,23 +222,46 @@ 
Repository properties##     knitr,
 ##     lubridate,
 ##     odbc,
+##     palmerpenguins,
+##     pool,
 ##     rJava,
 ##     rmarkdown,
 ##     RPostgres,
 ##     RSQLite,
+##     snakecase,
 ##     SqlRender,
 ##     testthat (>= 3.0.0),
 ##     tibble,
-##     zeallot
+##     tictoc
 ## Enhances:
-##     CirceR
+##     arrow
 ## VignetteBuilder:
 ##     knitr
-## Additional_repositories: https://OHDSI.github.io/drat
 ## Config/testthat/edition: 3
+## Config/testthat/parallel: false
 ## Encoding: UTF-8
 ## Roxygen: list(markdown = TRUE)
-## RoxygenNote: 7.2.3
+## RoxygenNote: 7.3.2 +## Collate: +## 'CDMConnector-package.R' +## 'Eunomia.R' +## 'benchmarkCDMConnector.R' +## 'cdm.R' +## 'cdmSubset.R' +## 'cdm_from_environment.R' +## 'cohortTransformations.R' +## 'cohort_ddl.R' +## 'compute.R' +## 'copy_cdm_to.R' +## 'dateadd.R' +## 'dbSource.R' +## 'reexports-omopgenerics.R' +## 'generateCohortSet.R' +## 'generateConceptCohortSet.R' +## 'summariseQuantile.R' +## 'utils.R' +## 'validate.R' +## 'zzz-deprecated.R'
@@ -248,60 +273,80 @@

File 
## $R
 ## $R[[1]]
 ## <File> <Code> <R6>
-## Name: cdm.R
-## # Lines: 709
+## Name: benchmarkCDMConnector.R
+## # Lines: 138
 ## $R[[2]]
 ## <File> <Code> <R6>
-## Name: cdm_reference_methods.R
-## # Lines: 40
+## Name: cdm.R
+## # Lines: 971
 ## $R[[3]]
 ## <File> <Code> <R6>
-## Name: cdm_select_tbl.R
-## # Lines: 40
+## Name: cdm_from_environment.R
+## # Lines: 196
 ## $R[[4]]
 ## <File> <Code> <R6>
 ## Name: CDMConnector-package.R
-## # Lines: 13
+## # Lines: 14
 ## $R[[5]]
 ## <File> <Code> <R6>
 ## Name: cdmSubset.R
-## # Lines: 497
+## # Lines: 520
 ## $R[[6]]
 ## <File> <Code> <R6>
-## Name: compute.R
-## # Lines: 362
+## Name: cohort_ddl.R
+## # Lines: 126
 ## $R[[7]]
 ## <File> <Code> <R6>
-## Name: dateadd.R
-## # Lines: 235
+## Name: cohortTransformations.R
+## # Lines: 380
 ## $R[[8]]
 ## <File> <Code> <R6>
-## Name: Eunomia.R
-## # Lines: 307
+## Name: compute.R
+## # Lines: 360
 ## $R[[9]]
 ## <File> <Code> <R6>
-## Name: generateCohortSet.R
-## # Lines: 821
+## Name: copy_cdm_to.R
+## # Lines: 103
 ## $R[[10]]
 ## <File> <Code> <R6>
-## Name: intersect.R
-## # Lines: 105
+## Name: dateadd.R
+## # Lines: 260
 ## $R[[11]]
 ## <File> <Code> <R6>
-## Name: listTables.R
-## # Lines: 66
+## Name: dbSource.R
+## # Lines: 281
 ## $R[[12]]
 ## <File> <Code> <R6>
-## Name: summarise_quantile.R
-## # Lines: 129
+## Name: Eunomia.R
+## # Lines: 406
 ## $R[[13]]
 ## <File> <Code> <R6>
-## Name: utils.R
-## # Lines: 109
+## Name: generateCohortSet.R
+## # Lines: 983
 ## $R[[14]]
 ## <File> <Code> <R6>
+## Name: generateConceptCohortSet.R
+## # Lines: 452
+## $R[[15]]
+## <File> <Code> <R6>
+## Name: reexports-omopgenerics.R
+## # Lines: 95
+## $R[[16]]
+## <File> <Code> <R6>
+## Name: summariseQuantile.R
+## # Lines: 146
+## $R[[17]]
+## <File> <Code> <R6>
+## Name: utils.R
+## # Lines: 280
+## $R[[18]]
+## <File> <Code> <R6>
 ## Name: validate.R
-## # Lines: 229
+## # Lines: 246
+## $R[[19]]
+## <File> <Code> <R6>
+## Name: zzz-deprecated.R
+## # Lines: 121
 ## 
 ## $cpp
 ## list()
@@ -321,56 +366,40 @@ 
File
 file <- files$R[[1]]
 file

## <File> <Code> <R6>
-## Name: cdm.R
-## # Lines: 709
+## Name: benchmarkCDMConnector.R +## # Lines: 138

File properties 

 file$getName()
-
## [1] "cdm.R"
+
## [1] "benchmarkCDMConnector.R"
 file$getNLines()
-
## [1] 709
+
## [1] 138
 file$getType()
## [1] "R"
 head(file$getLines())
-
## [1] "#' Create a CDM reference object from a database connection"                              
-## [2] "#'"                                                                                       
-## [3] "#' @param con A DBI database connection to a database where an OMOP CDM v5.4 or"          
-## [4] "#'   v5.3 instance is located."                                                           
-## [5] "#' @param cdm_schema,cdmSchema The schema where the OMOP CDM tables are located. Defaults"
-## [6] "#'   to NULL."
+
## [1] "# Copyright 2024 DARWIN EU®"                                        
+## [2] "#"                                                                  
+## [3] "# This file is part of CDMConnector"                                
+## [4] "#"                                                                  
+## [5] "# Licensed under the Apache License, Version 2.0 (the \"License\");"
+## [6] "# you may not use this file except in compliance with the License."
 tail(file$getLines())
-
## [1] "  DBI::dbDisconnect(attr(cdm, \"dbcon\"), shutdown = TRUE)"
-## [2] "}"                                                         
-## [3] ""                                                          
-## [4] "#' @rdname cdmDisconnect"                                  
-## [5] "#' @export"                                                
-## [6] "cdm_disconnect <- cdmDisconnect"
+
## [1] "                    dplyr::count() %>%"
+## [2] "                    dplyr::pull())"    
+## [3] ""                                      
+## [4] ""                                      
+## [5] "  return(timings)"                     
+## [6] "}"
 file$getFunctionTable()
-
##                     name lineStart lineEnd nArgs cycloComp
-## 1           cdm_from_con        20     175     7        22
-## 2             cdmFromCon       179     193     7         1
-## 3     detect_cdm_version       195     245     3        13
-## 4                version       265     273     1         2
-## 5                cdmName       298     301     1         1
-## 6    print.cdm_reference       315     321     2         1
-## 7    verify_write_access       326     362     4         3
-## 8              tbl_group       397     406     1         1
-## 9                   dbms       428     430     1         1
-## 10    dbms.cdm_reference       433     435     1         1
-## 11    dbms.DBIConnection       438     461     1         4
-## 12                  stow       480     511     4         1
-## 13        cdm_from_files       523     572     4         3
-## 14          cdmFromFiles       577     583     4         1
-## 15 collect.cdm_reference       607     613     2         3
-## 16              snapshot       641     693     1         3
-## 17         cdmDisconnect       700     705     1         2
+
##                    name lineStart lineEnd nArgs cycloComp
+## 1 benchmarkCDMConnector        33     138     1         1
@@ -381,72 +410,8 @@

Functionfunctions

## [[1]]
 ## <Function> <Code> <R6>
-## Name: cdm_from_con
-## # Lines: 156
-## [[2]]
-## <Function> <Code> <R6>
-## Name: cdmFromCon
-## # Lines: 15
-## [[3]]
-## <Function> <Code> <R6>
-## Name: detect_cdm_version
-## # Lines: 51
-## [[4]]
-## <Function> <Code> <R6>
-## Name: version
-## # Lines: 9
-## [[5]]
-## <Function> <Code> <R6>
-## Name: cdmName
-## # Lines: 4
-## [[6]]
-## <Function> <Code> <R6>
-## Name: print.cdm_reference
-## # Lines: 7
-## [[7]]
-## <Function> <Code> <R6>
-## Name: verify_write_access
-## # Lines: 37
-## [[8]]
-## <Function> <Code> <R6>
-## Name: tbl_group
-## # Lines: 10
-## [[9]]
-## <Function> <Code> <R6>
-## Name: dbms
-## # Lines: 3
-## [[10]]
-## <Function> <Code> <R6>
-## Name: dbms.cdm_reference
-## # Lines: 3
-## [[11]]
-## <Function> <Code> <R6>
-## Name: dbms.DBIConnection
-## # Lines: 24
-## [[12]]
-## <Function> <Code> <R6>
-## Name: stow
-## # Lines: 32
-## [[13]]
-## <Function> <Code> <R6>
-## Name: cdm_from_files
-## # Lines: 50
-## [[14]]
-## <Function> <Code> <R6>
-## Name: cdmFromFiles
-## # Lines: 7
-## [[15]]
-## <Function> <Code> <R6>
-## Name: collect.cdm_reference
-## # Lines: 7
-## [[16]]
-## <Function> <Code> <R6>
-## Name: snapshot
-## # Lines: 53
-## [[17]]
-## <Function> <Code> <R6>
-## Name: cdmDisconnect
-## # Lines: 6
+## Name: benchmarkCDMConnector +## # Lines: 106 
 funs <- unlist(lapply(files$R, function(file) {
   file$getFunctions()
@@ -455,36 +420,36 @@ 
Functionfun <- funs[[1]]
 fun
## <Function> <Code> <R6>
-## Name: cdm_from_con
-## # Lines: 156
+## Name: benchmarkCDMConnector +## # Lines: 106

Function properties 

 fun$getName()
-
## [1] "cdm_from_con"
+
## [1] "benchmarkCDMConnector"
 fun$getNLines()
-
## [1] 156
+
## [1] 106
 fun$getFunction()
-
##           name lineStart lineEnd nArgs cycloComp
-## 1 cdm_from_con        20     175     7        22
+
##                    name lineStart lineEnd nArgs cycloComp
+## 1 benchmarkCDMConnector        33     138     1         1
 head(fun$getLines())
-
## [1] "cdm_from_con <- function(con,"                  
-## [2] "                         cdm_schema = NULL,"    
-## [3] "                         write_schema = NULL,"  
-## [4] "                         cohort_tables = NULL," 
-## [5] "                         cdm_version = \"5.3\","
-## [6] "                         cdm_name = NULL) {"
+
## [1] "benchmarkCDMConnector <- function(cdm) {"        
+## [2] ""                                                
+## [3] "  checkmate::assertClass(cdm, \"cdm_reference\")"
+## [4] ""                                                
+## [5] "  # will add timings to list"                    
+## [6] "  timings <- list()"
 tail(fun$getLines())
-
## [1] "  # The following attributes can be used to communicate temp table preferences to downstream analytic packages."                 
-## [2] "  # This a feature for analytic package developers and users should not need to know about it unless there is an issue to debug."
-## [3] "  attr(cdm, \"cohort_as_temp\") <- FALSE"                                                                                        
-## [4] "  attr(cdm, \"intermediate_as_temp\") <- TRUE"                                                                                   
-## [5] "  return(cdm)"                                                                                                                   
+
## [1] "                    dplyr::count() %>%"
+## [2] "                    dplyr::pull())"    
+## [3] ""                                      
+## [4] ""                                      
+## [5] "  return(timings)"                     
 ## [6] "}"
@@ -500,15 +465,15 @@

ComPaRing main to develop## # A tibble: 2 × 7 ## R cpp o h java sql branch ## <int> <int> <int> <int> <int> <int> <chr> -## 1 3662 0 0 0 0 0 main +## 1 6078 0 0 0 0 0 main ## 2 2628 0 0 0 0 0 V0.1.0 -
-
+

+
 PaRe::pkgDiagram(dev)

-

-
+

+
 mainFunUse <- PaRe::getFunctionUse(repo) %>%
   mutate(branch = "main")
 
@@ -567,18 +532,16 @@ 
ComPaRing main to develop

 
-
## 
-
-
-
[32m✔
[39m Updated metadata database: 5.07 MB in 14 files.
-## 
-
[36mℹ
[39m Updating metadata database
-
-
[32m✔
[39m Updating metadata database ... done

-
-devGraph <- PaRe::getGraphData(dev)
-
-library(igraph)

+
## ✔ Updated metadata database: 5.54 MB in 15 files.
+## ℹ Updating metadata database✔ Updating metadata database ... done

+
## Warning in getParDeps(pkgs = deps, nThreads = nThreads): Could not fetch
+## dependencies for package: `methods`

+
+devGraph <- PaRe::getGraphData(dev)

+
## Warning in getParDeps(pkgs = deps, nThreads = nThreads): Could not fetch
+## dependencies for package: `methods`

+
 
## 
 ## Attaching package: 'igraph'
 ## 
@@ -593,7 +556,7 @@ 
ComPaRing main to develop## The following object is masked from 'package:base':
 ## 
 ##     union

-
+
 data.frame(
   branch = c("main", "V0.1.0"),
   countVertices = c(length(igraph::V(mainGraph)), length(igraph::V(devGraph))),
@@ -602,41 +565,41 @@ 
ComPaRing main to develop  meanDistance = c(round(mean(igraph::distances(mainGraph)), 2), round(mean(igraph::distances(devGraph)), 2))
 )

 
##   branch countVertices countEdges meanDegree meanDistance
-## 1   main            44        173       7.86         2.14
-## 2 V0.1.0            44        172       7.82         2.15

-
+## 1   main            45        526      23.38         2.15
+## 2 V0.1.0            43        348      16.19         2.15

+
 messages <- PaRe::lintRepo(repo)
 messages2 <- PaRe::lintRepo(dev)
 head(messages)

-
##   filename line_number column_number  type
-## 1    cdm.R           5            81 style
-## 2    cdm.R           7            81 style
-## 3    cdm.R           9            81 style
-## 4    cdm.R          11            81 style
-## 5    cdm.R          14            81 style
-## 6    cdm.R          20             1 style
-##                                                                     message
-## 1                              Lines should not be more than 80 characters.
-## 2                              Lines should not be more than 80 characters.
-## 3                              Lines should not be more than 80 characters.
-## 4                              Lines should not be more than 80 characters.
-## 5                              Lines should not be more than 80 characters.
-## 6 Functions should have cyclomatic complexity of less than 15, this has 22.
+
##                  filename line_number column_number  type
+## 1 benchmarkCDMConnector.R         110            81 style
+## 2                   cdm.R          21            81 style
+## 3                   cdm.R          23            81 style
+## 4                   cdm.R          25            81 style
+## 5                   cdm.R          27            81 style
+## 6                   cdm.R          30            81 style
+##                                                                    message
+## 1 Lines should not be more than 80 characters. This line is 82 characters.
+## 2 Lines should not be more than 80 characters. This line is 89 characters.
+## 3 Lines should not be more than 80 characters. This line is 91 characters.
+## 4 Lines should not be more than 80 characters. This line is 92 characters.
+## 5 Lines should not be more than 80 characters. This line is 85 characters.
+## 6 Lines should not be more than 80 characters. This line is 85 characters.
 ##                                                                                           line
-## 1    #' @param cdm_schema,cdmSchema The schema where the OMOP CDM tables are located. Defaults
-## 2  #' @param write_schema,writeSchema An optional schema in the CDM database that the user has
-## 3 #' @param cohort_tables,cohortTables A character vector listing the cohort table names to be
-## 4        #' @param cdm_version,cdmVersion The version of the OMOP CDM: "5.3" (default), "5.4",
-## 5        #' @param cdm_name,cdmName The name of the CDM. If NULL (default) the cdm_source_name
-## 6                                                                cdm_from_con <- function(con,
+## 1             task <- "summary of observation period start and end dates by gender concept id"
+## 2    #' @param cdm_schema,cdmSchema The schema where the OMOP CDM tables are located. Defaults
+## 3  #' @param write_schema,writeSchema An optional schema in the CDM database that the user has
+## 4 #' @param cohort_tables,cohortTables A character vector listing the cohort table names to be
+## 5        #' @param cdm_version,cdmVersion The version of the OMOP CDM: "5.3" (default), "5.4",
+## 6        #' @param cdm_name,cdmName The name of the CDM. If NULL (default) the cdm_source_name
 ##               linter
 ## 1 line_length_linter
 ## 2 line_length_linter
 ## 3 line_length_linter
 ## 4 line_length_linter
 ## 5 line_length_linter
-## 6   cyclocomp_linter

-

 

   

 
diff --git a/docs/articles/ComparingBranches_files/figure-html/unnamed-chunk-17-1.png b/docs/articles/ComparingBranches_files/figure-html/unnamed-chunk-17-1.png
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diff --git a/docs/articles/ComparingBranches_files/figure-html/unnamed-chunk-20-1.png b/docs/articles/ComparingBranches_files/figure-html/unnamed-chunk-20-1.png
index d29365b..eaa04ba 100644
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diff --git a/docs/articles/ComparingBranches_files/grViz-binding-1.0.11/grViz.js b/docs/articles/ComparingBranches_files/grViz-binding-1.0.11/grViz.js
new file mode 100644
index 0000000..f801317
--- /dev/null
+++ b/docs/articles/ComparingBranches_files/grViz-binding-1.0.11/grViz.js
@@ -0,0 +1,91 @@
+HTMLWidgets.widget({
+
+  name: 'grViz',
+
+  type: 'output',
+
+  initialize: function(el, width, height) {
+
+    return {
+      // TODO: add instance fields as required
+    };
+  },
+
+  renderValue: function(el, x, instance) {
+    //  Use this to sort of make our diagram responsive
+    //  or at a minimum fit within the bounds set by htmlwidgets
+    //  for the parent container
+    function makeResponsive(el){
+       var svg = el.getElementsByTagName("svg")[0];
+       if (svg) {
+        if (svg.width) {svg.removeAttribute("width")}
+        if (svg.height) {svg.removeAttribute("height")}
+        svg.style.width = "100%";
+        svg.style.height = "100%";
+       }
+    }
+
+    if (x.diagram !== "") {
+
+      if (typeof x.config === "undefined"){
+        x.config = {};
+        x.config.engine = "dot";
+        x.config.options = {};
+      }
+
+      try {
+
+        el.innerHTML = Viz(x.diagram, format="svg", engine=x.config.engine, options=x.config.options);
+
+        makeResponsive(el);
+
+        if (HTMLWidgets.shinyMode) {
+          // Get widget id
+          var id = el.id;
+
+          $("#" + id + " .node").click(function(e) {
+            // Get node id
+            var nodeid = e.currentTarget.id;
+            // Get node text object and make an array
+            var node_texts = $("#" + id + " #" + nodeid + " text");
+            //var node_path = $("#" + nodeid + " path")[0];
+            var text_array = node_texts.map(function() {return $(this).text(); }).toArray();
+            // Build return object *obj* with node-id, node text values and node fill
+            var obj = {
+              id: nodeid,
+              //fill: node_path.attributes.fill.nodeValue,
+              //outerHMTL: node_path.outerHTML,
+              nodeValues: text_array
+            };
+            // Send *obj* to Shiny's inputs (input$[id]+_click  e.g.: input$vtree_click))
+            Shiny.setInputValue(id + "_click", obj, {priority: "event"});
+          });
+        }
+
+        // set up a container for tasks to perform after completion
+        //  one example would be add callbacks for event handling
+        //  styling
+        if (typeof x.tasks !== "undefined") {
+          if ((typeof x.tasks.length === "undefined") ||
+           (typeof x.tasks === "function")) {
+             // handle a function not enclosed in array
+             // should be able to remove once using jsonlite
+             x.tasks = [x.tasks];
+          }
+          x.tasks.map(function(t){
+            // for each tasks add it to the mermaid.tasks with el
+            t.call(el);
+          });
+        }
+      } catch(e){
+        var p = document.createElement("pre");
+        p.innerText = e;
+        el.appendChild(p);
+      }
+    }
+
+  },
+
+  resize: function(el, width, height, instance) {
+  }
+});
diff --git a/docs/articles/ComparingBranches_files/htmltools-fill-0.5.8.1/fill.css b/docs/articles/ComparingBranches_files/htmltools-fill-0.5.8.1/fill.css
new file mode 100644
index 0000000..841ea9d
--- /dev/null
+++ b/docs/articles/ComparingBranches_files/htmltools-fill-0.5.8.1/fill.css
@@ -0,0 +1,21 @@
+@layer htmltools {
+  .html-fill-container {
+    display: flex;
+    flex-direction: column;
+    /* Prevent the container from expanding vertically or horizontally beyond its
+    parent's constraints. */
+    min-height: 0;
+    min-width: 0;
+  }
+  .html-fill-container > .html-fill-item {
+    /* Fill items can grow and shrink freely within
+    available vertical space in fillable container */
+    flex: 1 1 auto;
+    min-height: 0;
+    min-width: 0;
+  }
+  .html-fill-container > :not(.html-fill-item) {
+    /* Prevent shrinking or growing of non-fill items */
+    flex: 0 0 auto;
+  }
+}
diff --git a/docs/articles/ComparingBranches_files/htmlwidgets-1.6.4/htmlwidgets.js b/docs/articles/ComparingBranches_files/htmlwidgets-1.6.4/htmlwidgets.js
new file mode 100644
index 0000000..1067d02
--- /dev/null
+++ b/docs/articles/ComparingBranches_files/htmlwidgets-1.6.4/htmlwidgets.js
@@ -0,0 +1,901 @@
+(function() {
+  // If window.HTMLWidgets is already defined, then use it; otherwise create a
+  // new object. This allows preceding code to set options that affect the
+  // initialization process (though none currently exist).
+  window.HTMLWidgets = window.HTMLWidgets || {};
+
+  // See if we're running in a viewer pane. If not, we're in a web browser.
+  var viewerMode = window.HTMLWidgets.viewerMode =
+      /\bviewer_pane=1\b/.test(window.location);
+
+  // See if we're running in Shiny mode. If not, it's a static document.
+  // Note that static widgets can appear in both Shiny and static modes, but
+  // obviously, Shiny widgets can only appear in Shiny apps/documents.
+  var shinyMode = window.HTMLWidgets.shinyMode =
+      typeof(window.Shiny) !== "undefined" && !!window.Shiny.outputBindings;
+
+  // We can't count on jQuery being available, so we implement our own
+  // version if necessary.
+  function querySelectorAll(scope, selector) {
+    if (typeof(jQuery) !== "undefined" && scope instanceof jQuery) {
+      return scope.find(selector);
+    }
+    if (scope.querySelectorAll) {
+      return scope.querySelectorAll(selector);
+    }
+  }
+
+  function asArray(value) {
+    if (value === null)
+      return [];
+    if ($.isArray(value))
+      return value;
+    return [value];
+  }
+
+  // Implement jQuery's extend
+  function extend(target /*, ... */) {
+    if (arguments.length == 1) {
+      return target;
+    }
+    for (var i = 1; i < arguments.length; i++) {
+      var source = arguments[i];
+      for (var prop in source) {
+        if (source.hasOwnProperty(prop)) {
+          target[prop] = source[prop];
+        }
+      }
+    }
+    return target;
+  }
+
+  // IE8 doesn't support Array.forEach.
+  function forEach(values, callback, thisArg) {
+    if (values.forEach) {
+      values.forEach(callback, thisArg);
+    } else {
+      for (var i = 0; i < values.length; i++) {
+        callback.call(thisArg, values[i], i, values);
+      }
+    }
+  }
+
+  // Replaces the specified method with the return value of funcSource.
+  //
+  // Note that funcSource should not BE the new method, it should be a function
+  // that RETURNS the new method. funcSource receives a single argument that is
+  // the overridden method, it can be called from the new method. The overridden
+  // method can be called like a regular function, it has the target permanently
+  // bound to it so "this" will work correctly.
+  function overrideMethod(target, methodName, funcSource) {
+    var superFunc = target[methodName] || function() {};
+    var superFuncBound = function() {
+      return superFunc.apply(target, arguments);
+    };
+    target[methodName] = funcSource(superFuncBound);
+  }
+
+  // Add a method to delegator that, when invoked, calls
+  // delegatee.methodName. If there is no such method on
+  // the delegatee, but there was one on delegator before
+  // delegateMethod was called, then the original version
+  // is invoked instead.
+  // For example:
+  //
+  // var a = {
+  //   method1: function() { console.log('a1'); }
+  //   method2: function() { console.log('a2'); }
+  // };
+  // var b = {
+  //   method1: function() { console.log('b1'); }
+  // };
+  // delegateMethod(a, b, "method1");
+  // delegateMethod(a, b, "method2");
+  // a.method1();
+  // a.method2();
+  //
+  // The output would be "b1", "a2".
+  function delegateMethod(delegator, delegatee, methodName) {
+    var inherited = delegator[methodName];
+    delegator[methodName] = function() {
+      var target = delegatee;
+      var method = delegatee[methodName];
+
+      // The method doesn't exist on the delegatee. Instead,
+      // call the method on the delegator, if it exists.
+      if (!method) {
+        target = delegator;
+        method = inherited;
+      }
+
+      if (method) {
+        return method.apply(target, arguments);
+      }
+    };
+  }
+
+  // Implement a vague facsimilie of jQuery's data method
+  function elementData(el, name, value) {
+    if (arguments.length == 2) {
+      return el["htmlwidget_data_" + name];
+    } else if (arguments.length == 3) {
+      el["htmlwidget_data_" + name] = value;
+      return el;
+    } else {
+      throw new Error("Wrong number of arguments for elementData: " +
+        arguments.length);
+    }
+  }
+
+  // http://stackoverflow.com/questions/3446170/escape-string-for-use-in-javascript-regex
+  function escapeRegExp(str) {
+    return str.replace(/[\-\[\]\/\{\}\(\)\*\+\?\.\\\^\$\|]/g, "\\$&");
+  }
+
+  function hasClass(el, className) {
+    var re = new RegExp("\\b" + escapeRegExp(className) + "\\b");
+    return re.test(el.className);
+  }
+
+  // elements - array (or array-like object) of HTML elements
+  // className - class name to test for
+  // include - if true, only return elements with given className;
+  //   if false, only return elements *without* given className
+  function filterByClass(elements, className, include) {
+    var results = [];
+    for (var i = 0; i < elements.length; i++) {
+      if (hasClass(elements[i], className) == include)
+        results.push(elements[i]);
+    }
+    return results;
+  }
+
+  function on(obj, eventName, func) {
+    if (obj.addEventListener) {
+      obj.addEventListener(eventName, func, false);
+    } else if (obj.attachEvent) {
+      obj.attachEvent(eventName, func);
+    }
+  }
+
+  function off(obj, eventName, func) {
+    if (obj.removeEventListener)
+      obj.removeEventListener(eventName, func, false);
+    else if (obj.detachEvent) {
+      obj.detachEvent(eventName, func);
+    }
+  }
+
+  // Translate array of values to top/right/bottom/left, as usual with
+  // the "padding" CSS property
+  // https://developer.mozilla.org/en-US/docs/Web/CSS/padding
+  function unpackPadding(value) {
+    if (typeof(value) === "number")
+      value = [value];
+    if (value.length === 1) {
+      return {top: value[0], right: value[0], bottom: value[0], left: value[0]};
+    }
+    if (value.length === 2) {
+      return {top: value[0], right: value[1], bottom: value[0], left: value[1]};
+    }
+    if (value.length === 3) {
+      return {top: value[0], right: value[1], bottom: value[2], left: value[1]};
+    }
+    if (value.length === 4) {
+      return {top: value[0], right: value[1], bottom: value[2], left: value[3]};
+    }
+  }
+
+  // Convert an unpacked padding object to a CSS value
+  function paddingToCss(paddingObj) {
+    return paddingObj.top + "px " + paddingObj.right + "px " + paddingObj.bottom + "px " + paddingObj.left + "px";
+  }
+
+  // Makes a number suitable for CSS
+  function px(x) {
+    if (typeof(x) === "number")
+      return x + "px";
+    else
+      return x;
+  }
+
+  // Retrieves runtime widget sizing information for an element.
+  // The return value is either null, or an object with fill, padding,
+  // defaultWidth, defaultHeight fields.
+  function sizingPolicy(el) {
+    var sizingEl = document.querySelector("script[data-for='" + el.id + "'][type='application/htmlwidget-sizing']");
+    if (!sizingEl)
+      return null;
+    var sp = JSON.parse(sizingEl.textContent || sizingEl.text || "{}");
+    if (viewerMode) {
+      return sp.viewer;
+    } else {
+      return sp.browser;
+    }
+  }
+
+  // @param tasks Array of strings (or falsy value, in which case no-op).
+  //   Each element must be a valid JavaScript expression that yields a
+  //   function. Or, can be an array of objects with "code" and "data"
+  //   properties; in this case, the "code" property should be a string
+  //   of JS that's an expr that yields a function, and "data" should be
+  //   an object that will be added as an additional argument when that
+  //   function is called.
+  // @param target The object that will be "this" for each function
+  //   execution.
+  // @param args Array of arguments to be passed to the functions. (The
+  //   same arguments will be passed to all functions.)
+  function evalAndRun(tasks, target, args) {
+    if (tasks) {
+      forEach(tasks, function(task) {
+        var theseArgs = args;
+        if (typeof(task) === "object") {
+          theseArgs = theseArgs.concat([task.data]);
+          task = task.code;
+        }
+        var taskFunc = tryEval(task);
+        if (typeof(taskFunc) !== "function") {
+          throw new Error("Task must be a function! Source:\n" + task);
+        }
+        taskFunc.apply(target, theseArgs);
+      });
+    }
+  }
+
+  // Attempt eval() both with and without enclosing in parentheses.
+  // Note that enclosing coerces a function declaration into
+  // an expression that eval() can parse
+  // (otherwise, a SyntaxError is thrown)
+  function tryEval(code) {
+    var result = null;
+    try {
+      result = eval("(" + code + ")");
+    } catch(error) {
+      if (!(error instanceof SyntaxError)) {
+        throw error;
+      }
+      try {
+        result = eval(code);
+      } catch(e) {
+        if (e instanceof SyntaxError) {
+          throw error;
+        } else {
+          throw e;
+        }
+      }
+    }
+    return result;
+  }
+
+  function initSizing(el) {
+    var sizing = sizingPolicy(el);
+    if (!sizing)
+      return;
+
+    var cel = document.getElementById("htmlwidget_container");
+    if (!cel)
+      return;
+
+    if (typeof(sizing.padding) !== "undefined") {
+      document.body.style.margin = "0";
+      document.body.style.padding = paddingToCss(unpackPadding(sizing.padding));
+    }
+
+    if (sizing.fill) {
+      document.body.style.overflow = "hidden";
+      document.body.style.width = "100%";
+      document.body.style.height = "100%";
+      document.documentElement.style.width = "100%";
+      document.documentElement.style.height = "100%";
+      cel.style.position = "absolute";
+      var pad = unpackPadding(sizing.padding);
+      cel.style.top = pad.top + "px";
+      cel.style.right = pad.right + "px";
+      cel.style.bottom = pad.bottom + "px";
+      cel.style.left = pad.left + "px";
+      el.style.width = "100%";
+      el.style.height = "100%";
+
+      return {
+        getWidth: function() { return cel.getBoundingClientRect().width; },
+        getHeight: function() { return cel.getBoundingClientRect().height; }
+      };
+
+    } else {
+      el.style.width = px(sizing.width);
+      el.style.height = px(sizing.height);
+
+      return {
+        getWidth: function() { return cel.getBoundingClientRect().width; },
+        getHeight: function() { return cel.getBoundingClientRect().height; }
+      };
+    }
+  }
+
+  // Default implementations for methods
+  var defaults = {
+    find: function(scope) {
+      return querySelectorAll(scope, "." + this.name);
+    },
+    renderError: function(el, err) {
+      var $el = $(el);
+
+      this.clearError(el);
+
+      // Add all these error classes, as Shiny does
+      var errClass = "shiny-output-error";
+      if (err.type !== null) {
+        // use the classes of the error condition as CSS class names
+        errClass = errClass + " " + $.map(asArray(err.type), function(type) {
+          return errClass + "-" + type;
+        }).join(" ");
+      }
+      errClass = errClass + " htmlwidgets-error";
+
+      // Is el inline or block? If inline or inline-block, just display:none it
+      // and add an inline error.
+      var display = $el.css("display");
+      $el.data("restore-display-mode", display);
+
+      if (display === "inline" || display === "inline-block") {
+        $el.hide();
+        if (err.message !== "") {
+          var errorSpan = $("").addClass(errClass);
+          errorSpan.text(err.message);
+          $el.after(errorSpan);
+        }
+      } else if (display === "block") {
+        // If block, add an error just after the el, set visibility:none on the
+        // el, and position the error to be on top of the el.
+        // Mark it with a unique ID and CSS class so we can remove it later.
+        $el.css("visibility", "hidden");
+        if (err.message !== "") {
+          var errorDiv = $("
").addClass(errClass).css("position", "absolute")
+            .css("top", el.offsetTop)
+            .css("left", el.offsetLeft)
+            // setting width can push out the page size, forcing otherwise
+            // unnecessary scrollbars to appear and making it impossible for
+            // the element to shrink; so use max-width instead
+            .css("maxWidth", el.offsetWidth)
+            .css("height", el.offsetHeight);
+          errorDiv.text(err.message);
+          $el.after(errorDiv);
+
+          // Really dumb way to keep the size/position of the error in sync with
+          // the parent element as the window is resized or whatever.
+          var intId = setInterval(function() {
+            if (!errorDiv[0].parentElement) {
+              clearInterval(intId);
+              return;
+            }
+            errorDiv
+              .css("top", el.offsetTop)
+              .css("left", el.offsetLeft)
+              .css("maxWidth", el.offsetWidth)
+              .css("height", el.offsetHeight);
+          }, 500);
+        }
+      }
+    },
+    clearError: function(el) {
+      var $el = $(el);
+      var display = $el.data("restore-display-mode");
+      $el.data("restore-display-mode", null);
+
+      if (display === "inline" || display === "inline-block") {
+        if (display)
+          $el.css("display", display);
+        $(el.nextSibling).filter(".htmlwidgets-error").remove();
+      } else if (display === "block"){
+        $el.css("visibility", "inherit");
+        $(el.nextSibling).filter(".htmlwidgets-error").remove();
+      }
+    },
+    sizing: {}
+  };
+
+  // Called by widget bindings to register a new type of widget. The definition
+  // object can contain the following properties:
+  // - name (required) - A string indicating the binding name, which will be
+  //   used by default as the CSS classname to look for.
+  // - initialize (optional) - A function(el) that will be called once per
+  //   widget element; if a value is returned, it will be passed as the third
+  //   value to renderValue.
+  // - renderValue (required) - A function(el, data, initValue) that will be
+  //   called with data. Static contexts will cause this to be called once per
+  //   element; Shiny apps will cause this to be called multiple times per
+  //   element, as the data changes.
+  window.HTMLWidgets.widget = function(definition) {
+    if (!definition.name) {
+      throw new Error("Widget must have a name");
+    }
+    if (!definition.type) {
+      throw new Error("Widget must have a type");
+    }
+    // Currently we only support output widgets
+    if (definition.type !== "output") {
+      throw new Error("Unrecognized widget type '" + definition.type + "'");
+    }
+    // TODO: Verify that .name is a valid CSS classname
+
+    // Support new-style instance-bound definitions. Old-style class-bound
+    // definitions have one widget "object" per widget per type/class of
+    // widget; the renderValue and resize methods on such widget objects
+    // take el and instance arguments, because the widget object can't
+    // store them. New-style instance-bound definitions have one widget
+    // object per widget instance; the definition that's passed in doesn't
+    // provide renderValue or resize methods at all, just the single method
+    //   factory(el, width, height)
+    // which returns an object that has renderValue(x) and resize(w, h).
+    // This enables a far more natural programming style for the widget
+    // author, who can store per-instance state using either OO-style
+    // instance fields or functional-style closure variables (I guess this
+    // is in contrast to what can only be called C-style pseudo-OO which is
+    // what we required before).
+    if (definition.factory) {
+      definition = createLegacyDefinitionAdapter(definition);
+    }
+
+    if (!definition.renderValue) {
+      throw new Error("Widget must have a renderValue function");
+    }
+
+    // For static rendering (non-Shiny), use a simple widget registration
+    // scheme. We also use this scheme for Shiny apps/documents that also
+    // contain static widgets.
+    window.HTMLWidgets.widgets = window.HTMLWidgets.widgets || [];
+    // Merge defaults into the definition; don't mutate the original definition.
+    var staticBinding = extend({}, defaults, definition);
+    overrideMethod(staticBinding, "find", function(superfunc) {
+      return function(scope) {
+        var results = superfunc(scope);
+        // Filter out Shiny outputs, we only want the static kind
+        return filterByClass(results, "html-widget-output", false);
+      };
+    });
+    window.HTMLWidgets.widgets.push(staticBinding);
+
+    if (shinyMode) {
+      // Shiny is running. Register the definition with an output binding.
+      // The definition itself will not be the output binding, instead
+      // we will make an output binding object that delegates to the
+      // definition. This is because we foolishly used the same method
+      // name (renderValue) for htmlwidgets definition and Shiny bindings
+      // but they actually have quite different semantics (the Shiny
+      // bindings receive data that includes lots of metadata that it
+      // strips off before calling htmlwidgets renderValue). We can't
+      // just ignore the difference because in some widgets it's helpful
+      // to call this.renderValue() from inside of resize(), and if
+      // we're not delegating, then that call will go to the Shiny
+      // version instead of the htmlwidgets version.
+
+      // Merge defaults with definition, without mutating either.
+      var bindingDef = extend({}, defaults, definition);
+
+      // This object will be our actual Shiny binding.
+      var shinyBinding = new Shiny.OutputBinding();
+
+      // With a few exceptions, we'll want to simply use the bindingDef's
+      // version of methods if they are available, otherwise fall back to
+      // Shiny's defaults. NOTE: If Shiny's output bindings gain additional
+      // methods in the future, and we want them to be overrideable by
+      // HTMLWidget binding definitions, then we'll need to add them to this
+      // list.
+      delegateMethod(shinyBinding, bindingDef, "getId");
+      delegateMethod(shinyBinding, bindingDef, "onValueChange");
+      delegateMethod(shinyBinding, bindingDef, "onValueError");
+      delegateMethod(shinyBinding, bindingDef, "renderError");
+      delegateMethod(shinyBinding, bindingDef, "clearError");
+      delegateMethod(shinyBinding, bindingDef, "showProgress");
+
+      // The find, renderValue, and resize are handled differently, because we
+      // want to actually decorate the behavior of the bindingDef methods.
+
+      shinyBinding.find = function(scope) {
+        var results = bindingDef.find(scope);
+
+        // Only return elements that are Shiny outputs, not static ones
+        var dynamicResults = results.filter(".html-widget-output");
+
+        // It's possible that whatever caused Shiny to think there might be
+        // new dynamic outputs, also caused there to be new static outputs.
+        // Since there might be lots of different htmlwidgets bindings, we
+        // schedule execution for later--no need to staticRender multiple
+        // times.
+        if (results.length !== dynamicResults.length)
+          scheduleStaticRender();
+
+        return dynamicResults;
+      };
+
+      // Wrap renderValue to handle initialization, which unfortunately isn't
+      // supported natively by Shiny at the time of this writing.
+
+      shinyBinding.renderValue = function(el, data) {
+        Shiny.renderDependencies(data.deps);
+        // Resolve strings marked as javascript literals to objects
+        if (!(data.evals instanceof Array)) data.evals = [data.evals];
+        for (var i = 0; data.evals && i < data.evals.length; i++) {
+          window.HTMLWidgets.evaluateStringMember(data.x, data.evals[i]);
+        }
+        if (!bindingDef.renderOnNullValue) {
+          if (data.x === null) {
+            el.style.visibility = "hidden";
+            return;
+          } else {
+            el.style.visibility = "inherit";
+          }
+        }
+        if (!elementData(el, "initialized")) {
+          initSizing(el);
+
+          elementData(el, "initialized", true);
+          if (bindingDef.initialize) {
+            var rect = el.getBoundingClientRect();
+            var result = bindingDef.initialize(el, rect.width, rect.height);
+            elementData(el, "init_result", result);
+          }
+        }
+        bindingDef.renderValue(el, data.x, elementData(el, "init_result"));
+        evalAndRun(data.jsHooks.render, elementData(el, "init_result"), [el, data.x]);
+      };
+
+      // Only override resize if bindingDef implements it
+      if (bindingDef.resize) {
+        shinyBinding.resize = function(el, width, height) {
+          // Shiny can call resize before initialize/renderValue have been
+          // called, which doesn't make sense for widgets.
+          if (elementData(el, "initialized")) {
+            bindingDef.resize(el, width, height, elementData(el, "init_result"));
+          }
+        };
+      }
+
+      Shiny.outputBindings.register(shinyBinding, bindingDef.name);
+    }
+  };
+
+  var scheduleStaticRenderTimerId = null;
+  function scheduleStaticRender() {
+    if (!scheduleStaticRenderTimerId) {
+      scheduleStaticRenderTimerId = setTimeout(function() {
+        scheduleStaticRenderTimerId = null;
+        window.HTMLWidgets.staticRender();
+      }, 1);
+    }
+  }
+
+  // Render static widgets after the document finishes loading
+  // Statically render all elements that are of this widget's class
+  window.HTMLWidgets.staticRender = function() {
+    var bindings = window.HTMLWidgets.widgets || [];
+    forEach(bindings, function(binding) {
+      var matches = binding.find(document.documentElement);
+      forEach(matches, function(el) {
+        var sizeObj = initSizing(el, binding);
+
+        var getSize = function(el) {
+          if (sizeObj) {
+            return {w: sizeObj.getWidth(), h: sizeObj.getHeight()}
+          } else {
+            var rect = el.getBoundingClientRect();
+            return {w: rect.width, h: rect.height}
+          }
+        };
+
+        if (hasClass(el, "html-widget-static-bound"))
+          return;
+        el.className = el.className + " html-widget-static-bound";
+
+        var initResult;
+        if (binding.initialize) {
+          var size = getSize(el);
+          initResult = binding.initialize(el, size.w, size.h);
+          elementData(el, "init_result", initResult);
+        }
+
+        if (binding.resize) {
+          var lastSize = getSize(el);
+          var resizeHandler = function(e) {
+            var size = getSize(el);
+            if (size.w === 0 && size.h === 0)
+              return;
+            if (size.w === lastSize.w && size.h === lastSize.h)
+              return;
+            lastSize = size;
+            binding.resize(el, size.w, size.h, initResult);
+          };
+
+          on(window, "resize", resizeHandler);
+
+          // This is needed for cases where we're running in a Shiny
+          // app, but the widget itself is not a Shiny output, but
+          // rather a simple static widget. One example of this is
+          // an rmarkdown document that has runtime:shiny and widget
+          // that isn't in a render function. Shiny only knows to
+          // call resize handlers for Shiny outputs, not for static
+          // widgets, so we do it ourselves.
+          if (window.jQuery) {
+            window.jQuery(document).on(
+              "shown.htmlwidgets shown.bs.tab.htmlwidgets shown.bs.collapse.htmlwidgets",
+              resizeHandler
+            );
+            window.jQuery(document).on(
+              "hidden.htmlwidgets hidden.bs.tab.htmlwidgets hidden.bs.collapse.htmlwidgets",
+              resizeHandler
+            );
+          }
+
+          // This is needed for the specific case of ioslides, which
+          // flips slides between display:none and display:block.
+          // Ideally we would not have to have ioslide-specific code
+          // here, but rather have ioslides raise a generic event,
+          // but the rmarkdown package just went to CRAN so the
+          // window to getting that fixed may be long.
+          if (window.addEventListener) {
+            // It's OK to limit this to window.addEventListener
+            // browsers because ioslides itself only supports
+            // such browsers.
+            on(document, "slideenter", resizeHandler);
+            on(document, "slideleave", resizeHandler);
+          }
+        }
+
+        var scriptData = document.querySelector("script[data-for='" + el.id + "'][type='application/json']");
+        if (scriptData) {
+          var data = JSON.parse(scriptData.textContent || scriptData.text);
+          // Resolve strings marked as javascript literals to objects
+          if (!(data.evals instanceof Array)) data.evals = [data.evals];
+          for (var k = 0; data.evals && k < data.evals.length; k++) {
+            window.HTMLWidgets.evaluateStringMember(data.x, data.evals[k]);
+          }
+          binding.renderValue(el, data.x, initResult);
+          evalAndRun(data.jsHooks.render, initResult, [el, data.x]);
+        }
+      });
+    });
+
+    invokePostRenderHandlers();
+  }
+
+
+  function has_jQuery3() {
+    if (!window.jQuery) {
+      return false;
+    }
+    var $version = window.jQuery.fn.jquery;
+    var $major_version = parseInt($version.split(".")[0]);
+    return $major_version >= 3;
+  }
+
+  /*
+  / Shiny 1.4 bumped jQuery from 1.x to 3.x which means jQuery's
+  / on-ready handler (i.e., $(fn)) is now asyncronous (i.e., it now
+  / really means $(setTimeout(fn)).
+  / https://jquery.com/upgrade-guide/3.0/#breaking-change-document-ready-handlers-are-now-asynchronous
+  /
+  / Since Shiny uses $() to schedule initShiny, shiny>=1.4 calls initShiny
+  / one tick later than it did before, which means staticRender() is
+  / called renderValue() earlier than (advanced) widget authors might be expecting.
+  / https://github.com/rstudio/shiny/issues/2630
+  /
+  / For a concrete example, leaflet has some methods (e.g., updateBounds)
+  / which reference Shiny methods registered in initShiny (e.g., setInputValue).
+  / Since leaflet is privy to this life-cycle, it knows to use setTimeout() to
+  / delay execution of those methods (until Shiny methods are ready)
+  / https://github.com/rstudio/leaflet/blob/18ec981/javascript/src/index.js#L266-L268
+  /
+  / Ideally widget authors wouldn't need to use this setTimeout() hack that
+  / leaflet uses to call Shiny methods on a staticRender(). In the long run,
+  / the logic initShiny should be broken up so that method registration happens
+  / right away, but binding happens later.
+  */
+  function maybeStaticRenderLater() {
+    if (shinyMode && has_jQuery3()) {
+      window.jQuery(window.HTMLWidgets.staticRender);
+    } else {
+      window.HTMLWidgets.staticRender();
+    }
+  }
+
+  if (document.addEventListener) {
+    document.addEventListener("DOMContentLoaded", function() {
+      document.removeEventListener("DOMContentLoaded", arguments.callee, false);
+      maybeStaticRenderLater();
+    }, false);
+  } else if (document.attachEvent) {
+    document.attachEvent("onreadystatechange", function() {
+      if (document.readyState === "complete") {
+        document.detachEvent("onreadystatechange", arguments.callee);
+        maybeStaticRenderLater();
+      }
+    });
+  }
+
+
+  window.HTMLWidgets.getAttachmentUrl = function(depname, key) {
+    // If no key, default to the first item
+    if (typeof(key) === "undefined")
+      key = 1;
+
+    var link = document.getElementById(depname + "-" + key + "-attachment");
+    if (!link) {
+      throw new Error("Attachment " + depname + "/" + key + " not found in document");
+    }
+    return link.getAttribute("href");
+  };
+
+  window.HTMLWidgets.dataframeToD3 = function(df) {
+    var names = [];
+    var length;
+    for (var name in df) {
+        if (df.hasOwnProperty(name))
+            names.push(name);
+        if (typeof(df[name]) !== "object" || typeof(df[name].length) === "undefined") {
+            throw new Error("All fields must be arrays");
+        } else if (typeof(length) !== "undefined" && length !== df[name].length) {
+            throw new Error("All fields must be arrays of the same length");
+        }
+        length = df[name].length;
+    }
+    var results = [];
+    var item;
+    for (var row = 0; row < length; row++) {
+        item = {};
+        for (var col = 0; col < names.length; col++) {
+            item[names[col]] = df[names[col]][row];
+        }
+        results.push(item);
+    }
+    return results;
+  };
+
+  window.HTMLWidgets.transposeArray2D = function(array) {
+      if (array.length === 0) return array;
+      var newArray = array[0].map(function(col, i) {
+          return array.map(function(row) {
+              return row[i]
+          })
+      });
+      return newArray;
+  };
+  // Split value at splitChar, but allow splitChar to be escaped
+  // using escapeChar. Any other characters escaped by escapeChar
+  // will be included as usual (including escapeChar itself).
+  function splitWithEscape(value, splitChar, escapeChar) {
+    var results = [];
+    var escapeMode = false;
+    var currentResult = "";
+    for (var pos = 0; pos < value.length; pos++) {
+      if (!escapeMode) {
+        if (value[pos] === splitChar) {
+          results.push(currentResult);
+          currentResult = "";
+        } else if (value[pos] === escapeChar) {
+          escapeMode = true;
+        } else {
+          currentResult += value[pos];
+        }
+      } else {
+        currentResult += value[pos];
+        escapeMode = false;
+      }
+    }
+    if (currentResult !== "") {
+      results.push(currentResult);
+    }
+    return results;
+  }
+  // Function authored by Yihui/JJ Allaire
+  window.HTMLWidgets.evaluateStringMember = function(o, member) {
+    var parts = splitWithEscape(member, '.', '\\');
+    for (var i = 0, l = parts.length; i < l; i++) {
+      var part = parts[i];
+      // part may be a character or 'numeric' member name
+      if (o !== null && typeof o === "object" && part in o) {
+        if (i == (l - 1)) { // if we are at the end of the line then evalulate
+          if (typeof o[part] === "string")
+            o[part] = tryEval(o[part]);
+        } else { // otherwise continue to next embedded object
+          o = o[part];
+        }
+      }
+    }
+  };
+
+  // Retrieve the HTMLWidget instance (i.e. the return value of an
+  // HTMLWidget binding's initialize() or factory() function)
+  // associated with an element, or null if none.
+  window.HTMLWidgets.getInstance = function(el) {
+    return elementData(el, "init_result");
+  };
+
+  // Finds the first element in the scope that matches the selector,
+  // and returns the HTMLWidget instance (i.e. the return value of
+  // an HTMLWidget binding's initialize() or factory() function)
+  // associated with that element, if any. If no element matches the
+  // selector, or the first matching element has no HTMLWidget
+  // instance associated with it, then null is returned.
+  //
+  // The scope argument is optional, and defaults to window.document.
+  window.HTMLWidgets.find = function(scope, selector) {
+    if (arguments.length == 1) {
+      selector = scope;
+      scope = document;
+    }
+
+    var el = scope.querySelector(selector);
+    if (el === null) {
+      return null;
+    } else {
+      return window.HTMLWidgets.getInstance(el);
+    }
+  };
+
+  // Finds all elements in the scope that match the selector, and
+  // returns the HTMLWidget instances (i.e. the return values of
+  // an HTMLWidget binding's initialize() or factory() function)
+  // associated with the elements, in an array. If elements that
+  // match the selector don't have an associated HTMLWidget
+  // instance, the returned array will contain nulls.
+  //
+  // The scope argument is optional, and defaults to window.document.
+  window.HTMLWidgets.findAll = function(scope, selector) {
+    if (arguments.length == 1) {
+      selector = scope;
+      scope = document;
+    }
+
+    var nodes = scope.querySelectorAll(selector);
+    var results = [];
+    for (var i = 0; i < nodes.length; i++) {
+      results.push(window.HTMLWidgets.getInstance(nodes[i]));
+    }
+    return results;
+  };
+
+  var postRenderHandlers = [];
+  function invokePostRenderHandlers() {
+    while (postRenderHandlers.length) {
+      var handler = postRenderHandlers.shift();
+      if (handler) {
+        handler();
+      }
+    }
+  }
+
+  // Register the given callback function to be invoked after the
+  // next time static widgets are rendered.
+  window.HTMLWidgets.addPostRenderHandler = function(callback) {
+    postRenderHandlers.push(callback);
+  };
+
+  // Takes a new-style instance-bound definition, and returns an
+  // old-style class-bound definition. This saves us from having
+  // to rewrite all the logic in this file to accomodate both
+  // types of definitions.
+  function createLegacyDefinitionAdapter(defn) {
+    var result = {
+      name: defn.name,
+      type: defn.type,
+      initialize: function(el, width, height) {
+        return defn.factory(el, width, height);
+      },
+      renderValue: function(el, x, instance) {
+        return instance.renderValue(x);
+      },
+      resize: function(el, width, height, instance) {
+        return instance.resize(width, height);
+      }
+    };
+
+    if (defn.find)
+      result.find = defn.find;
+    if (defn.renderError)
+      result.renderError = defn.renderError;
+    if (defn.clearError)
+      result.clearError = defn.clearError;
+
+    return result;
+  }
+})();
diff --git a/docs/articles/Contributing.html b/docs/articles/Contributing.html
index a68579f..05e9752 100644
--- a/docs/articles/Contributing.html
+++ b/docs/articles/Contributing.html
@@ -40,7 +40,7 @@
       
       
         PaRe
-        0.1.12
+        0.1.14
       
     

 
@@ -101,7 +101,7 @@ 
Contributing to PaRe

                         
Maarten van
 Kessel

             
-            
2023-08-11

+            
2024-11-28

       
       Source: vignettes/articles/Contributing.Rmd
       
diff --git a/docs/articles/Documentation.html b/docs/articles/Documentation.html
index 3d585d7..11a2062 100644
--- a/docs/articles/Documentation.html
+++ b/docs/articles/Documentation.html
@@ -40,7 +40,7 @@
       
       
         PaRe
-        0.1.12
+        0.1.14
       
     

 
@@ -101,7 +101,7 @@ 
Documentation

                         
Maarten van
 Kessel

             
-            
2023-08-11

+            
2024-11-28

       
       Source: vignettes/Documentation.Rmd
       
@@ -250,18 +250,18 @@ 
Setting up a Repository object)
 
 repo <- PaRe::Repository$new(path = pathToRepo)

-
#> cloning into 'C:\Users\MVANKE~1\AppData\Local\Temp\RtmpQRpwDq/glue'...
-#> Receiving objects:   1% (50/4925),   63 kb
-#> Receiving objects:  11% (542/4925),  352 kb
-#> Receiving objects:  21% (1035/4925), 1768 kb
-#> Receiving objects:  31% (1527/4925), 2345 kb
-#> Receiving objects:  41% (2020/4925), 2737 kb
-#> Receiving objects:  51% (2512/4925), 2849 kb
-#> Receiving objects:  61% (3005/4925), 3241 kb
-#> Receiving objects:  71% (3497/4925), 3746 kb
-#> Receiving objects:  81% (3990/4925), 3858 kb
-#> Receiving objects:  91% (4482/4925), 4026 kb
-#> Receiving objects: 100% (4925/4925), 4892 kb, done.

+
#> cloning into 'C:\Users\MVANKE~1\AppData\Local\Temp\RtmpYrand7/glue'...
+#> Receiving objects:   1% (63/6253),   63 kb
+#> Receiving objects:  11% (688/6253),  592 kb
+#> Receiving objects:  21% (1314/6253), 2320 kb
+#> Receiving objects:  31% (1939/6253), 2744 kb
+#> Receiving objects:  41% (2564/6253), 2856 kb
+#> Receiving objects:  51% (3190/6253), 3600 kb
+#> Receiving objects:  61% (3815/6253), 3808 kb
+#> Receiving objects:  71% (4440/6253), 3920 kb
+#> Receiving objects:  81% (5065/6253), 4088 kb
+#> Receiving objects:  91% (5691/6253), 4448 kb
+#> Receiving objects: 100% (6253/6253), 12641 kb, done.

checkDependencies @@ -368,7 +368,7 @@

summariseFunctionUse
 funsUsed <- PaRe::getFunctionUse(repo = repo)
 funsUsed

-
#> # A tibble: 426 × 4
+
#> # A tibble: 367 × 4
 #>    file     line pkg     fun         
 #>    <chr>   <int> <chr>   <chr>       
 #>  1 color.R    59 base    function    
@@ -381,7 +381,7 @@ 
summariseFunctionUse#>  8 color.R    70 base    function    
 #>  9 color.R    70 base    parse       
 #> 10 color.R    70 base    tryCatch    
-#> # ℹ 416 more rows

+#> # ℹ 357 more rows

getDefinedFunctions @@ -389,13 +389,13 @@

getDefinedFunctions
 defFuns <- PaRe::getDefinedFunctions(repo = repo)
 head(defFuns)

-
#>                name lineStart lineEnd nArgs cycloComp             fileName
-#> 1          glue_col        59      61     3         1              color.R
-#> 2     glue_data_col        65      67     4         1              color.R
-#> 3 color_transformer        69      99     2         8              color.R
-#> 4           .onLoad        47      50     1         1 compat-s3-register.R
-#> 5       s3_register        53     122     4         8 compat-s3-register.R
-#> 6    get_method_env        64      71     1         2 compat-s3-register.R
+
#>                name lineStart lineEnd nArgs cycloComp fileName
+#> 1          glue_col        59      61     3         1  color.R
+#> 2     glue_data_col        65      67     4         1  color.R
+#> 3 color_transformer        69      99     2         8  color.R
+#> 4             intro        67      69     3         1   glue.R
+#> 5         glue_data        92     200     6        21   glue.R
+#> 6                 f       150     176     1         3   glue.R

Besides the location of each function being displayed, the number of arguments for each function, and the cyclometic complexity is also included in the result.

@@ -403,24 +403,29 @@

getDefinedFunctionsPaRe::pkgDiagram(repo = repo) %>% DiagrammeRsvg::export_svg() %>% magick::image_read_svg() -

+
#> Loading required package: DiagrammeRsvg
+#> Loading required package: magick
+#> Linking to ImageMagick 6.9.12.98
+#> Enabled features: cairo, freetype, fftw, ghostscript, heic, lcms, pango, raw, rsvg, webp
+#> Disabled features: fontconfig, x11
+

Lines of code

-
+
 PaRe::countPackageLines(repo = repo)

 
#> # A tibble: 1 × 6
 #>       R   cpp     o     h  java   sql
 #>   <int> <int> <int> <int> <int> <int>
-#> 1  1118     0     0     0     0     0

+#> 1   984     0     0     0     0     0

glue contains 1056 lines of R-code.

Linting

-
+
 messages <- PaRe::lintRepo(repo = repo)
 PaRe::lintScore(repo = repo, messages = messages)

 
#> Warning: Returning more (or less) than 1 row per `summarise()` group was deprecated in
@@ -436,9 +441,9 @@ 
Linting#> # A tibble: 2 × 2
 #>   type      pct
 #>   <chr>   <dbl>
-#> 1 style   10.2 
-#> 2 warning  3.94

-
+#> 1 style   11.9 
+#> 2 warning  4.07

+
 head(messages)

 
#>   filename line_number column_number    type
 #> 1  color.R           8            81   style
@@ -447,13 +452,13 @@ 
Linting#> 4  color.R          59            81   style
 #> 5  color.R          60             3 warning
 #> 6  color.R          60            81   style
-#>                                                 message
-#> 1          Lines should not be more than 80 characters.
-#> 2          Lines should not be more than 80 characters.
-#> 3 Variable and function name style should be camelCase.
-#> 4          Lines should not be more than 80 characters.
-#> 5      no visible global function definition for 'glue'
-#> 6          Lines should not be more than 80 characters.
+#>                                                                    message
+#> 1 Lines should not be more than 80 characters. This line is 93 characters.
+#> 2 Lines should not be more than 80 characters. This line is 81 characters.
+#> 3                 Variable and function name style should match camelCase.
+#> 4 Lines should not be more than 80 characters. This line is 82 characters.
+#> 5                         no visible global function definition for 'glue'
+#> 6 Lines should not be more than 80 characters. This line is 94 characters.
 #>                                                                                             line
 #> 1  #' Using the following syntax will apply the function [crayon::blue()] to the text 'foo bar'.
 #> 2              #' If you want an expression to be evaluated, simply place that in a normal brace
diff --git a/docs/articles/Documentation_files/figure-html/pkgDiagram-1.png b/docs/articles/Documentation_files/figure-html/pkgDiagram-1.png
index f0b9ce6..9690878 100644
Binary files a/docs/articles/Documentation_files/figure-html/pkgDiagram-1.png and b/docs/articles/Documentation_files/figure-html/pkgDiagram-1.png differ
diff --git a/docs/articles/PareReport.html b/docs/articles/PareReport.html
index d65b2c0..374de8c 100644
--- a/docs/articles/PareReport.html
+++ b/docs/articles/PareReport.html
@@ -40,7 +40,7 @@
       
       
         PaRe
-        0.1.12
+        0.1.14
       
     

 
@@ -94,19 +94,20 @@
 
       
 
-      
-
-
-
-
+      
+
+
+
+
+
 

   

     

       
PaRe Report: PaRe [0.1.12]

                         
PaRe
-0.1.12

+0.1.14

-

2023-08-11

+

2024-11-28

Source: vignettes/articles/PareReport.Rmd @@ -123,22 +124,22 @@

Package overview

Summary of package functions

-
-

-
- +
+

+
+

Function details

-
- +
+

Use of other programming languages

-
- +
+

Style adherence, syntax errors and possible semantic issues @@ -146,20 +147,20 @@

Style adhere

Summary

-
- +
+

Warnings

-
- +
+

Style

-
- +
+

@@ -169,8 +170,8 @@

Dependency reviewCheck dependencies against whitelist 

## All dependencies are approved.
-
- +
+

Dependency characteristics @@ -189,14 +190,14 @@

Dependency characteristicsmeanDistance: The average dependency layers between PaRe and all other recursive dependencies. -
- +
+

Function use per dependency

-
-

+
+

diff --git a/docs/articles/PareReportBranches.html b/docs/articles/PareReportBranches.html index 17a7cc9..e40c0d8 100644 --- a/docs/articles/PareReportBranches.html +++ b/docs/articles/PareReportBranches.html @@ -40,7 +40,7 @@ PaRe - 0.1.12 + 0.1.14
@@ -94,19 +94,20 @@ - - - - - -
+ + + + + + +

ComPaRe branches: main, rc, dev

Maarten van Kessel

-

2023-08-11

+

2024-11-28

Source: vignettes/articles/PareReportBranches.Rmd @@ -115,21 +116,21 @@

2023-08-11

-
## cloning into 'C:\Users\MVANKE~1\AppData\Local\Temp\Rtmpaa1BYM/PaRe'...
-## Receiving objects:   1% (19/1817),   63 kb
-## Receiving objects:  11% (200/1817),  239 kb
-## Receiving objects:  21% (382/1817), 1584 kb
-## Receiving objects:  31% (564/1817), 3489 kb
-## Receiving objects:  41% (745/1817), 6779 kb
-## Receiving objects:  51% (927/1817), 9413 kb
-## Receiving objects:  61% (1109/1817), 9637 kb
-## Receiving objects:  71% (1291/1817), 9693 kb
-## Receiving objects:  81% (1472/1817), 9693 kb
-## Receiving objects:  91% (1654/1817), 9749 kb
-## Receiving objects: 100% (1817/1817), 14151 kb, done.
-
## Local:    main C:/Users/mvankessel/AppData/Local/Temp/Rtmpaa1BYM/PaRe
+
## cloning into 'C:\Users\MVANKE~1\AppData\Local\Temp\RtmpwtWKvB/PaRe'...
+## Receiving objects:   1% (23/2278),   63 kb
+## Receiving objects:  11% (251/2278), 1080 kb
+## Receiving objects:  21% (479/2278), 4778 kb
+## Receiving objects:  31% (707/2278), 8196 kb
+## Receiving objects:  41% (934/2278), 8364 kb
+## Receiving objects:  51% (1162/2278), 10998 kb
+## Receiving objects:  61% (1390/2278), 13015 kb
+## Receiving objects:  71% (1618/2278), 15593 kb
+## Receiving objects:  81% (1846/2278), 15817 kb
+## Receiving objects:  91% (2073/2278), 15929 kb
+## Receiving objects: 100% (2278/2278), 15965 kb, done.

+
## Local:    main C:/Users/mvankessel/AppData/Local/Temp/RtmpwtWKvB/PaRe
 ## Remote:   main @ origin (https://github.com/darwin-eu-dev/PaRe.git)
-## Head:     [8b216fc] 2023-07-17: Merge pull request #46 from darwin-eu-dev/rc

+## Head:     [72d3e48] 2024-11-01: Update feature_request.md
##  [1] "CRAN-SUBMISSION" "DESCRIPTION"     "docs"            "extras"         
 ##  [5] "inst"            "man"             "NAMESPACE"       "NEWS.md"        
 ##  [9] "PaRe.Rproj"      "pkgdown"         "R"               "README.md"      
@@ -152,20 +153,20 @@ 
Package Diagram
 
Main
 

-

-
+

+

rc

-
- +
+

dev

-
- +
+
@@ -177,16 +178,28 @@

Function Use

Depencies

-
## 
-
[36mℹ
[39m Loading metadata database
-
-
[32m✔
[39m Loading metadata database ... done
-## All dependencies are approved.
-## All dependencies are approved.
-## All dependencies are approved.
-
-
- +
## ✔ Updated metadata database: 5.12 MB in 4 files.
+## ℹ Updating metadata database✔ Updating metadata database ... done
+
## Warning in getParDeps(pkgs = customWhiteList$package, nThreads = nThreads):
+## Could not fetch dependencies for package: `PaRe`
+
## All dependencies are approved.
+
## Warning in getParDeps(pkgs = customWhiteList$package, nThreads = nThreads):
+## Could not fetch dependencies for package: `PaRe`
+
## All dependencies are approved.
+
## Warning in getParDeps(pkgs = customWhiteList$package, nThreads = nThreads):
+## Could not fetch dependencies for package: `PaRe`
+
## All dependencies are approved.
+
+
## Warning in getParDeps(pkgs = deps, nThreads = nThreads): Could not fetch
+## dependencies for package: `utils`
+
## Warning in getParDeps(pkgs = deps, nThreads = nThreads): Could not fetch
+## dependencies for package: `utils`Could not fetch dependencies for package:
+## `parallel`
+## Warning in getParDeps(pkgs = deps, nThreads = nThreads): Could not fetch
+## dependencies for package: `utils`Could not fetch dependencies for package:
+## `parallel`
+
+

diff --git a/docs/articles/PareReportBranches_files/crosstalk-1.2.1/css/crosstalk.min.css b/docs/articles/PareReportBranches_files/crosstalk-1.2.1/css/crosstalk.min.css new file mode 100644 index 0000000..6b45382 --- /dev/null +++ b/docs/articles/PareReportBranches_files/crosstalk-1.2.1/css/crosstalk.min.css @@ -0,0 +1 @@ +.container-fluid.crosstalk-bscols{margin-left:-30px;margin-right:-30px;white-space:normal}body>.container-fluid.crosstalk-bscols{margin-left:auto;margin-right:auto}.crosstalk-input-checkboxgroup .crosstalk-options-group .crosstalk-options-column{display:inline-block;padding-right:12px;vertical-align:top}@media only screen and (max-width: 480px){.crosstalk-input-checkboxgroup .crosstalk-options-group .crosstalk-options-column{display:block;padding-right:inherit}}.crosstalk-input{margin-bottom:15px}.crosstalk-input .control-label{margin-bottom:0;vertical-align:middle}.crosstalk-input input[type="checkbox"]{margin:4px 0 0;margin-top:1px;line-height:normal}.crosstalk-input .checkbox{position:relative;display:block;margin-top:10px;margin-bottom:10px}.crosstalk-input .checkbox>label{padding-left:20px;margin-bottom:0;font-weight:400;cursor:pointer}.crosstalk-input .checkbox input[type="checkbox"],.crosstalk-input .checkbox-inline input[type="checkbox"]{position:absolute;margin-top:2px;margin-left:-20px}.crosstalk-input .checkbox+.checkbox{margin-top:-5px}.crosstalk-input .checkbox-inline{position:relative;display:inline-block;padding-left:20px;margin-bottom:0;font-weight:400;vertical-align:middle;cursor:pointer}.crosstalk-input .checkbox-inline+.checkbox-inline{margin-top:0;margin-left:10px} diff --git a/docs/articles/PareReportBranches_files/crosstalk-1.2.1/js/crosstalk.js b/docs/articles/PareReportBranches_files/crosstalk-1.2.1/js/crosstalk.js new file mode 100644 index 0000000..fd9eb53 --- /dev/null +++ b/docs/articles/PareReportBranches_files/crosstalk-1.2.1/js/crosstalk.js @@ -0,0 +1,1474 @@ +(function(){function e(t,n,r){function s(o,u){if(!n[o]){if(!t[o]){var a=typeof require=="function"&&require;if(!u&&a)return a(o,!0);if(i)return i(o,!0);var f=new Error("Cannot find module '"+o+"'");throw f.code="MODULE_NOT_FOUND",f}var l=n[o]={exports:{}};t[o][0].call(l.exports,function(e){var n=t[o][1][e];return s(n?n:e)},l,l.exports,e,t,n,r)}return n[o].exports}var i=typeof require=="function"&&require;for(var o=0;o b) { + return 1; + } +} + +/** + * @private + */ + +var FilterSet = function () { + function FilterSet() { + _classCallCheck(this, FilterSet); + + this.reset(); + } + + _createClass(FilterSet, [{ + key: "reset", + value: function reset() { + // Key: handle ID, Value: array of selected keys, or null + this._handles = {}; + // Key: key string, Value: count of handles that include it + this._keys = {}; + this._value = null; + this._activeHandles = 0; + } + }, { + key: "update", + value: function update(handleId, keys) { + if (keys !== null) { + keys = keys.slice(0); // clone before sorting + keys.sort(naturalComparator); + } + + var _diffSortedLists = (0, _util.diffSortedLists)(this._handles[handleId], keys), + added = _diffSortedLists.added, + removed = _diffSortedLists.removed; + + this._handles[handleId] = keys; + + for (var i = 0; i < added.length; i++) { + this._keys[added[i]] = (this._keys[added[i]] || 0) + 1; + } + for (var _i = 0; _i < removed.length; _i++) { + this._keys[removed[_i]]--; + } + + this._updateValue(keys); + } + + /** + * @param {string[]} keys Sorted array of strings that indicate + * a superset of possible keys. + * @private + */ + + }, { + key: "_updateValue", + value: function _updateValue() { + var keys = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : this._allKeys; + + var handleCount = Object.keys(this._handles).length; + if (handleCount === 0) { + this._value = null; + } else { + this._value = []; + for (var i = 0; i < keys.length; i++) { + var count = this._keys[keys[i]]; + if (count === handleCount) { + this._value.push(keys[i]); + } + } + } + } + }, { + key: "clear", + value: function clear(handleId) { + if (typeof this._handles[handleId] === "undefined") { + return; + } + + var keys = this._handles[handleId]; + if (!keys) { + keys = []; + } + + for (var i = 0; i < keys.length; i++) { + this._keys[keys[i]]--; + } + delete this._handles[handleId]; + + this._updateValue(); + } + }, { + key: "value", + get: function get() { + return this._value; + } + }, { + key: "_allKeys", + get: function get() { + var allKeys = Object.keys(this._keys); + allKeys.sort(naturalComparator); + return allKeys; + } + }]); + + return FilterSet; +}(); + +exports.default = FilterSet; + +},{"./util":11}],4:[function(require,module,exports){ +(function (global){ +"use strict"; + +Object.defineProperty(exports, "__esModule", { + value: true +}); + +var _createClass = function () { function defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if ("value" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } } return function (Constructor, protoProps, staticProps) { if (protoProps) defineProperties(Constructor.prototype, protoProps); if (staticProps) defineProperties(Constructor, staticProps); return Constructor; }; }(); + +var _typeof = typeof Symbol === "function" && typeof Symbol.iterator === "symbol" ? function (obj) { return typeof obj; } : function (obj) { return obj && typeof Symbol === "function" && obj.constructor === Symbol && obj !== Symbol.prototype ? "symbol" : typeof obj; }; + +exports.default = group; + +var _var2 = require("./var"); + +var _var3 = _interopRequireDefault(_var2); + +function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; } + +function _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError("Cannot call a class as a function"); } } + +// Use a global so that multiple copies of crosstalk.js can be loaded and still +// have groups behave as singletons across all copies. +global.__crosstalk_groups = global.__crosstalk_groups || {}; +var groups = global.__crosstalk_groups; + +function group(groupName) { + if (groupName && typeof groupName === "string") { + if (!groups.hasOwnProperty(groupName)) { + groups[groupName] = new Group(groupName); + } + return groups[groupName]; + } else if ((typeof groupName === "undefined" ? "undefined" : _typeof(groupName)) === "object" && groupName._vars && groupName.var) { + // Appears to already be a group object + return groupName; + } else if (Array.isArray(groupName) && groupName.length == 1 && typeof groupName[0] === "string") { + return group(groupName[0]); + } else { + throw new Error("Invalid groupName argument"); + } +} + +var Group = function () { + function Group(name) { + _classCallCheck(this, Group); + + this.name = name; + this._vars = {}; + } + + _createClass(Group, [{ + key: "var", + value: function _var(name) { + if (!name || typeof name !== "string") { + throw new Error("Invalid var name"); + } + + if (!this._vars.hasOwnProperty(name)) this._vars[name] = new _var3.default(this, name); + return this._vars[name]; + } + }, { + key: "has", + value: function has(name) { + if (!name || typeof name !== "string") { + throw new Error("Invalid var name"); + } + + return this._vars.hasOwnProperty(name); + } + }]); + + return Group; +}(); + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) + +},{"./var":12}],5:[function(require,module,exports){ +(function (global){ +"use strict"; + +Object.defineProperty(exports, "__esModule", { + value: true +}); + +var _group = require("./group"); + +var _group2 = _interopRequireDefault(_group); + +var _selection = require("./selection"); + +var _filter = require("./filter"); + +var _input = require("./input"); + +require("./input_selectize"); + +require("./input_checkboxgroup"); + +require("./input_slider"); + +function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; } + +var defaultGroup = (0, _group2.default)("default"); + +function var_(name) { + return defaultGroup.var(name); +} + +function has(name) { + return defaultGroup.has(name); +} + +if (global.Shiny) { + global.Shiny.addCustomMessageHandler("update-client-value", function (message) { + if (typeof message.group === "string") { + (0, _group2.default)(message.group).var(message.name).set(message.value); + } else { + var_(message.name).set(message.value); + } + }); +} + +var crosstalk = { + group: _group2.default, + var: var_, + has: has, + SelectionHandle: _selection.SelectionHandle, + FilterHandle: _filter.FilterHandle, + bind: _input.bind +}; + +/** + * @namespace crosstalk + */ +exports.default = crosstalk; + +global.crosstalk = crosstalk; + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) + +},{"./filter":2,"./group":4,"./input":6,"./input_checkboxgroup":7,"./input_selectize":8,"./input_slider":9,"./selection":10}],6:[function(require,module,exports){ +(function (global){ +"use strict"; + +Object.defineProperty(exports, "__esModule", { + value: true +}); +exports.register = register; +exports.bind = bind; +var $ = global.jQuery; + +var bindings = {}; + +function register(reg) { + bindings[reg.className] = reg; + if (global.document && global.document.readyState !== "complete") { + $(function () { + bind(); + }); + } else if (global.document) { + setTimeout(bind, 100); + } +} + +function bind() { + Object.keys(bindings).forEach(function (className) { + var binding = bindings[className]; + $("." + binding.className).not(".crosstalk-input-bound").each(function (i, el) { + bindInstance(binding, el); + }); + }); +} + +// Escape jQuery identifier +function $escape(val) { + return val.replace(/([!"#$%&'()*+,./:;<=>?@[\\\]^`{|}~])/g, "\\$1"); +} + +function bindEl(el) { + var $el = $(el); + Object.keys(bindings).forEach(function (className) { + if ($el.hasClass(className) && !$el.hasClass("crosstalk-input-bound")) { + var binding = bindings[className]; + bindInstance(binding, el); + } + }); +} + +function bindInstance(binding, el) { + var jsonEl = $(el).find("script[type='application/json'][data-for='" + $escape(el.id) + "']"); + var data = JSON.parse(jsonEl[0].innerText); + + var instance = binding.factory(el, data); + $(el).data("crosstalk-instance", instance); + $(el).addClass("crosstalk-input-bound"); +} + +if (global.Shiny) { + var inputBinding = new global.Shiny.InputBinding(); + var _$ = global.jQuery; + _$.extend(inputBinding, { + find: function find(scope) { + return _$(scope).find(".crosstalk-input"); + }, + initialize: function initialize(el) { + if (!_$(el).hasClass("crosstalk-input-bound")) { + bindEl(el); + } + }, + getId: function getId(el) { + return el.id; + }, + getValue: function getValue(el) {}, + setValue: function setValue(el, value) {}, + receiveMessage: function receiveMessage(el, data) {}, + subscribe: function subscribe(el, callback) { + _$(el).data("crosstalk-instance").resume(); + }, + unsubscribe: function unsubscribe(el) { + _$(el).data("crosstalk-instance").suspend(); + } + }); + global.Shiny.inputBindings.register(inputBinding, "crosstalk.inputBinding"); +} + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) + +},{}],7:[function(require,module,exports){ +(function (global){ +"use strict"; + +var _input = require("./input"); + +var input = _interopRequireWildcard(_input); + +var _filter = require("./filter"); + +function _interopRequireWildcard(obj) { if (obj && obj.__esModule) { return obj; } else { var newObj = {}; if (obj != null) { for (var key in obj) { if (Object.prototype.hasOwnProperty.call(obj, key)) newObj[key] = obj[key]; } } newObj.default = obj; return newObj; } } + +var $ = global.jQuery; + +input.register({ + className: "crosstalk-input-checkboxgroup", + + factory: function factory(el, data) { + /* + * map: {"groupA": ["keyA", "keyB", ...], ...} + * group: "ct-groupname" + */ + var ctHandle = new _filter.FilterHandle(data.group); + + var lastKnownKeys = void 0; + var $el = $(el); + $el.on("change", "input[type='checkbox']", function () { + var checked = $el.find("input[type='checkbox']:checked"); + if (checked.length === 0) { + lastKnownKeys = null; + ctHandle.clear(); + } else { + var keys = {}; + checked.each(function () { + data.map[this.value].forEach(function (key) { + keys[key] = true; + }); + }); + var keyArray = Object.keys(keys); + keyArray.sort(); + lastKnownKeys = keyArray; + ctHandle.set(keyArray); + } + }); + + return { + suspend: function suspend() { + ctHandle.clear(); + }, + resume: function resume() { + if (lastKnownKeys) ctHandle.set(lastKnownKeys); + } + }; + } +}); + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) + +},{"./filter":2,"./input":6}],8:[function(require,module,exports){ +(function (global){ +"use strict"; + +var _input = require("./input"); + +var input = _interopRequireWildcard(_input); + +var _util = require("./util"); + +var util = _interopRequireWildcard(_util); + +var _filter = require("./filter"); + +function _interopRequireWildcard(obj) { if (obj && obj.__esModule) { return obj; } else { var newObj = {}; if (obj != null) { for (var key in obj) { if (Object.prototype.hasOwnProperty.call(obj, key)) newObj[key] = obj[key]; } } newObj.default = obj; return newObj; } } + +var $ = global.jQuery; + +input.register({ + className: "crosstalk-input-select", + + factory: function factory(el, data) { + /* + * items: {value: [...], label: [...]} + * map: {"groupA": ["keyA", "keyB", ...], ...} + * group: "ct-groupname" + */ + + var first = [{ value: "", label: "(All)" }]; + var items = util.dataframeToD3(data.items); + var opts = { + options: first.concat(items), + valueField: "value", + labelField: "label", + searchField: "label" + }; + + var select = $(el).find("select")[0]; + + var selectize = $(select).selectize(opts)[0].selectize; + + var ctHandle = new _filter.FilterHandle(data.group); + + var lastKnownKeys = void 0; + selectize.on("change", function () { + if (selectize.items.length === 0) { + lastKnownKeys = null; + ctHandle.clear(); + } else { + var keys = {}; + selectize.items.forEach(function (group) { + data.map[group].forEach(function (key) { + keys[key] = true; + }); + }); + var keyArray = Object.keys(keys); + keyArray.sort(); + lastKnownKeys = keyArray; + ctHandle.set(keyArray); + } + }); + + return { + suspend: function suspend() { + ctHandle.clear(); + }, + resume: function resume() { + if (lastKnownKeys) ctHandle.set(lastKnownKeys); + } + }; + } +}); + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) + +},{"./filter":2,"./input":6,"./util":11}],9:[function(require,module,exports){ +(function (global){ +"use strict"; + +var _slicedToArray = function () { function sliceIterator(arr, i) { var _arr = []; var _n = true; var _d = false; var _e = undefined; try { for (var _i = arr[Symbol.iterator](), _s; !(_n = (_s = _i.next()).done); _n = true) { _arr.push(_s.value); if (i && _arr.length === i) break; } } catch (err) { _d = true; _e = err; } finally { try { if (!_n && _i["return"]) _i["return"](); } finally { if (_d) throw _e; } } return _arr; } return function (arr, i) { if (Array.isArray(arr)) { return arr; } else if (Symbol.iterator in Object(arr)) { return sliceIterator(arr, i); } else { throw new TypeError("Invalid attempt to destructure non-iterable instance"); } }; }(); + +var _input = require("./input"); + +var input = _interopRequireWildcard(_input); + +var _filter = require("./filter"); + +function _interopRequireWildcard(obj) { if (obj && obj.__esModule) { return obj; } else { var newObj = {}; if (obj != null) { for (var key in obj) { if (Object.prototype.hasOwnProperty.call(obj, key)) newObj[key] = obj[key]; } } newObj.default = obj; return newObj; } } + +var $ = global.jQuery; +var strftime = global.strftime; + +input.register({ + className: "crosstalk-input-slider", + + factory: function factory(el, data) { + /* + * map: {"groupA": ["keyA", "keyB", ...], ...} + * group: "ct-groupname" + */ + var ctHandle = new _filter.FilterHandle(data.group); + + var opts = {}; + var $el = $(el).find("input"); + var dataType = $el.data("data-type"); + var timeFormat = $el.data("time-format"); + var round = $el.data("round"); + var timeFormatter = void 0; + + // Set up formatting functions + if (dataType === "date") { + timeFormatter = strftime.utc(); + opts.prettify = function (num) { + return timeFormatter(timeFormat, new Date(num)); + }; + } else if (dataType === "datetime") { + var timezone = $el.data("timezone"); + if (timezone) timeFormatter = strftime.timezone(timezone);else timeFormatter = strftime; + + opts.prettify = function (num) { + return timeFormatter(timeFormat, new Date(num)); + }; + } else if (dataType === "number") { + if (typeof round !== "undefined") opts.prettify = function (num) { + var factor = Math.pow(10, round); + return Math.round(num * factor) / factor; + }; + } + + $el.ionRangeSlider(opts); + + function getValue() { + var result = $el.data("ionRangeSlider").result; + + // Function for converting numeric value from slider to appropriate type. + var convert = void 0; + var dataType = $el.data("data-type"); + if (dataType === "date") { + convert = function convert(val) { + return formatDateUTC(new Date(+val)); + }; + } else if (dataType === "datetime") { + convert = function convert(val) { + // Convert ms to s + return +val / 1000; + }; + } else { + convert = function convert(val) { + return +val; + }; + } + + if ($el.data("ionRangeSlider").options.type === "double") { + return [convert(result.from), convert(result.to)]; + } else { + return convert(result.from); + } + } + + var lastKnownKeys = null; + + $el.on("change.crosstalkSliderInput", function (event) { + if (!$el.data("updating") && !$el.data("animating")) { + var _getValue = getValue(), + _getValue2 = _slicedToArray(_getValue, 2), + from = _getValue2[0], + to = _getValue2[1]; + + var keys = []; + for (var i = 0; i < data.values.length; i++) { + var val = data.values[i]; + if (val >= from && val <= to) { + keys.push(data.keys[i]); + } + } + keys.sort(); + ctHandle.set(keys); + lastKnownKeys = keys; + } + }); + + // let $el = $(el); + // $el.on("change", "input[type="checkbox"]", function() { + // let checked = $el.find("input[type="checkbox"]:checked"); + // if (checked.length === 0) { + // ctHandle.clear(); + // } else { + // let keys = {}; + // checked.each(function() { + // data.map[this.value].forEach(function(key) { + // keys[key] = true; + // }); + // }); + // let keyArray = Object.keys(keys); + // keyArray.sort(); + // ctHandle.set(keyArray); + // } + // }); + + return { + suspend: function suspend() { + ctHandle.clear(); + }, + resume: function resume() { + if (lastKnownKeys) ctHandle.set(lastKnownKeys); + } + }; + } +}); + +// Convert a number to a string with leading zeros +function padZeros(n, digits) { + var str = n.toString(); + while (str.length < digits) { + str = "0" + str; + }return str; +} + +// Given a Date object, return a string in yyyy-mm-dd format, using the +// UTC date. This may be a day off from the date in the local time zone. +function formatDateUTC(date) { + if (date instanceof Date) { + return date.getUTCFullYear() + "-" + padZeros(date.getUTCMonth() + 1, 2) + "-" + padZeros(date.getUTCDate(), 2); + } else { + return null; + } +} + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) + +},{"./filter":2,"./input":6}],10:[function(require,module,exports){ +"use strict"; + +Object.defineProperty(exports, "__esModule", { + value: true +}); +exports.SelectionHandle = undefined; + +var _createClass = function () { function defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if ("value" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } } return function (Constructor, protoProps, staticProps) { if (protoProps) defineProperties(Constructor.prototype, protoProps); if (staticProps) defineProperties(Constructor, staticProps); return Constructor; }; }(); + +var _events = require("./events"); + +var _events2 = _interopRequireDefault(_events); + +var _group = require("./group"); + +var _group2 = _interopRequireDefault(_group); + +var _util = require("./util"); + +var util = _interopRequireWildcard(_util); + +function _interopRequireWildcard(obj) { if (obj && obj.__esModule) { return obj; } else { var newObj = {}; if (obj != null) { for (var key in obj) { if (Object.prototype.hasOwnProperty.call(obj, key)) newObj[key] = obj[key]; } } newObj.default = obj; return newObj; } } + +function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; } + +function _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError("Cannot call a class as a function"); } } + +/** + * Use this class to read and write (and listen for changes to) the selection + * for a Crosstalk group. This is intended to be used for linked brushing. + * + * If two (or more) `SelectionHandle` instances in the same webpage share the + * same group name, they will share the same state. Setting the selection using + * one `SelectionHandle` instance will result in the `value` property instantly + * changing across the others, and `"change"` event listeners on all instances + * (including the one that initiated the sending) will fire. + * + * @param {string} [group] - The name of the Crosstalk group, or if none, + * null or undefined (or any other falsy value). This can be changed later + * via the [SelectionHandle#setGroup](#setGroup) method. + * @param {Object} [extraInfo] - An object whose properties will be copied to + * the event object whenever an event is emitted. + */ +var SelectionHandle = exports.SelectionHandle = function () { + function SelectionHandle() { + var group = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : null; + var extraInfo = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : null; + + _classCallCheck(this, SelectionHandle); + + this._eventRelay = new _events2.default(); + this._emitter = new util.SubscriptionTracker(this._eventRelay); + + // Name of the group we're currently tracking, if any. Can change over time. + this._group = null; + // The Var we're currently tracking, if any. Can change over time. + this._var = null; + // The event handler subscription we currently have on var.on("change"). + this._varOnChangeSub = null; + + this._extraInfo = util.extend({ sender: this }, extraInfo); + + this.setGroup(group); + } + + /** + * Changes the Crosstalk group membership of this SelectionHandle. The group + * being switched away from (if any) will not have its selection value + * modified as a result of calling `setGroup`, even if this handle was the + * most recent handle to set the selection of the group. + * + * The group being switched to (if any) will also not have its selection value + * modified as a result of calling `setGroup`. If you want to set the + * selection value of the new group, call `set` explicitly. + * + * @param {string} group - The name of the Crosstalk group, or null (or + * undefined) to clear the group. + */ + + + _createClass(SelectionHandle, [{ + key: "setGroup", + value: function setGroup(group) { + var _this = this; + + // If group is unchanged, do nothing + if (this._group === group) return; + // Treat null, undefined, and other falsy values the same + if (!this._group && !group) return; + + if (this._var) { + this._var.off("change", this._varOnChangeSub); + this._var = null; + this._varOnChangeSub = null; + } + + this._group = group; + + if (group) { + this._var = (0, _group2.default)(group).var("selection"); + var sub = this._var.on("change", function (e) { + _this._eventRelay.trigger("change", e, _this); + }); + this._varOnChangeSub = sub; + } + } + + /** + * Retrieves the current selection for the group represented by this + * `SelectionHandle`. + * + * - If no selection is active, then this value will be falsy. + * - If a selection is active, but no data points are selected, then this + * value will be an empty array. + * - If a selection is active, and data points are selected, then the keys + * of the selected data points will be present in the array. + */ + + }, { + key: "_mergeExtraInfo", + + + /** + * Combines the given `extraInfo` (if any) with the handle's default + * `_extraInfo` (if any). + * @private + */ + value: function _mergeExtraInfo(extraInfo) { + // Important incidental effect: shallow clone is returned + return util.extend({}, this._extraInfo ? this._extraInfo : null, extraInfo ? extraInfo : null); + } + + /** + * Overwrites the current selection for the group, and raises the `"change"` + * event among all of the group's '`SelectionHandle` instances (including + * this one). + * + * @fires SelectionHandle#change + * @param {string[]} selectedKeys - Falsy, empty array, or array of keys (see + * {@link SelectionHandle#value}). + * @param {Object} [extraInfo] - Extra properties to be included on the event + * object that's passed to listeners (in addition to any options that were + * passed into the `SelectionHandle` constructor). + */ + + }, { + key: "set", + value: function set(selectedKeys, extraInfo) { + if (this._var) this._var.set(selectedKeys, this._mergeExtraInfo(extraInfo)); + } + + /** + * Overwrites the current selection for the group, and raises the `"change"` + * event among all of the group's '`SelectionHandle` instances (including + * this one). + * + * @fires SelectionHandle#change + * @param {Object} [extraInfo] - Extra properties to be included on the event + * object that's passed to listeners (in addition to any that were passed + * into the `SelectionHandle` constructor). + */ + + }, { + key: "clear", + value: function clear(extraInfo) { + if (this._var) this.set(void 0, this._mergeExtraInfo(extraInfo)); + } + + /** + * Subscribes to events on this `SelectionHandle`. + * + * @param {string} eventType - Indicates the type of events to listen to. + * Currently, only `"change"` is supported. + * @param {SelectionHandle~listener} listener - The callback function that + * will be invoked when the event occurs. + * @return {string} - A token to pass to {@link SelectionHandle#off} to cancel + * this subscription. + */ + + }, { + key: "on", + value: function on(eventType, listener) { + return this._emitter.on(eventType, listener); + } + + /** + * Cancels event subscriptions created by {@link SelectionHandle#on}. + * + * @param {string} eventType - The type of event to unsubscribe. + * @param {string|SelectionHandle~listener} listener - Either the callback + * function previously passed into {@link SelectionHandle#on}, or the + * string that was returned from {@link SelectionHandle#on}. + */ + + }, { + key: "off", + value: function off(eventType, listener) { + return this._emitter.off(eventType, listener); + } + + /** + * Shuts down the `SelectionHandle` object. + * + * Removes all event listeners that were added through this handle. + */ + + }, { + key: "close", + value: function close() { + this._emitter.removeAllListeners(); + this.setGroup(null); + } + }, { + key: "value", + get: function get() { + return this._var ? this._var.get() : null; + } + }]); + + return SelectionHandle; +}(); + +/** + * @callback SelectionHandle~listener + * @param {Object} event - An object containing details of the event. For + * `"change"` events, this includes the properties `value` (the new + * value of the selection, or `undefined` if no selection is active), + * `oldValue` (the previous value of the selection), and `sender` (the + * `SelectionHandle` instance that made the change). + */ + +/** + * @event SelectionHandle#change + * @type {object} + * @property {object} value - The new value of the selection, or `undefined` + * if no selection is active. + * @property {object} oldValue - The previous value of the selection. + * @property {SelectionHandle} sender - The `SelectionHandle` instance that + * changed the value. + */ + +},{"./events":1,"./group":4,"./util":11}],11:[function(require,module,exports){ +"use strict"; + +Object.defineProperty(exports, "__esModule", { + value: true +}); + +var _createClass = function () { function defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if ("value" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } } return function (Constructor, protoProps, staticProps) { if (protoProps) defineProperties(Constructor.prototype, protoProps); if (staticProps) defineProperties(Constructor, staticProps); return Constructor; }; }(); + +var _typeof = typeof Symbol === "function" && typeof Symbol.iterator === "symbol" ? function (obj) { return typeof obj; } : function (obj) { return obj && typeof Symbol === "function" && obj.constructor === Symbol && obj !== Symbol.prototype ? "symbol" : typeof obj; }; + +exports.extend = extend; +exports.checkSorted = checkSorted; +exports.diffSortedLists = diffSortedLists; +exports.dataframeToD3 = dataframeToD3; + +function _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError("Cannot call a class as a function"); } } + +function extend(target) { + for (var _len = arguments.length, sources = Array(_len > 1 ? _len - 1 : 0), _key = 1; _key < _len; _key++) { + sources[_key - 1] = arguments[_key]; + } + + for (var i = 0; i < sources.length; i++) { + var src = sources[i]; + if (typeof src === "undefined" || src === null) continue; + + for (var key in src) { + if (src.hasOwnProperty(key)) { + target[key] = src[key]; + } + } + } + return target; +} + +function checkSorted(list) { + for (var i = 1; i < list.length; i++) { + if (list[i] <= list[i - 1]) { + throw new Error("List is not sorted or contains duplicate"); + } + } +} + +function diffSortedLists(a, b) { + var i_a = 0; + var i_b = 0; + + if (!a) a = []; + if (!b) b = []; + + var a_only = []; + var b_only = []; + + checkSorted(a); + checkSorted(b); + + while (i_a < a.length && i_b < b.length) { + if (a[i_a] === b[i_b]) { + i_a++; + i_b++; + } else if (a[i_a] < b[i_b]) { + a_only.push(a[i_a++]); + } else { + b_only.push(b[i_b++]); + } + } + + if (i_a < a.length) a_only = a_only.concat(a.slice(i_a)); + if (i_b < b.length) b_only = b_only.concat(b.slice(i_b)); + return { + removed: a_only, + added: b_only + }; +} + +// Convert from wide: { colA: [1,2,3], colB: [4,5,6], ... } +// to long: [ {colA: 1, colB: 4}, {colA: 2, colB: 5}, ... ] +function dataframeToD3(df) { + var names = []; + var length = void 0; + for (var name in df) { + if (df.hasOwnProperty(name)) names.push(name); + if (_typeof(df[name]) !== "object" || typeof df[name].length === "undefined") { + throw new Error("All fields must be arrays"); + } else if (typeof length !== "undefined" && length !== df[name].length) { + throw new Error("All fields must be arrays of the same length"); + } + length = df[name].length; + } + var results = []; + var item = void 0; + for (var row = 0; row < length; row++) { + item = {}; + for (var col = 0; col < names.length; col++) { + item[names[col]] = df[names[col]][row]; + } + results.push(item); + } + return results; +} + +/** + * Keeps track of all event listener additions/removals and lets all active + * listeners be removed with a single operation. + * + * @private + */ + +var SubscriptionTracker = exports.SubscriptionTracker = function () { + function SubscriptionTracker(emitter) { + _classCallCheck(this, SubscriptionTracker); + + this._emitter = emitter; + this._subs = {}; + } + + _createClass(SubscriptionTracker, [{ + key: "on", + value: function on(eventType, listener) { + var sub = this._emitter.on(eventType, listener); + this._subs[sub] = eventType; + return sub; + } + }, { + key: "off", + value: function off(eventType, listener) { + var sub = this._emitter.off(eventType, listener); + if (sub) { + delete this._subs[sub]; + } + return sub; + } + }, { + key: "removeAllListeners", + value: function removeAllListeners() { + var _this = this; + + var current_subs = this._subs; + this._subs = {}; + Object.keys(current_subs).forEach(function (sub) { + _this._emitter.off(current_subs[sub], sub); + }); + } + }]); + + return SubscriptionTracker; +}(); + +},{}],12:[function(require,module,exports){ +(function (global){ +"use strict"; + +Object.defineProperty(exports, "__esModule", { + value: true +}); + +var _typeof = typeof Symbol === "function" && typeof Symbol.iterator === "symbol" ? function (obj) { return typeof obj; } : function (obj) { return obj && typeof Symbol === "function" && obj.constructor === Symbol && obj !== Symbol.prototype ? "symbol" : typeof obj; }; + +var _createClass = function () { function defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if ("value" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } } return function (Constructor, protoProps, staticProps) { if (protoProps) defineProperties(Constructor.prototype, protoProps); if (staticProps) defineProperties(Constructor, staticProps); return Constructor; }; }(); + +var _events = require("./events"); + +var _events2 = _interopRequireDefault(_events); + +function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; } + +function _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError("Cannot call a class as a function"); } } + +var Var = function () { + function Var(group, name, /*optional*/value) { + _classCallCheck(this, Var); + + this._group = group; + this._name = name; + this._value = value; + this._events = new _events2.default(); + } + + _createClass(Var, [{ + key: "get", + value: function get() { + return this._value; + } + }, { + key: "set", + value: function set(value, /*optional*/event) { + if (this._value === value) { + // Do nothing; the value hasn't changed + return; + } + var oldValue = this._value; + this._value = value; + // Alert JavaScript listeners that the value has changed + var evt = {}; + if (event && (typeof event === "undefined" ? "undefined" : _typeof(event)) === "object") { + for (var k in event) { + if (event.hasOwnProperty(k)) evt[k] = event[k]; + } + } + evt.oldValue = oldValue; + evt.value = value; + this._events.trigger("change", evt, this); + + // TODO: Make this extensible, to let arbitrary back-ends know that + // something has changed + if (global.Shiny && global.Shiny.onInputChange) { + global.Shiny.onInputChange(".clientValue-" + (this._group.name !== null ? this._group.name + "-" : "") + this._name, typeof value === "undefined" ? null : value); + } + } + }, { + key: "on", + value: function on(eventType, listener) { + return this._events.on(eventType, listener); + } + }, { + key: "off", + value: function off(eventType, listener) { + return this._events.off(eventType, listener); + } + }]); + + return Var; +}(); + +exports.default = Var; + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) + 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+ "file": "generated.js", + "sourceRoot": "", + "sourcesContent": [ + "(function(){function e(t,n,r){function s(o,u){if(!n[o]){if(!t[o]){var a=typeof require==\"function\"&&require;if(!u&&a)return a(o,!0);if(i)return i(o,!0);var f=new Error(\"Cannot find module '\"+o+\"'\");throw f.code=\"MODULE_NOT_FOUND\",f}var l=n[o]={exports:{}};t[o][0].call(l.exports,function(e){var n=t[o][1][e];return s(n?n:e)},l,l.exports,e,t,n,r)}return n[o].exports}var i=typeof require==\"function\"&&require;for(var o=0;o {\n this._eventRelay.trigger(\"change\", e, this);\n });\n this._varOnChangeSub = sub;\n }\n }\n\n /**\n * Combine the given `extraInfo` (if any) with the handle's default\n * `_extraInfo` (if any).\n * @private\n */\n _mergeExtraInfo(extraInfo) {\n return util.extend({},\n this._extraInfo ? this._extraInfo : null,\n extraInfo ? extraInfo : null);\n }\n\n /**\n * Close the handle. This clears this handle's contribution to the filter set,\n * and unsubscribes all event listeners.\n */\n close() {\n this._emitter.removeAllListeners();\n this.clear();\n this.setGroup(null);\n }\n\n /**\n * Clear this handle's contribution to the filter set.\n *\n * @param {Object} [extraInfo] - Extra properties to be included on the event\n * object that's passed to listeners (in addition to any options that were\n * passed into the `FilterHandle` constructor).\n * \n * @fires FilterHandle#change\n */\n clear(extraInfo) {\n if (!this._filterSet)\n return;\n this._filterSet.clear(this._id);\n this._onChange(extraInfo);\n }\n\n /**\n * Set this handle's contribution to the filter set. This array should consist\n * of the keys of the rows that _should_ be displayed; any keys that are not\n * present in the array will be considered _filtered out_. Note that multiple\n * `FilterHandle` instances in the group may each contribute an array of keys,\n * and only those keys that appear in _all_ of the arrays make it through the\n * filter.\n *\n * @param {string[]} keys - Empty array, or array of keys. To clear the\n * filter, don't pass an empty array; instead, use the\n * {@link FilterHandle#clear} method.\n * @param {Object} [extraInfo] - Extra properties to be included on the event\n * object that's passed to listeners (in addition to any options that were\n * passed into the `FilterHandle` constructor).\n * \n * @fires FilterHandle#change\n */\n set(keys, extraInfo) {\n if (!this._filterSet)\n return;\n this._filterSet.update(this._id, keys);\n this._onChange(extraInfo);\n }\n\n /**\n * @return {string[]|null} - Either: 1) an array of keys that made it through\n * all of the `FilterHandle` instances, or, 2) `null`, which means no filter\n * is being applied (all data should be displayed).\n */\n get filteredKeys() {\n return this._filterSet ? this._filterSet.value : null;\n }\n\n /**\n * Subscribe to events on this `FilterHandle`.\n *\n * @param {string} eventType - Indicates the type of events to listen to.\n * Currently, only `\"change\"` is supported.\n * @param {FilterHandle~listener} listener - The callback function that\n * will be invoked when the event occurs.\n * @return {string} - A token to pass to {@link FilterHandle#off} to cancel\n * this subscription.\n */\n on(eventType, listener) {\n return this._emitter.on(eventType, listener);\n }\n\n /**\n * Cancel event subscriptions created by {@link FilterHandle#on}.\n *\n * @param {string} eventType - The type of event to unsubscribe.\n * @param {string|FilterHandle~listener} listener - Either the callback\n * function previously passed into {@link FilterHandle#on}, or the\n * string that was returned from {@link FilterHandle#on}.\n */\n off(eventType, listener) {\n return this._emitter.off(eventType, listener);\n }\n\n _onChange(extraInfo) {\n if (!this._filterSet)\n return;\n this._filterVar.set(this._filterSet.value, this._mergeExtraInfo(extraInfo));\n }\n\n /**\n * @callback FilterHandle~listener\n * @param {Object} event - An object containing details of the event. For\n * `\"change\"` events, this includes the properties `value` (the new\n * value of the filter set, or `null` if no filter set is active),\n * `oldValue` (the previous value of the filter set), and `sender` (the\n * `FilterHandle` instance that made the change).\n */\n\n}\n\n/**\n * @event FilterHandle#change\n * @type {object}\n * @property {object} value - The new value of the filter set, or `null`\n * if no filter set is active.\n * @property {object} oldValue - The previous value of the filter set.\n * @property {FilterHandle} sender - The `FilterHandle` instance that\n * changed the value.\n */\n", + "import { diffSortedLists } from \"./util\";\n\nfunction naturalComparator(a, b) {\n if (a === b) {\n return 0;\n } else if (a < b) {\n return -1;\n } else if (a > b) {\n return 1;\n }\n}\n\n/**\n * @private\n */\nexport default class FilterSet {\n constructor() {\n this.reset();\n }\n\n reset() {\n // Key: handle ID, Value: array of selected keys, or null\n this._handles = {};\n // Key: key string, Value: count of handles that include it\n this._keys = {};\n this._value = null;\n this._activeHandles = 0;\n }\n\n get value() {\n return this._value;\n }\n\n update(handleId, keys) {\n if (keys !== null) {\n keys = keys.slice(0); // clone before sorting\n keys.sort(naturalComparator);\n }\n\n let {added, removed} = diffSortedLists(this._handles[handleId], keys);\n this._handles[handleId] = keys;\n\n for (let i = 0; i < added.length; i++) {\n this._keys[added[i]] = (this._keys[added[i]] || 0) + 1;\n }\n for (let i = 0; i < removed.length; i++) {\n this._keys[removed[i]]--;\n }\n\n this._updateValue(keys);\n }\n\n /**\n * @param {string[]} keys Sorted array of strings that indicate\n * a superset of possible keys.\n * @private\n */\n _updateValue(keys = this._allKeys) {\n let handleCount = Object.keys(this._handles).length;\n if (handleCount === 0) {\n this._value = null;\n } else {\n this._value = [];\n for (let i = 0; i < keys.length; i++) {\n let count = this._keys[keys[i]];\n if (count === handleCount) {\n this._value.push(keys[i]);\n }\n }\n }\n }\n\n clear(handleId) {\n if (typeof(this._handles[handleId]) === \"undefined\") {\n return;\n }\n\n let keys = this._handles[handleId];\n if (!keys) {\n keys = [];\n }\n\n for (let i = 0; i < keys.length; i++) {\n this._keys[keys[i]]--;\n }\n delete this._handles[handleId];\n\n this._updateValue();\n }\n\n get _allKeys() {\n let allKeys = Object.keys(this._keys);\n allKeys.sort(naturalComparator);\n return allKeys;\n }\n}\n", + "import Var from \"./var\";\n\n// Use a global so that multiple copies of crosstalk.js can be loaded and still\n// have groups behave as singletons across all copies.\nglobal.__crosstalk_groups = global.__crosstalk_groups || {};\nlet groups = global.__crosstalk_groups;\n\nexport default function group(groupName) {\n if (groupName && typeof(groupName) === \"string\") {\n if (!groups.hasOwnProperty(groupName)) {\n groups[groupName] = new Group(groupName);\n }\n return groups[groupName];\n } else if (typeof(groupName) === \"object\" && groupName._vars && groupName.var) {\n // Appears to already be a group object\n return groupName;\n } else if (Array.isArray(groupName) &&\n groupName.length == 1 &&\n typeof(groupName[0]) === \"string\") {\n return group(groupName[0]);\n } else {\n throw new Error(\"Invalid groupName argument\");\n }\n}\n\nclass Group {\n constructor(name) {\n this.name = name;\n this._vars = {};\n }\n\n var(name) {\n if (!name || typeof(name) !== \"string\") {\n throw new Error(\"Invalid var name\");\n }\n\n if (!this._vars.hasOwnProperty(name))\n this._vars[name] = new Var(this, name);\n return this._vars[name];\n }\n\n has(name) {\n if (!name || typeof(name) !== \"string\") {\n throw new Error(\"Invalid var name\");\n }\n\n return this._vars.hasOwnProperty(name);\n }\n}\n", + "import group from \"./group\";\nimport { SelectionHandle } from \"./selection\";\nimport { FilterHandle } from \"./filter\";\nimport { bind } from \"./input\";\nimport \"./input_selectize\";\nimport \"./input_checkboxgroup\";\nimport \"./input_slider\";\n\nconst defaultGroup = group(\"default\");\n\nfunction var_(name) {\n return defaultGroup.var(name);\n}\n\nfunction has(name) {\n return defaultGroup.has(name);\n}\n\nif (global.Shiny) {\n global.Shiny.addCustomMessageHandler(\"update-client-value\", function(message) {\n if (typeof(message.group) === \"string\") {\n group(message.group).var(message.name).set(message.value);\n } else {\n var_(message.name).set(message.value);\n }\n });\n}\n\nconst crosstalk = {\n group: group,\n var: var_,\n has: has,\n SelectionHandle: SelectionHandle,\n FilterHandle: FilterHandle,\n bind: bind\n};\n\n/**\n * @namespace crosstalk\n */\nexport default crosstalk;\nglobal.crosstalk = crosstalk;\n", + "let $ = global.jQuery;\n\nlet bindings = {};\n\nexport function register(reg) {\n bindings[reg.className] = reg;\n if (global.document && global.document.readyState !== \"complete\") {\n $(() => {\n bind();\n });\n } else if (global.document) {\n setTimeout(bind, 100);\n }\n}\n\nexport function bind() {\n Object.keys(bindings).forEach(function(className) {\n let binding = bindings[className];\n $(\".\" + binding.className).not(\".crosstalk-input-bound\").each(function(i, el) {\n bindInstance(binding, el);\n });\n });\n}\n\n// Escape jQuery identifier\nfunction $escape(val) {\n return val.replace(/([!\"#$%&'()*+,./:;<=>?@[\\\\\\]^`{|}~])/g, \"\\\\$1\");\n}\n\nfunction bindEl(el) {\n let $el = $(el);\n Object.keys(bindings).forEach(function(className) {\n if ($el.hasClass(className) && !$el.hasClass(\"crosstalk-input-bound\")) {\n let binding = bindings[className];\n bindInstance(binding, el);\n }\n });\n}\n\nfunction bindInstance(binding, el) {\n let jsonEl = $(el).find(\"script[type='application/json'][data-for='\" + $escape(el.id) + \"']\");\n let data = JSON.parse(jsonEl[0].innerText);\n\n let instance = binding.factory(el, data);\n $(el).data(\"crosstalk-instance\", instance);\n $(el).addClass(\"crosstalk-input-bound\");\n}\n\nif (global.Shiny) {\n let inputBinding = new global.Shiny.InputBinding();\n let $ = global.jQuery;\n $.extend(inputBinding, {\n find: function(scope) {\n return $(scope).find(\".crosstalk-input\");\n },\n initialize: function(el) {\n if (!$(el).hasClass(\"crosstalk-input-bound\")) {\n bindEl(el);\n }\n },\n getId: function(el) {\n return el.id;\n },\n getValue: function(el) {\n\n },\n setValue: function(el, value) {\n\n },\n receiveMessage: function(el, data) {\n\n },\n subscribe: function(el, callback) {\n $(el).data(\"crosstalk-instance\").resume();\n },\n unsubscribe: function(el) {\n $(el).data(\"crosstalk-instance\").suspend();\n }\n });\n global.Shiny.inputBindings.register(inputBinding, \"crosstalk.inputBinding\");\n}\n", + "import * as input from \"./input\";\nimport { FilterHandle } from \"./filter\";\n\nlet $ = global.jQuery;\n\ninput.register({\n className: \"crosstalk-input-checkboxgroup\",\n\n factory: function(el, data) {\n /*\n * map: {\"groupA\": [\"keyA\", \"keyB\", ...], ...}\n * group: \"ct-groupname\"\n */\n let ctHandle = new FilterHandle(data.group);\n\n let lastKnownKeys;\n let $el = $(el);\n $el.on(\"change\", \"input[type='checkbox']\", function() {\n let checked = $el.find(\"input[type='checkbox']:checked\");\n if (checked.length === 0) {\n lastKnownKeys = null;\n ctHandle.clear();\n } else {\n let keys = {};\n checked.each(function() {\n data.map[this.value].forEach(function(key) {\n keys[key] = true;\n });\n });\n let keyArray = Object.keys(keys);\n keyArray.sort();\n lastKnownKeys = keyArray;\n ctHandle.set(keyArray);\n }\n });\n\n return {\n suspend: function() {\n ctHandle.clear();\n },\n resume: function() {\n if (lastKnownKeys)\n ctHandle.set(lastKnownKeys);\n }\n };\n }\n});\n", + "import * as input from \"./input\";\nimport * as util from \"./util\";\nimport { FilterHandle } from \"./filter\";\n\nlet $ = global.jQuery;\n\ninput.register({\n className: \"crosstalk-input-select\",\n\n factory: function(el, data) {\n /*\n * items: {value: [...], label: [...]}\n * map: {\"groupA\": [\"keyA\", \"keyB\", ...], ...}\n * group: \"ct-groupname\"\n */\n\n let first = [{value: \"\", label: \"(All)\"}];\n let items = util.dataframeToD3(data.items);\n let opts = {\n options: first.concat(items),\n valueField: \"value\",\n labelField: \"label\",\n searchField: \"label\"\n };\n\n let select = $(el).find(\"select\")[0];\n\n let selectize = $(select).selectize(opts)[0].selectize;\n\n let ctHandle = new FilterHandle(data.group);\n\n let lastKnownKeys;\n selectize.on(\"change\", function() {\n if (selectize.items.length === 0) {\n lastKnownKeys = null;\n ctHandle.clear();\n } else {\n let keys = {};\n selectize.items.forEach(function(group) {\n data.map[group].forEach(function(key) {\n keys[key] = true;\n });\n });\n let keyArray = Object.keys(keys);\n keyArray.sort();\n lastKnownKeys = keyArray;\n ctHandle.set(keyArray);\n }\n });\n\n return {\n suspend: function() {\n ctHandle.clear();\n },\n resume: function() {\n if (lastKnownKeys)\n ctHandle.set(lastKnownKeys);\n }\n };\n }\n});\n", + "import * as input from \"./input\";\nimport { FilterHandle } from \"./filter\";\n\nlet $ = global.jQuery;\nlet strftime = global.strftime;\n\ninput.register({\n className: \"crosstalk-input-slider\",\n\n factory: function(el, data) {\n /*\n * map: {\"groupA\": [\"keyA\", \"keyB\", ...], ...}\n * group: \"ct-groupname\"\n */\n let ctHandle = new FilterHandle(data.group);\n\n let opts = {};\n let $el = $(el).find(\"input\");\n let dataType = $el.data(\"data-type\");\n let timeFormat = $el.data(\"time-format\");\n let round = $el.data(\"round\");\n let timeFormatter;\n\n // Set up formatting functions\n if (dataType === \"date\") {\n timeFormatter = strftime.utc();\n opts.prettify = function(num) {\n return timeFormatter(timeFormat, new Date(num));\n };\n\n } else if (dataType === \"datetime\") {\n let timezone = $el.data(\"timezone\");\n if (timezone)\n timeFormatter = strftime.timezone(timezone);\n else\n timeFormatter = strftime;\n\n opts.prettify = function(num) {\n return timeFormatter(timeFormat, new Date(num));\n };\n } else if (dataType === \"number\") {\n if (typeof round !== \"undefined\")\n opts.prettify = function(num) {\n let factor = Math.pow(10, round);\n return Math.round(num * factor) / factor;\n };\n }\n\n $el.ionRangeSlider(opts);\n\n function getValue() {\n let result = $el.data(\"ionRangeSlider\").result;\n\n // Function for converting numeric value from slider to appropriate type.\n let convert;\n let dataType = $el.data(\"data-type\");\n if (dataType === \"date\") {\n convert = function(val) {\n return formatDateUTC(new Date(+val));\n };\n } else if (dataType === \"datetime\") {\n convert = function(val) {\n // Convert ms to s\n return +val / 1000;\n };\n } else {\n convert = function(val) { return +val; };\n }\n\n if ($el.data(\"ionRangeSlider\").options.type === \"double\") {\n return [convert(result.from), convert(result.to)];\n } else {\n return convert(result.from);\n }\n }\n\n let lastKnownKeys = null;\n\n $el.on(\"change.crosstalkSliderInput\", function(event) {\n if (!$el.data(\"updating\") && !$el.data(\"animating\")) {\n let [from, to] = getValue();\n let keys = [];\n for (let i = 0; i < data.values.length; i++) {\n let val = data.values[i];\n if (val >= from && val <= to) {\n keys.push(data.keys[i]);\n }\n }\n keys.sort();\n ctHandle.set(keys);\n lastKnownKeys = keys;\n }\n });\n\n\n // let $el = $(el);\n // $el.on(\"change\", \"input[type=\"checkbox\"]\", function() {\n // let checked = $el.find(\"input[type=\"checkbox\"]:checked\");\n // if (checked.length === 0) {\n // ctHandle.clear();\n // } else {\n // let keys = {};\n // checked.each(function() {\n // data.map[this.value].forEach(function(key) {\n // keys[key] = true;\n // });\n // });\n // let keyArray = Object.keys(keys);\n // keyArray.sort();\n // ctHandle.set(keyArray);\n // }\n // });\n\n return {\n suspend: function() {\n ctHandle.clear();\n },\n resume: function() {\n if (lastKnownKeys)\n ctHandle.set(lastKnownKeys);\n }\n };\n }\n});\n\n\n// Convert a number to a string with leading zeros\nfunction padZeros(n, digits) {\n let str = n.toString();\n while (str.length < digits)\n str = \"0\" + str;\n return str;\n}\n\n// Given a Date object, return a string in yyyy-mm-dd format, using the\n// UTC date. This may be a day off from the date in the local time zone.\nfunction formatDateUTC(date) {\n if (date instanceof Date) {\n return date.getUTCFullYear() + \"-\" +\n padZeros(date.getUTCMonth()+1, 2) + \"-\" +\n padZeros(date.getUTCDate(), 2);\n\n } else {\n return null;\n }\n}\n", + "import Events from \"./events\";\nimport grp from \"./group\";\nimport * as util from \"./util\";\n\n/**\n * Use this class to read and write (and listen for changes to) the selection\n * for a Crosstalk group. This is intended to be used for linked brushing.\n *\n * If two (or more) `SelectionHandle` instances in the same webpage share the\n * same group name, they will share the same state. Setting the selection using\n * one `SelectionHandle` instance will result in the `value` property instantly\n * changing across the others, and `\"change\"` event listeners on all instances\n * (including the one that initiated the sending) will fire.\n *\n * @param {string} [group] - The name of the Crosstalk group, or if none,\n * null or undefined (or any other falsy value). This can be changed later\n * via the [SelectionHandle#setGroup](#setGroup) method.\n * @param {Object} [extraInfo] - An object whose properties will be copied to\n * the event object whenever an event is emitted.\n */\nexport class SelectionHandle {\n\n constructor(group = null, extraInfo = null) {\n this._eventRelay = new Events();\n this._emitter = new util.SubscriptionTracker(this._eventRelay);\n\n // Name of the group we're currently tracking, if any. Can change over time.\n this._group = null;\n // The Var we're currently tracking, if any. Can change over time.\n this._var = null;\n // The event handler subscription we currently have on var.on(\"change\").\n this._varOnChangeSub = null;\n\n this._extraInfo = util.extend({ sender: this }, extraInfo);\n\n this.setGroup(group);\n }\n\n /**\n * Changes the Crosstalk group membership of this SelectionHandle. The group\n * being switched away from (if any) will not have its selection value\n * modified as a result of calling `setGroup`, even if this handle was the\n * most recent handle to set the selection of the group.\n *\n * The group being switched to (if any) will also not have its selection value\n * modified as a result of calling `setGroup`. If you want to set the\n * selection value of the new group, call `set` explicitly.\n *\n * @param {string} group - The name of the Crosstalk group, or null (or\n * undefined) to clear the group.\n */\n setGroup(group) {\n // If group is unchanged, do nothing\n if (this._group === group)\n return;\n // Treat null, undefined, and other falsy values the same\n if (!this._group && !group)\n return;\n\n if (this._var) {\n this._var.off(\"change\", this._varOnChangeSub);\n this._var = null;\n this._varOnChangeSub = null;\n }\n\n this._group = group;\n\n if (group) {\n this._var = grp(group).var(\"selection\");\n let sub = this._var.on(\"change\", (e) => {\n this._eventRelay.trigger(\"change\", e, this);\n });\n this._varOnChangeSub = sub;\n }\n }\n\n /**\n * Retrieves the current selection for the group represented by this\n * `SelectionHandle`.\n *\n * - If no selection is active, then this value will be falsy.\n * - If a selection is active, but no data points are selected, then this\n * value will be an empty array.\n * - If a selection is active, and data points are selected, then the keys\n * of the selected data points will be present in the array.\n */\n get value() {\n return this._var ? this._var.get() : null;\n }\n\n /**\n * Combines the given `extraInfo` (if any) with the handle's default\n * `_extraInfo` (if any).\n * @private\n */\n _mergeExtraInfo(extraInfo) {\n // Important incidental effect: shallow clone is returned\n return util.extend({},\n this._extraInfo ? this._extraInfo : null,\n extraInfo ? extraInfo : null);\n }\n\n /**\n * Overwrites the current selection for the group, and raises the `\"change\"`\n * event among all of the group's '`SelectionHandle` instances (including\n * this one).\n *\n * @fires SelectionHandle#change\n * @param {string[]} selectedKeys - Falsy, empty array, or array of keys (see\n * {@link SelectionHandle#value}).\n * @param {Object} [extraInfo] - Extra properties to be included on the event\n * object that's passed to listeners (in addition to any options that were\n * passed into the `SelectionHandle` constructor).\n */\n set(selectedKeys, extraInfo) {\n if (this._var)\n this._var.set(selectedKeys, this._mergeExtraInfo(extraInfo));\n }\n\n /**\n * Overwrites the current selection for the group, and raises the `\"change\"`\n * event among all of the group's '`SelectionHandle` instances (including\n * this one).\n *\n * @fires SelectionHandle#change\n * @param {Object} [extraInfo] - Extra properties to be included on the event\n * object that's passed to listeners (in addition to any that were passed\n * into the `SelectionHandle` constructor).\n */\n clear(extraInfo) {\n if (this._var)\n this.set(void 0, this._mergeExtraInfo(extraInfo));\n }\n\n /**\n * Subscribes to events on this `SelectionHandle`.\n *\n * @param {string} eventType - Indicates the type of events to listen to.\n * Currently, only `\"change\"` is supported.\n * @param {SelectionHandle~listener} listener - The callback function that\n * will be invoked when the event occurs.\n * @return {string} - A token to pass to {@link SelectionHandle#off} to cancel\n * this subscription.\n */\n on(eventType, listener) {\n return this._emitter.on(eventType, listener);\n }\n\n /**\n * Cancels event subscriptions created by {@link SelectionHandle#on}.\n *\n * @param {string} eventType - The type of event to unsubscribe.\n * @param {string|SelectionHandle~listener} listener - Either the callback\n * function previously passed into {@link SelectionHandle#on}, or the\n * string that was returned from {@link SelectionHandle#on}.\n */\n off(eventType, listener) {\n return this._emitter.off(eventType, listener);\n }\n\n /**\n * Shuts down the `SelectionHandle` object.\n *\n * Removes all event listeners that were added through this handle.\n */\n close() {\n this._emitter.removeAllListeners();\n this.setGroup(null);\n }\n}\n\n/**\n * @callback SelectionHandle~listener\n * @param {Object} event - An object containing details of the event. For\n * `\"change\"` events, this includes the properties `value` (the new\n * value of the selection, or `undefined` if no selection is active),\n * `oldValue` (the previous value of the selection), and `sender` (the\n * `SelectionHandle` instance that made the change).\n */\n\n/**\n * @event SelectionHandle#change\n * @type {object}\n * @property {object} value - The new value of the selection, or `undefined`\n * if no selection is active.\n * @property {object} oldValue - The previous value of the selection.\n * @property {SelectionHandle} sender - The `SelectionHandle` instance that\n * changed the value.\n */\n", + "export function extend(target, ...sources) {\n for (let i = 0; i < sources.length; i++) {\n let src = sources[i];\n if (typeof(src) === \"undefined\" || src === null)\n continue;\n\n for (let key in src) {\n if (src.hasOwnProperty(key)) {\n target[key] = src[key];\n }\n }\n }\n return target;\n}\n\nexport function checkSorted(list) {\n for (let i = 1; i < list.length; i++) {\n if (list[i] <= list[i-1]) {\n throw new Error(\"List is not sorted or contains duplicate\");\n }\n }\n}\n\nexport function diffSortedLists(a, b) {\n let i_a = 0;\n let i_b = 0;\n\n if (!a) a = [];\n if (!b) b = [];\n\n let a_only = [];\n let b_only = [];\n\n checkSorted(a);\n checkSorted(b);\n\n while (i_a < a.length && i_b < b.length) {\n if (a[i_a] === b[i_b]) {\n i_a++;\n i_b++;\n } else if (a[i_a] < b[i_b]) {\n a_only.push(a[i_a++]);\n } else {\n b_only.push(b[i_b++]);\n }\n }\n\n if (i_a < a.length)\n a_only = a_only.concat(a.slice(i_a));\n if (i_b < b.length)\n b_only = b_only.concat(b.slice(i_b));\n return {\n removed: a_only,\n added: b_only\n };\n}\n\n// Convert from wide: { colA: [1,2,3], colB: [4,5,6], ... }\n// to long: [ {colA: 1, colB: 4}, {colA: 2, colB: 5}, ... ]\nexport function dataframeToD3(df) {\n let names = [];\n let length;\n for (let name in df) {\n if (df.hasOwnProperty(name))\n names.push(name);\n if (typeof(df[name]) !== \"object\" || typeof(df[name].length) === \"undefined\") {\n throw new Error(\"All fields must be arrays\");\n } else if (typeof(length) !== \"undefined\" && length !== df[name].length) {\n throw new Error(\"All fields must be arrays of the same length\");\n }\n length = df[name].length;\n }\n let results = [];\n let item;\n for (let row = 0; row < length; row++) {\n item = {};\n for (let col = 0; col < names.length; col++) {\n item[names[col]] = df[names[col]][row];\n }\n results.push(item);\n }\n return results;\n}\n\n/**\n * Keeps track of all event listener additions/removals and lets all active\n * listeners be removed with a single operation.\n *\n * @private\n */\nexport class SubscriptionTracker {\n constructor(emitter) {\n this._emitter = emitter;\n this._subs = {};\n }\n\n on(eventType, listener) {\n let sub = this._emitter.on(eventType, listener);\n this._subs[sub] = eventType;\n return sub;\n }\n\n off(eventType, listener) {\n let sub = this._emitter.off(eventType, listener);\n if (sub) {\n delete this._subs[sub];\n }\n return sub;\n }\n\n removeAllListeners() {\n let current_subs = this._subs;\n this._subs = {};\n Object.keys(current_subs).forEach((sub) => {\n this._emitter.off(current_subs[sub], sub);\n });\n }\n}\n", + "import Events from \"./events\";\n\nexport default class Var {\n constructor(group, name, /*optional*/ value) {\n this._group = group;\n this._name = name;\n this._value = value;\n this._events = new Events();\n }\n\n get() {\n return this._value;\n }\n\n set(value, /*optional*/ event) {\n if (this._value === value) {\n // Do nothing; the value hasn't changed\n return;\n }\n let oldValue = this._value;\n this._value = value;\n // Alert JavaScript listeners that the value has changed\n let evt = {};\n if (event && typeof(event) === \"object\") {\n for (let k in event) {\n if (event.hasOwnProperty(k))\n evt[k] = event[k];\n }\n }\n evt.oldValue = oldValue;\n evt.value = value;\n this._events.trigger(\"change\", evt, this);\n\n // TODO: Make this extensible, to let arbitrary back-ends know that\n // something has changed\n if (global.Shiny && global.Shiny.onInputChange) {\n global.Shiny.onInputChange(\n \".clientValue-\" +\n (this._group.name !== null ? this._group.name + \"-\" : \"\") +\n this._name,\n typeof(value) === \"undefined\" ? null : value\n );\n }\n }\n\n on(eventType, listener) {\n return this._events.on(eventType, listener);\n }\n\n off(eventType, listener) {\n return this._events.off(eventType, listener);\n }\n}\n" + ] +} \ No newline at end of file diff --git a/docs/articles/PareReportBranches_files/crosstalk-1.2.1/js/crosstalk.min.js b/docs/articles/PareReportBranches_files/crosstalk-1.2.1/js/crosstalk.min.js new file mode 100644 index 0000000..b7ec0ac --- /dev/null +++ b/docs/articles/PareReportBranches_files/crosstalk-1.2.1/js/crosstalk.min.js @@ -0,0 +1,2 @@ +!function o(u,a,l){function s(n,e){if(!a[n]){if(!u[n]){var t="function"==typeof require&&require;if(!e&&t)return t(n,!0);if(f)return f(n,!0);var r=new Error("Cannot find module '"+n+"'");throw r.code="MODULE_NOT_FOUND",r}var i=a[n]={exports:{}};u[n][0].call(i.exports,function(e){var t=u[n][1][e];return s(t||e)},i,i.exports,o,u,a,l)}return a[n].exports}for(var f="function"==typeof require&&require,e=0;e?@[\\\]^`{|}~])/g,"\\$1")+"']"),r=JSON.parse(n[0].innerText),i=e.factory(t,r);o(t).data("crosstalk-instance",i),o(t).addClass("crosstalk-input-bound")}if(t.Shiny){var e=new t.Shiny.InputBinding,u=t.jQuery;u.extend(e,{find:function(e){return u(e).find(".crosstalk-input")},initialize:function(e){var t,n;u(e).hasClass("crosstalk-input-bound")||(n=o(t=e),Object.keys(r).forEach(function(e){n.hasClass(e)&&!n.hasClass("crosstalk-input-bound")&&i(r[e],t)}))},getId:function(e){return e.id},getValue:function(e){},setValue:function(e,t){},receiveMessage:function(e,t){},subscribe:function(e,t){u(e).data("crosstalk-instance").resume()},unsubscribe:function(e){u(e).data("crosstalk-instance").suspend()}}),t.Shiny.inputBindings.register(e,"crosstalk.inputBinding")}}).call(this,"undefined"!=typeof global?global:"undefined"!=typeof self?self:"undefined"!=typeof window?window:{})},{}],7:[function(r,e,t){(function(e){"use strict";var t=function(e){{if(e&&e.__esModule)return e;var t={};if(null!=e)for(var n in e)Object.prototype.hasOwnProperty.call(e,n)&&(t[n]=e[n]);return t.default=e,t}}(r("./input")),n=r("./filter");var a=e.jQuery;t.register({className:"crosstalk-input-checkboxgroup",factory:function(e,r){var i=new n.FilterHandle(r.group),o=void 0,u=a(e);return u.on("change","input[type='checkbox']",function(){var e=u.find("input[type='checkbox']:checked");if(0===e.length)o=null,i.clear();else{var t={};e.each(function(){r.map[this.value].forEach(function(e){t[e]=!0})});var n=Object.keys(t);n.sort(),o=n,i.set(n)}}),{suspend:function(){i.clear()},resume:function(){o&&i.set(o)}}}})}).call(this,"undefined"!=typeof global?global:"undefined"!=typeof self?self:"undefined"!=typeof window?window:{})},{"./filter":2,"./input":6}],8:[function(r,e,t){(function(e){"use strict";var t=n(r("./input")),l=n(r("./util")),s=r("./filter");function n(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var n in e)Object.prototype.hasOwnProperty.call(e,n)&&(t[n]=e[n]);return t.default=e,t}var f=e.jQuery;t.register({className:"crosstalk-input-select",factory:function(e,n){var t=l.dataframeToD3(n.items),r={options:[{value:"",label:"(All)"}].concat(t),valueField:"value",labelField:"label",searchField:"label"},i=f(e).find("select")[0],o=f(i).selectize(r)[0].selectize,u=new s.FilterHandle(n.group),a=void 0;return o.on("change",function(){if(0===o.items.length)a=null,u.clear();else{var t={};o.items.forEach(function(e){n.map[e].forEach(function(e){t[e]=!0})});var e=Object.keys(t);e.sort(),a=e,u.set(e)}}),{suspend:function(){u.clear()},resume:function(){a&&u.set(a)}}}})}).call(this,"undefined"!=typeof global?global:"undefined"!=typeof self?self:"undefined"!=typeof window?window:{})},{"./filter":2,"./input":6,"./util":11}],9:[function(n,e,t){(function(e){"use strict";var d=function(e,t){if(Array.isArray(e))return e;if(Symbol.iterator in Object(e))return function(e,t){var n=[],r=!0,i=!1,o=void 0;try{for(var u,a=e[Symbol.iterator]();!(r=(u=a.next()).done)&&(n.push(u.value),!t||n.length!==t);r=!0);}catch(e){i=!0,o=e}finally{try{!r&&a.return&&a.return()}finally{if(i)throw o}}return n}(e,t);throw new TypeError("Invalid attempt to destructure non-iterable instance")},t=function(e){{if(e&&e.__esModule)return e;var t={};if(null!=e)for(var n in e)Object.prototype.hasOwnProperty.call(e,n)&&(t[n]=e[n]);return t.default=e,t}}(n("./input")),a=n("./filter");var v=e.jQuery,p=e.strftime;function y(e,t){for(var n=e.toString();n.length {\n this._eventRelay.trigger(\"change\", e, this);\n });\n this._varOnChangeSub = sub;\n }\n }\n\n /**\n * Combine the given `extraInfo` (if any) with the handle's default\n * `_extraInfo` (if any).\n * @private\n */\n _mergeExtraInfo(extraInfo) {\n return util.extend({},\n this._extraInfo ? this._extraInfo : null,\n extraInfo ? extraInfo : null);\n }\n\n /**\n * Close the handle. This clears this handle's contribution to the filter set,\n * and unsubscribes all event listeners.\n */\n close() {\n this._emitter.removeAllListeners();\n this.clear();\n this.setGroup(null);\n }\n\n /**\n * Clear this handle's contribution to the filter set.\n *\n * @param {Object} [extraInfo] - Extra properties to be included on the event\n * object that's passed to listeners (in addition to any options that were\n * passed into the `FilterHandle` constructor).\n * \n * @fires FilterHandle#change\n */\n clear(extraInfo) {\n if (!this._filterSet)\n return;\n this._filterSet.clear(this._id);\n this._onChange(extraInfo);\n }\n\n /**\n * Set this handle's contribution to the filter set. This array should consist\n * of the keys of the rows that _should_ be displayed; any keys that are not\n * present in the array will be considered _filtered out_. Note that multiple\n * `FilterHandle` instances in the group may each contribute an array of keys,\n * and only those keys that appear in _all_ of the arrays make it through the\n * filter.\n *\n * @param {string[]} keys - Empty array, or array of keys. To clear the\n * filter, don't pass an empty array; instead, use the\n * {@link FilterHandle#clear} method.\n * @param {Object} [extraInfo] - Extra properties to be included on the event\n * object that's passed to listeners (in addition to any options that were\n * passed into the `FilterHandle` constructor).\n * \n * @fires FilterHandle#change\n */\n set(keys, extraInfo) {\n if (!this._filterSet)\n return;\n this._filterSet.update(this._id, keys);\n this._onChange(extraInfo);\n }\n\n /**\n * @return {string[]|null} - Either: 1) an array of keys that made it through\n * all of the `FilterHandle` instances, or, 2) `null`, which means no filter\n * is being applied (all data should be displayed).\n */\n get filteredKeys() {\n return this._filterSet ? this._filterSet.value : null;\n }\n\n /**\n * Subscribe to events on this `FilterHandle`.\n *\n * @param {string} eventType - Indicates the type of events to listen to.\n * Currently, only `\"change\"` is supported.\n * @param {FilterHandle~listener} listener - The callback function that\n * will be invoked when the event occurs.\n * @return {string} - A token to pass to {@link FilterHandle#off} to cancel\n * this subscription.\n */\n on(eventType, listener) {\n return this._emitter.on(eventType, listener);\n }\n\n /**\n * Cancel event subscriptions created by {@link FilterHandle#on}.\n *\n * @param {string} eventType - The type of event to unsubscribe.\n * @param {string|FilterHandle~listener} listener - Either the callback\n * function previously passed into {@link FilterHandle#on}, or the\n * string that was returned from {@link FilterHandle#on}.\n */\n off(eventType, listener) {\n return this._emitter.off(eventType, listener);\n }\n\n _onChange(extraInfo) {\n if (!this._filterSet)\n return;\n this._filterVar.set(this._filterSet.value, this._mergeExtraInfo(extraInfo));\n }\n\n /**\n * @callback FilterHandle~listener\n * @param {Object} event - An object containing details of the event. For\n * `\"change\"` events, this includes the properties `value` (the new\n * value of the filter set, or `null` if no filter set is active),\n * `oldValue` (the previous value of the filter set), and `sender` (the\n * `FilterHandle` instance that made the change).\n */\n\n}\n\n/**\n * @event FilterHandle#change\n * @type {object}\n * @property {object} value - The new value of the filter set, or `null`\n * if no filter set is active.\n * @property {object} oldValue - The previous value of the filter set.\n * @property {FilterHandle} sender - The `FilterHandle` instance that\n * changed the value.\n */\n","import { diffSortedLists } from \"./util\";\n\nfunction naturalComparator(a, b) {\n if (a === b) {\n return 0;\n } else if (a < b) {\n return -1;\n } else if (a > b) {\n return 1;\n }\n}\n\n/**\n * @private\n */\nexport default class FilterSet {\n constructor() {\n this.reset();\n }\n\n reset() {\n // Key: handle ID, Value: array of selected keys, or null\n this._handles = {};\n // Key: key string, Value: count of handles that include it\n this._keys = {};\n this._value = null;\n this._activeHandles = 0;\n }\n\n get value() {\n return this._value;\n }\n\n update(handleId, keys) {\n if (keys !== null) {\n keys = keys.slice(0); // clone before sorting\n keys.sort(naturalComparator);\n }\n\n let {added, removed} = diffSortedLists(this._handles[handleId], keys);\n this._handles[handleId] = keys;\n\n for (let i = 0; i < added.length; i++) {\n this._keys[added[i]] = (this._keys[added[i]] || 0) + 1;\n }\n for (let i = 0; i < removed.length; i++) {\n this._keys[removed[i]]--;\n }\n\n this._updateValue(keys);\n }\n\n /**\n * @param {string[]} keys Sorted array of strings that indicate\n * a superset of possible keys.\n * @private\n */\n _updateValue(keys = this._allKeys) {\n let handleCount = Object.keys(this._handles).length;\n if (handleCount === 0) {\n this._value = null;\n } else {\n this._value = [];\n for (let i = 0; i < keys.length; i++) {\n let count = this._keys[keys[i]];\n if (count === handleCount) {\n this._value.push(keys[i]);\n }\n }\n }\n }\n\n clear(handleId) {\n if (typeof(this._handles[handleId]) === \"undefined\") {\n return;\n }\n\n let keys = this._handles[handleId];\n if (!keys) {\n keys = [];\n }\n\n for (let i = 0; i < keys.length; i++) {\n this._keys[keys[i]]--;\n }\n delete this._handles[handleId];\n\n this._updateValue();\n }\n\n get _allKeys() {\n let allKeys = Object.keys(this._keys);\n allKeys.sort(naturalComparator);\n return allKeys;\n }\n}\n","import Var from \"./var\";\n\n// Use a global so that multiple copies of crosstalk.js can be loaded and still\n// have groups behave as singletons across all copies.\nglobal.__crosstalk_groups = global.__crosstalk_groups || {};\nlet groups = global.__crosstalk_groups;\n\nexport default function group(groupName) {\n if (groupName && typeof(groupName) === \"string\") {\n if (!groups.hasOwnProperty(groupName)) {\n groups[groupName] = new Group(groupName);\n }\n return groups[groupName];\n } else if (typeof(groupName) === \"object\" && groupName._vars && groupName.var) {\n // Appears to already be a group object\n return groupName;\n } else if (Array.isArray(groupName) &&\n groupName.length == 1 &&\n typeof(groupName[0]) === \"string\") {\n return group(groupName[0]);\n } else {\n throw new Error(\"Invalid groupName argument\");\n }\n}\n\nclass Group {\n constructor(name) {\n this.name = name;\n this._vars = {};\n }\n\n var(name) {\n if (!name || typeof(name) !== \"string\") {\n throw new Error(\"Invalid var name\");\n }\n\n if (!this._vars.hasOwnProperty(name))\n this._vars[name] = new Var(this, name);\n return this._vars[name];\n }\n\n has(name) {\n if (!name || typeof(name) !== \"string\") {\n throw new Error(\"Invalid var name\");\n }\n\n return this._vars.hasOwnProperty(name);\n }\n}\n","import group from \"./group\";\nimport { SelectionHandle } from \"./selection\";\nimport { FilterHandle } from \"./filter\";\nimport { bind } from \"./input\";\nimport \"./input_selectize\";\nimport \"./input_checkboxgroup\";\nimport \"./input_slider\";\n\nconst defaultGroup = group(\"default\");\n\nfunction var_(name) {\n return defaultGroup.var(name);\n}\n\nfunction has(name) {\n return defaultGroup.has(name);\n}\n\nif (global.Shiny) {\n global.Shiny.addCustomMessageHandler(\"update-client-value\", function(message) {\n if (typeof(message.group) === \"string\") {\n group(message.group).var(message.name).set(message.value);\n } else {\n var_(message.name).set(message.value);\n }\n });\n}\n\nconst crosstalk = {\n group: group,\n var: var_,\n has: has,\n SelectionHandle: SelectionHandle,\n FilterHandle: FilterHandle,\n bind: bind\n};\n\n/**\n * @namespace crosstalk\n */\nexport default crosstalk;\nglobal.crosstalk = crosstalk;\n","let $ = global.jQuery;\n\nlet bindings = {};\n\nexport function register(reg) {\n bindings[reg.className] = reg;\n if (global.document && global.document.readyState !== \"complete\") {\n $(() => {\n bind();\n });\n } else if (global.document) {\n setTimeout(bind, 100);\n }\n}\n\nexport function bind() {\n Object.keys(bindings).forEach(function(className) {\n let binding = bindings[className];\n $(\".\" + binding.className).not(\".crosstalk-input-bound\").each(function(i, el) {\n bindInstance(binding, el);\n });\n });\n}\n\n// Escape jQuery identifier\nfunction $escape(val) {\n return val.replace(/([!\"#$%&'()*+,./:;<=>?@[\\\\\\]^`{|}~])/g, \"\\\\$1\");\n}\n\nfunction bindEl(el) {\n let $el = $(el);\n Object.keys(bindings).forEach(function(className) {\n if ($el.hasClass(className) && !$el.hasClass(\"crosstalk-input-bound\")) {\n let binding = bindings[className];\n bindInstance(binding, el);\n }\n });\n}\n\nfunction bindInstance(binding, el) {\n let jsonEl = $(el).find(\"script[type='application/json'][data-for='\" + $escape(el.id) + \"']\");\n let data = JSON.parse(jsonEl[0].innerText);\n\n let instance = binding.factory(el, data);\n $(el).data(\"crosstalk-instance\", instance);\n $(el).addClass(\"crosstalk-input-bound\");\n}\n\nif (global.Shiny) {\n let inputBinding = new global.Shiny.InputBinding();\n let $ = global.jQuery;\n $.extend(inputBinding, {\n find: function(scope) {\n return $(scope).find(\".crosstalk-input\");\n },\n initialize: function(el) {\n if (!$(el).hasClass(\"crosstalk-input-bound\")) {\n bindEl(el);\n }\n },\n getId: function(el) {\n return el.id;\n },\n getValue: function(el) {\n\n },\n setValue: function(el, value) {\n\n },\n receiveMessage: function(el, data) {\n\n },\n subscribe: function(el, callback) {\n $(el).data(\"crosstalk-instance\").resume();\n },\n unsubscribe: function(el) {\n $(el).data(\"crosstalk-instance\").suspend();\n }\n });\n global.Shiny.inputBindings.register(inputBinding, \"crosstalk.inputBinding\");\n}\n","import * as input from \"./input\";\nimport { FilterHandle } from \"./filter\";\n\nlet $ = global.jQuery;\n\ninput.register({\n className: \"crosstalk-input-checkboxgroup\",\n\n factory: function(el, data) {\n /*\n * map: {\"groupA\": [\"keyA\", \"keyB\", ...], ...}\n * group: \"ct-groupname\"\n */\n let ctHandle = new FilterHandle(data.group);\n\n let lastKnownKeys;\n let $el = $(el);\n $el.on(\"change\", \"input[type='checkbox']\", function() {\n let checked = $el.find(\"input[type='checkbox']:checked\");\n if (checked.length === 0) {\n lastKnownKeys = null;\n ctHandle.clear();\n } else {\n let keys = {};\n checked.each(function() {\n data.map[this.value].forEach(function(key) {\n keys[key] = true;\n });\n });\n let keyArray = Object.keys(keys);\n keyArray.sort();\n lastKnownKeys = keyArray;\n ctHandle.set(keyArray);\n }\n });\n\n return {\n suspend: function() {\n ctHandle.clear();\n },\n resume: function() {\n if (lastKnownKeys)\n ctHandle.set(lastKnownKeys);\n }\n };\n }\n});\n","import * as input from \"./input\";\nimport * as util from \"./util\";\nimport { FilterHandle } from \"./filter\";\n\nlet $ = global.jQuery;\n\ninput.register({\n className: \"crosstalk-input-select\",\n\n factory: function(el, data) {\n /*\n * items: {value: [...], label: [...]}\n * map: {\"groupA\": [\"keyA\", \"keyB\", ...], ...}\n * group: \"ct-groupname\"\n */\n\n let first = [{value: \"\", label: \"(All)\"}];\n let items = util.dataframeToD3(data.items);\n let opts = {\n options: first.concat(items),\n valueField: \"value\",\n labelField: \"label\",\n searchField: \"label\"\n };\n\n let select = $(el).find(\"select\")[0];\n\n let selectize = $(select).selectize(opts)[0].selectize;\n\n let ctHandle = new FilterHandle(data.group);\n\n let lastKnownKeys;\n selectize.on(\"change\", function() {\n if (selectize.items.length === 0) {\n lastKnownKeys = null;\n ctHandle.clear();\n } else {\n let keys = {};\n selectize.items.forEach(function(group) {\n data.map[group].forEach(function(key) {\n keys[key] = true;\n });\n });\n let keyArray = Object.keys(keys);\n keyArray.sort();\n lastKnownKeys = keyArray;\n ctHandle.set(keyArray);\n }\n });\n\n return {\n suspend: function() {\n ctHandle.clear();\n },\n resume: function() {\n if (lastKnownKeys)\n ctHandle.set(lastKnownKeys);\n }\n };\n }\n});\n","import * as input from \"./input\";\nimport { FilterHandle } from \"./filter\";\n\nlet $ = global.jQuery;\nlet strftime = global.strftime;\n\ninput.register({\n className: \"crosstalk-input-slider\",\n\n factory: function(el, data) {\n /*\n * map: {\"groupA\": [\"keyA\", \"keyB\", ...], ...}\n * group: \"ct-groupname\"\n */\n let ctHandle = new FilterHandle(data.group);\n\n let opts = {};\n let $el = $(el).find(\"input\");\n let dataType = $el.data(\"data-type\");\n let timeFormat = $el.data(\"time-format\");\n let round = $el.data(\"round\");\n let timeFormatter;\n\n // Set up formatting functions\n if (dataType === \"date\") {\n timeFormatter = strftime.utc();\n opts.prettify = function(num) {\n return timeFormatter(timeFormat, new Date(num));\n };\n\n } else if (dataType === \"datetime\") {\n let timezone = $el.data(\"timezone\");\n if (timezone)\n timeFormatter = strftime.timezone(timezone);\n else\n timeFormatter = strftime;\n\n opts.prettify = function(num) {\n return timeFormatter(timeFormat, new Date(num));\n };\n } else if (dataType === \"number\") {\n if (typeof round !== \"undefined\")\n opts.prettify = function(num) {\n let factor = Math.pow(10, round);\n return Math.round(num * factor) / factor;\n };\n }\n\n $el.ionRangeSlider(opts);\n\n function getValue() {\n let result = $el.data(\"ionRangeSlider\").result;\n\n // Function for converting numeric value from slider to appropriate type.\n let convert;\n let dataType = $el.data(\"data-type\");\n if (dataType === \"date\") {\n convert = function(val) {\n return formatDateUTC(new Date(+val));\n };\n } else if (dataType === \"datetime\") {\n convert = function(val) {\n // Convert ms to s\n return +val / 1000;\n };\n } else {\n convert = function(val) { return +val; };\n }\n\n if ($el.data(\"ionRangeSlider\").options.type === \"double\") {\n return [convert(result.from), convert(result.to)];\n } else {\n return convert(result.from);\n }\n }\n\n let lastKnownKeys = null;\n\n $el.on(\"change.crosstalkSliderInput\", function(event) {\n if (!$el.data(\"updating\") && !$el.data(\"animating\")) {\n let [from, to] = getValue();\n let keys = [];\n for (let i = 0; i < data.values.length; i++) {\n let val = data.values[i];\n if (val >= from && val <= to) {\n keys.push(data.keys[i]);\n }\n }\n keys.sort();\n ctHandle.set(keys);\n lastKnownKeys = keys;\n }\n });\n\n\n // let $el = $(el);\n // $el.on(\"change\", \"input[type=\"checkbox\"]\", function() {\n // let checked = $el.find(\"input[type=\"checkbox\"]:checked\");\n // if (checked.length === 0) {\n // ctHandle.clear();\n // } else {\n // let keys = {};\n // checked.each(function() {\n // data.map[this.value].forEach(function(key) {\n // keys[key] = true;\n // });\n // });\n // let keyArray = Object.keys(keys);\n // keyArray.sort();\n // ctHandle.set(keyArray);\n // }\n // });\n\n return {\n suspend: function() {\n ctHandle.clear();\n },\n resume: function() {\n if (lastKnownKeys)\n ctHandle.set(lastKnownKeys);\n }\n };\n }\n});\n\n\n// Convert a number to a string with leading zeros\nfunction padZeros(n, digits) {\n let str = n.toString();\n while (str.length < digits)\n str = \"0\" + str;\n return str;\n}\n\n// Given a Date object, return a string in yyyy-mm-dd format, using the\n// UTC date. This may be a day off from the date in the local time zone.\nfunction formatDateUTC(date) {\n if (date instanceof Date) {\n return date.getUTCFullYear() + \"-\" +\n padZeros(date.getUTCMonth()+1, 2) + \"-\" +\n padZeros(date.getUTCDate(), 2);\n\n } else {\n return null;\n }\n}\n","import Events from \"./events\";\nimport grp from \"./group\";\nimport * as util from \"./util\";\n\n/**\n * Use this class to read and write (and listen for changes to) the selection\n * for a Crosstalk group. This is intended to be used for linked brushing.\n *\n * If two (or more) `SelectionHandle` instances in the same webpage share the\n * same group name, they will share the same state. Setting the selection using\n * one `SelectionHandle` instance will result in the `value` property instantly\n * changing across the others, and `\"change\"` event listeners on all instances\n * (including the one that initiated the sending) will fire.\n *\n * @param {string} [group] - The name of the Crosstalk group, or if none,\n * null or undefined (or any other falsy value). This can be changed later\n * via the [SelectionHandle#setGroup](#setGroup) method.\n * @param {Object} [extraInfo] - An object whose properties will be copied to\n * the event object whenever an event is emitted.\n */\nexport class SelectionHandle {\n\n constructor(group = null, extraInfo = null) {\n this._eventRelay = new Events();\n this._emitter = new util.SubscriptionTracker(this._eventRelay);\n\n // Name of the group we're currently tracking, if any. Can change over time.\n this._group = null;\n // The Var we're currently tracking, if any. Can change over time.\n this._var = null;\n // The event handler subscription we currently have on var.on(\"change\").\n this._varOnChangeSub = null;\n\n this._extraInfo = util.extend({ sender: this }, extraInfo);\n\n this.setGroup(group);\n }\n\n /**\n * Changes the Crosstalk group membership of this SelectionHandle. The group\n * being switched away from (if any) will not have its selection value\n * modified as a result of calling `setGroup`, even if this handle was the\n * most recent handle to set the selection of the group.\n *\n * The group being switched to (if any) will also not have its selection value\n * modified as a result of calling `setGroup`. If you want to set the\n * selection value of the new group, call `set` explicitly.\n *\n * @param {string} group - The name of the Crosstalk group, or null (or\n * undefined) to clear the group.\n */\n setGroup(group) {\n // If group is unchanged, do nothing\n if (this._group === group)\n return;\n // Treat null, undefined, and other falsy values the same\n if (!this._group && !group)\n return;\n\n if (this._var) {\n this._var.off(\"change\", this._varOnChangeSub);\n this._var = null;\n this._varOnChangeSub = null;\n }\n\n this._group = group;\n\n if (group) {\n this._var = grp(group).var(\"selection\");\n let sub = this._var.on(\"change\", (e) => {\n this._eventRelay.trigger(\"change\", e, this);\n });\n this._varOnChangeSub = sub;\n }\n }\n\n /**\n * Retrieves the current selection for the group represented by this\n * `SelectionHandle`.\n *\n * - If no selection is active, then this value will be falsy.\n * - If a selection is active, but no data points are selected, then this\n * value will be an empty array.\n * - If a selection is active, and data points are selected, then the keys\n * of the selected data points will be present in the array.\n */\n get value() {\n return this._var ? this._var.get() : null;\n }\n\n /**\n * Combines the given `extraInfo` (if any) with the handle's default\n * `_extraInfo` (if any).\n * @private\n */\n _mergeExtraInfo(extraInfo) {\n // Important incidental effect: shallow clone is returned\n return util.extend({},\n this._extraInfo ? this._extraInfo : null,\n extraInfo ? extraInfo : null);\n }\n\n /**\n * Overwrites the current selection for the group, and raises the `\"change\"`\n * event among all of the group's '`SelectionHandle` instances (including\n * this one).\n *\n * @fires SelectionHandle#change\n * @param {string[]} selectedKeys - Falsy, empty array, or array of keys (see\n * {@link SelectionHandle#value}).\n * @param {Object} [extraInfo] - Extra properties to be included on the event\n * object that's passed to listeners (in addition to any options that were\n * passed into the `SelectionHandle` constructor).\n */\n set(selectedKeys, extraInfo) {\n if (this._var)\n this._var.set(selectedKeys, this._mergeExtraInfo(extraInfo));\n }\n\n /**\n * Overwrites the current selection for the group, and raises the `\"change\"`\n * event among all of the group's '`SelectionHandle` instances (including\n * this one).\n *\n * @fires SelectionHandle#change\n * @param {Object} [extraInfo] - Extra properties to be included on the event\n * object that's passed to listeners (in addition to any that were passed\n * into the `SelectionHandle` constructor).\n */\n clear(extraInfo) {\n if (this._var)\n this.set(void 0, this._mergeExtraInfo(extraInfo));\n }\n\n /**\n * Subscribes to events on this `SelectionHandle`.\n *\n * @param {string} eventType - Indicates the type of events to listen to.\n * Currently, only `\"change\"` is supported.\n * @param {SelectionHandle~listener} listener - The callback function that\n * will be invoked when the event occurs.\n * @return {string} - A token to pass to {@link SelectionHandle#off} to cancel\n * this subscription.\n */\n on(eventType, listener) {\n return this._emitter.on(eventType, listener);\n }\n\n /**\n * Cancels event subscriptions created by {@link SelectionHandle#on}.\n *\n * @param {string} eventType - The type of event to unsubscribe.\n * @param {string|SelectionHandle~listener} listener - Either the callback\n * function previously passed into {@link SelectionHandle#on}, or the\n * string that was returned from {@link SelectionHandle#on}.\n */\n off(eventType, listener) {\n return this._emitter.off(eventType, listener);\n }\n\n /**\n * Shuts down the `SelectionHandle` object.\n *\n * Removes all event listeners that were added through this handle.\n */\n close() {\n this._emitter.removeAllListeners();\n this.setGroup(null);\n }\n}\n\n/**\n * @callback SelectionHandle~listener\n * @param {Object} event - An object containing details of the event. For\n * `\"change\"` events, this includes the properties `value` (the new\n * value of the selection, or `undefined` if no selection is active),\n * `oldValue` (the previous value of the selection), and `sender` (the\n * `SelectionHandle` instance that made the change).\n */\n\n/**\n * @event SelectionHandle#change\n * @type {object}\n * @property {object} value - The new value of the selection, or `undefined`\n * if no selection is active.\n * @property {object} oldValue - The previous value of the selection.\n * @property {SelectionHandle} sender - The `SelectionHandle` instance that\n * changed the value.\n */\n","export function extend(target, ...sources) {\n for (let i = 0; i < sources.length; i++) {\n let src = sources[i];\n if (typeof(src) === \"undefined\" || src === null)\n continue;\n\n for (let key in src) {\n if (src.hasOwnProperty(key)) {\n target[key] = src[key];\n }\n }\n }\n return target;\n}\n\nexport function checkSorted(list) {\n for (let i = 1; i < list.length; i++) {\n if (list[i] <= list[i-1]) {\n throw new Error(\"List is not sorted or contains duplicate\");\n }\n }\n}\n\nexport function diffSortedLists(a, b) {\n let i_a = 0;\n let i_b = 0;\n\n if (!a) a = [];\n if (!b) b = [];\n\n let a_only = [];\n let b_only = [];\n\n checkSorted(a);\n checkSorted(b);\n\n while (i_a < a.length && i_b < b.length) {\n if (a[i_a] === b[i_b]) {\n i_a++;\n i_b++;\n } else if (a[i_a] < b[i_b]) {\n a_only.push(a[i_a++]);\n } else {\n b_only.push(b[i_b++]);\n }\n }\n\n if (i_a < a.length)\n a_only = a_only.concat(a.slice(i_a));\n if (i_b < b.length)\n b_only = b_only.concat(b.slice(i_b));\n return {\n removed: a_only,\n added: b_only\n };\n}\n\n// Convert from wide: { colA: [1,2,3], colB: [4,5,6], ... }\n// to long: [ {colA: 1, colB: 4}, {colA: 2, colB: 5}, ... ]\nexport function dataframeToD3(df) {\n let names = [];\n let length;\n for (let name in df) {\n if (df.hasOwnProperty(name))\n names.push(name);\n if (typeof(df[name]) !== \"object\" || typeof(df[name].length) === \"undefined\") {\n throw new Error(\"All fields must be arrays\");\n } else if (typeof(length) !== \"undefined\" && length !== df[name].length) {\n throw new Error(\"All fields must be arrays of the same length\");\n }\n length = df[name].length;\n }\n let results = [];\n let item;\n for (let row = 0; row < length; row++) {\n item = {};\n for (let col = 0; col < names.length; col++) {\n item[names[col]] = df[names[col]][row];\n }\n results.push(item);\n }\n return results;\n}\n\n/**\n * Keeps track of all event listener additions/removals and lets all active\n * listeners be removed with a single operation.\n *\n * @private\n */\nexport class SubscriptionTracker {\n constructor(emitter) {\n this._emitter = emitter;\n this._subs = {};\n }\n\n on(eventType, listener) {\n let sub = this._emitter.on(eventType, listener);\n this._subs[sub] = eventType;\n return sub;\n }\n\n off(eventType, listener) {\n let sub = this._emitter.off(eventType, listener);\n if (sub) {\n delete this._subs[sub];\n }\n return sub;\n }\n\n removeAllListeners() {\n let current_subs = this._subs;\n this._subs = {};\n Object.keys(current_subs).forEach((sub) => {\n this._emitter.off(current_subs[sub], sub);\n });\n }\n}\n","import Events from \"./events\";\n\nexport default class Var {\n constructor(group, name, /*optional*/ value) {\n this._group = group;\n this._name = name;\n this._value = value;\n this._events = new Events();\n }\n\n get() {\n return this._value;\n }\n\n set(value, /*optional*/ event) {\n if (this._value === value) {\n // Do nothing; the value hasn't changed\n return;\n }\n let oldValue = this._value;\n this._value = value;\n // Alert JavaScript listeners that the value has changed\n let evt = {};\n if (event && typeof(event) === \"object\") {\n for (let k in event) {\n if (event.hasOwnProperty(k))\n evt[k] = event[k];\n }\n }\n evt.oldValue = oldValue;\n evt.value = value;\n this._events.trigger(\"change\", evt, this);\n\n // TODO: Make this extensible, to let arbitrary back-ends know that\n // something has changed\n if (global.Shiny && global.Shiny.onInputChange) {\n global.Shiny.onInputChange(\n \".clientValue-\" +\n (this._group.name !== null ? this._group.name + \"-\" : \"\") +\n this._name,\n typeof(value) === \"undefined\" ? null : value\n );\n }\n }\n\n on(eventType, listener) {\n return this._events.on(eventType, listener);\n }\n\n off(eventType, listener) {\n return this._events.off(eventType, listener);\n }\n}\n"]} \ No newline at end of file diff --git a/docs/articles/PareReportBranches_files/crosstalk-1.2.1/scss/crosstalk.scss b/docs/articles/PareReportBranches_files/crosstalk-1.2.1/scss/crosstalk.scss new file mode 100644 index 0000000..3566561 --- /dev/null +++ b/docs/articles/PareReportBranches_files/crosstalk-1.2.1/scss/crosstalk.scss @@ -0,0 +1,75 @@ +/* Adjust margins outwards, so column contents line up with the edges of the + parent of container-fluid. */ +.container-fluid.crosstalk-bscols { + margin-left: -30px; + margin-right: -30px; + white-space: normal; +} + +/* But don't adjust the margins outwards if we're directly under the body, + i.e. we were the top-level of something at the console. */ +body > .container-fluid.crosstalk-bscols { + margin-left: auto; + margin-right: auto; +} + +.crosstalk-input-checkboxgroup .crosstalk-options-group .crosstalk-options-column { + display: inline-block; + padding-right: 12px; + vertical-align: top; +} + +@media only screen and (max-width:480px) { + .crosstalk-input-checkboxgroup .crosstalk-options-group .crosstalk-options-column { + display: block; + padding-right: inherit; + } +} + +/* Relevant BS3 styles to make filter_checkbox() look reasonable without Bootstrap */ +.crosstalk-input { + margin-bottom: 15px; /* a la .form-group */ + .control-label { + margin-bottom: 0; + vertical-align: middle; + } + input[type="checkbox"] { + margin: 4px 0 0; + margin-top: 1px; + line-height: normal; + } + .checkbox { + position: relative; + display: block; + margin-top: 10px; + margin-bottom: 10px; + } + .checkbox > label{ + padding-left: 20px; + margin-bottom: 0; + font-weight: 400; + cursor: pointer; + } + .checkbox input[type="checkbox"], + .checkbox-inline input[type="checkbox"] { + position: absolute; + margin-top: 2px; + margin-left: -20px; + } + .checkbox + .checkbox { + margin-top: -5px; + } + .checkbox-inline { + position: relative; + display: inline-block; + padding-left: 20px; + margin-bottom: 0; + font-weight: 400; + vertical-align: middle; + cursor: pointer; + } + .checkbox-inline + .checkbox-inline { + margin-top: 0; + margin-left: 10px; + } +} diff --git a/docs/articles/PareReportBranches_files/datatables-binding-0.33/datatables.js b/docs/articles/PareReportBranches_files/datatables-binding-0.33/datatables.js new file mode 100644 index 0000000..765b53c --- /dev/null +++ b/docs/articles/PareReportBranches_files/datatables-binding-0.33/datatables.js @@ -0,0 +1,1539 @@ +(function() { + +// some helper functions: using a global object DTWidget so that it can be used +// in JS() code, e.g. datatable(options = list(foo = JS('code'))); unlike R's +// dynamic scoping, when 'code' is eval'ed, JavaScript does not know objects +// from the "parent frame", e.g. JS('DTWidget') will not work unless it was made +// a global object +var DTWidget = {}; + +// 123456666.7890 -> 123,456,666.7890 +var markInterval = function(d, digits, interval, mark, decMark, precision) { + x = precision ? d.toPrecision(digits) : d.toFixed(digits); + if (!/^-?[\d.]+$/.test(x)) return x; + var xv = x.split('.'); + if (xv.length > 2) return x; // should have at most one decimal point + xv[0] = xv[0].replace(new RegExp('\\B(?=(\\d{' + interval + '})+(?!\\d))', 'g'), mark); + return xv.join(decMark); +}; + +DTWidget.formatCurrency = function(data, currency, digits, interval, mark, decMark, before, zeroPrint) { + var d = parseFloat(data); + if (isNaN(d)) return ''; + if (zeroPrint !== null && d === 0.0) return zeroPrint; + var res = markInterval(d, digits, interval, mark, decMark); + res = before ? (/^-/.test(res) ? '-' + currency + res.replace(/^-/, '') : currency + res) : + res + currency; + return res; +}; + +DTWidget.formatString = function(data, prefix, suffix) { + var d = data; + if (d === null) return ''; + return prefix + d + suffix; +}; + +DTWidget.formatPercentage = function(data, digits, interval, mark, decMark, zeroPrint) { + var d = parseFloat(data); + if (isNaN(d)) return ''; + if (zeroPrint !== null && d === 0.0) return zeroPrint; + return markInterval(d * 100, digits, interval, mark, decMark) + '%'; +}; + +DTWidget.formatRound = function(data, digits, interval, mark, decMark, zeroPrint) { + var d = parseFloat(data); + if (isNaN(d)) return ''; + if (zeroPrint !== null && d === 0.0) return zeroPrint; + return markInterval(d, digits, interval, mark, decMark); +}; + +DTWidget.formatSignif = function(data, digits, interval, mark, decMark, zeroPrint) { + var d = parseFloat(data); + if (isNaN(d)) return ''; + if (zeroPrint !== null && d === 0.0) return zeroPrint; + return markInterval(d, digits, interval, mark, decMark, true); +}; + +DTWidget.formatDate = function(data, method, params) { + var d = data; + if (d === null) return ''; + // (new Date('2015-10-28')).toDateString() may return 2015-10-27 because the + // actual time created could be like 'Tue Oct 27 2015 19:00:00 GMT-0500 (CDT)', + // i.e. the date-only string is treated as UTC time instead of local time + if ((method === 'toDateString' || method === 'toLocaleDateString') && /^\d{4,}\D\d{2}\D\d{2}$/.test(d)) { + d = d.split(/\D/); + d = new Date(d[0], d[1] - 1, d[2]); + } else { + d = new Date(d); + } + return d[method].apply(d, params); +}; + +window.DTWidget = DTWidget; + +// A helper function to update the properties of existing filters +var setFilterProps = function(td, props) { + // Update enabled/disabled state + var $input = $(td).find('input').first(); + var searchable = $input.data('searchable'); + $input.prop('disabled', !searchable || props.disabled); + + // Based on the filter type, set its new values + var type = td.getAttribute('data-type'); + if (['factor', 'logical'].includes(type)) { + // Reformat the new dropdown options for use with selectize + var new_vals = props.params.options.map(function(item) { + return { text: item, value: item }; + }); + + // Find the selectize object + var dropdown = $(td).find('.selectized').eq(0)[0].selectize; + + // Note the current values + var old_vals = dropdown.getValue(); + + // Remove the existing values + dropdown.clearOptions(); + + // Add the new options + dropdown.addOption(new_vals); + + // Preserve the existing values + dropdown.setValue(old_vals); + + } else if (['number', 'integer', 'date', 'time'].includes(type)) { + // Apply internal scaling to new limits. Updating scale not yet implemented. + var slider = $(td).find('.noUi-target').eq(0); + var scale = Math.pow(10, Math.max(0, +slider.data('scale') || 0)); + var new_vals = [props.params.min * scale, props.params.max * scale]; + + // Note what the new limits will be just for this filter + var new_lims = new_vals.slice(); + + // Determine the current values and limits + var old_vals = slider.val().map(Number); + var old_lims = slider.noUiSlider('options').range; + old_lims = [old_lims.min, old_lims.max]; + + // Preserve the current values if filters have been applied; otherwise, apply no filtering + if (old_vals[0] != old_lims[0]) { + new_vals[0] = Math.max(old_vals[0], new_vals[0]); + } + + if (old_vals[1] != old_lims[1]) { + new_vals[1] = Math.min(old_vals[1], new_vals[1]); + } + + // Update the endpoints of the slider + slider.noUiSlider({ + start: new_vals, + range: {'min': new_lims[0], 'max': new_lims[1]} + }, true); + } +}; + +var transposeArray2D = function(a) { + return a.length === 0 ? a : HTMLWidgets.transposeArray2D(a); +}; + +var crosstalkPluginsInstalled = false; + +function maybeInstallCrosstalkPlugins() { + if (crosstalkPluginsInstalled) + return; + crosstalkPluginsInstalled = true; + + $.fn.dataTable.ext.afnFiltering.push( + function(oSettings, aData, iDataIndex) { + var ctfilter = oSettings.nTable.ctfilter; + if (ctfilter && !ctfilter[iDataIndex]) + return false; + + var ctselect = oSettings.nTable.ctselect; + if (ctselect && !ctselect[iDataIndex]) + return false; + + return true; + } + ); +} + +HTMLWidgets.widget({ + name: "datatables", + type: "output", + renderOnNullValue: true, + initialize: function(el, width, height) { + // in order that the type=number inputs return a number + $.valHooks.number = { + get: function(el) { + var value = parseFloat(el.value); + return isNaN(value) ? "" : value; + } + }; + $(el).html(' '); + return { + data: null, + ctfilterHandle: new crosstalk.FilterHandle(), + ctfilterSubscription: null, + ctselectHandle: new crosstalk.SelectionHandle(), + ctselectSubscription: null + }; + }, + renderValue: function(el, data, instance) { + if (el.offsetWidth === 0 || el.offsetHeight === 0) { + instance.data = data; + return; + } + instance.data = null; + var $el = $(el); + $el.empty(); + + if (data === null) { + $el.append(' '); + // clear previous Shiny inputs (if any) + for (var i in instance.clearInputs) instance.clearInputs[i](); + instance.clearInputs = {}; + return; + } + + var crosstalkOptions = data.crosstalkOptions; + if (!crosstalkOptions) crosstalkOptions = { + 'key': null, 'group': null + }; + if (crosstalkOptions.group) { + maybeInstallCrosstalkPlugins(); + instance.ctfilterHandle.setGroup(crosstalkOptions.group); + instance.ctselectHandle.setGroup(crosstalkOptions.group); + } + + // if we are in the viewer then we always want to fillContainer and + // and autoHideNavigation (unless the user has explicitly set these) + if (window.HTMLWidgets.viewerMode) { + if (!data.hasOwnProperty("fillContainer")) + data.fillContainer = true; + if (!data.hasOwnProperty("autoHideNavigation")) + data.autoHideNavigation = true; + } + + // propagate fillContainer to instance (so we have it in resize) + instance.fillContainer = data.fillContainer; + + var cells = data.data; + + if (cells instanceof Array) cells = transposeArray2D(cells); + + $el.append(data.container); + var $table = $el.find('table'); + if (data.class) $table.addClass(data.class); + if (data.caption) $table.prepend(data.caption); + + if (!data.selection) data.selection = { + mode: 'none', selected: null, target: 'row', selectable: null + }; + if (HTMLWidgets.shinyMode && data.selection.mode !== 'none' && + data.selection.target === 'row+column') { + if ($table.children('tfoot').length === 0) { + $table.append($('')); + $table.find('thead tr').clone().appendTo($table.find('tfoot')); + } + } + + // column filters + var filterRow; + switch (data.filter) { + case 'top': + $table.children('thead').append(data.filterHTML); + filterRow = $table.find('thead tr:last td'); + break; + case 'bottom': + if ($table.children('tfoot').length === 0) { + $table.append($('')); + } + $table.children('tfoot').prepend(data.filterHTML); + filterRow = $table.find('tfoot tr:first td'); + break; + } + + var options = { searchDelay: 1000 }; + if (cells !== null) $.extend(options, { + data: cells + }); + + // options for fillContainer + var bootstrapActive = typeof($.fn.popover) != 'undefined'; + if (instance.fillContainer) { + + // force scrollX/scrollY and turn off autoWidth + options.scrollX = true; + options.scrollY = "100px"; // can be any value, we'll adjust below + + // if we aren't paginating then move around the info/filter controls + // to save space at the bottom and rephrase the info callback + if (data.options.paging === false) { + + // we know how to do this cleanly for bootstrap, not so much + // for other themes/layouts + if (bootstrapActive) { + options.dom = "<'row'<'col-sm-4'i><'col-sm-8'f>>" + + "<'row'<'col-sm-12'tr>>"; + } + + options.fnInfoCallback = function(oSettings, iStart, iEnd, + iMax, iTotal, sPre) { + return Number(iTotal).toLocaleString() + " records"; + }; + } + } + + // auto hide navigation if requested + // Note, this only works on client-side processing mode as on server-side, + // cells (data.data) is null; In addition, we require the pageLength option + // being provided explicitly to enable this. Despite we may be able to deduce + // the default value of pageLength, it may complicate things so we'd rather + // put this responsiblity to users and warn them on the R side. + if (data.autoHideNavigation === true && data.options.paging !== false) { + // strip all nav if length >= cells + if ((cells instanceof Array) && data.options.pageLength >= cells.length) + options.dom = bootstrapActive ? "<'row'<'col-sm-12'tr>>" : "t"; + // alternatively lean things out for flexdashboard mobile portrait + else if (bootstrapActive && window.FlexDashboard && window.FlexDashboard.isMobilePhone()) + options.dom = "<'row'<'col-sm-12'f>>" + + "<'row'<'col-sm-12'tr>>" + + "<'row'<'col-sm-12'p>>"; + } + + $.extend(true, options, data.options || {}); + + var searchCols = options.searchCols; + if (searchCols) { + searchCols = searchCols.map(function(x) { + return x === null ? '' : x.search; + }); + // FIXME: this means I don't respect the escapeRegex setting + delete options.searchCols; + } + + // server-side processing? + var server = options.serverSide === true; + + // use the dataSrc function to pre-process JSON data returned from R + var DT_rows_all = [], DT_rows_current = []; + if (server && HTMLWidgets.shinyMode && typeof options.ajax === 'object' && + /^session\/[\da-z]+\/dataobj/.test(options.ajax.url) && !options.ajax.dataSrc) { + options.ajax.dataSrc = function(json) { + DT_rows_all = $.makeArray(json.DT_rows_all); + DT_rows_current = $.makeArray(json.DT_rows_current); + var data = json.data; + if (!colReorderEnabled()) return data; + var table = $table.DataTable(), order = table.colReorder.order(), flag = true, i, j, row; + for (i = 0; i < order.length; ++i) if (order[i] !== i) flag = false; + if (flag) return data; + for (i = 0; i < data.length; ++i) { + row = data[i].slice(); + for (j = 0; j < order.length; ++j) data[i][j] = row[order[j]]; + } + return data; + }; + } + + var thiz = this; + if (instance.fillContainer) $table.on('init.dt', function(e) { + thiz.fillAvailableHeight(el, $(el).innerHeight()); + }); + // If the page contains serveral datatables and one of which enables colReorder, + // the table.colReorder.order() function will exist but throws error when called. + // So it seems like the only way to know if colReorder is enabled or not is to + // check the options. + var colReorderEnabled = function() { return "colReorder" in options; }; + var table = $table.DataTable(options); + $el.data('datatable', table); + + if ('rowGroup' in options) { + // Maintain RowGroup dataSrc when columns are reordered (#1109) + table.on('column-reorder', function(e, settings, details) { + var oldDataSrc = table.rowGroup().dataSrc(); + var newDataSrc = details.mapping[oldDataSrc]; + table.rowGroup().dataSrc(newDataSrc); + }); + } + + // Unregister previous Crosstalk event subscriptions, if they exist + if (instance.ctfilterSubscription) { + instance.ctfilterHandle.off("change", instance.ctfilterSubscription); + instance.ctfilterSubscription = null; + } + if (instance.ctselectSubscription) { + instance.ctselectHandle.off("change", instance.ctselectSubscription); + instance.ctselectSubscription = null; + } + + if (!crosstalkOptions.group) { + $table[0].ctfilter = null; + $table[0].ctselect = null; + } else { + var key = crosstalkOptions.key; + function keysToMatches(keys) { + if (!keys) { + return null; + } else { + var selectedKeys = {}; + for (var i = 0; i < keys.length; i++) { + selectedKeys[keys[i]] = true; + } + var matches = {}; + for (var j = 0; j < key.length; j++) { + if (selectedKeys[key[j]]) + matches[j] = true; + } + return matches; + } + } + + function applyCrosstalkFilter(e) { + $table[0].ctfilter = keysToMatches(e.value); + table.draw(); + } + instance.ctfilterSubscription = instance.ctfilterHandle.on("change", applyCrosstalkFilter); + applyCrosstalkFilter({value: instance.ctfilterHandle.filteredKeys}); + + function applyCrosstalkSelection(e) { + if (e.sender !== instance.ctselectHandle) { + table + .rows('.' + selClass, {search: 'applied'}) + .nodes() + .to$() + .removeClass(selClass); + if (selectedRows) + changeInput('rows_selected', selectedRows(), void 0, true); + } + + if (e.sender !== instance.ctselectHandle && e.value && e.value.length) { + var matches = keysToMatches(e.value); + + // persistent selection with plotly (& leaflet) + var ctOpts = crosstalk.var("plotlyCrosstalkOpts").get() || {}; + if (ctOpts.persistent === true) { + var matches = $.extend(matches, $table[0].ctselect); + } + + $table[0].ctselect = matches; + table.draw(); + } else { + if ($table[0].ctselect) { + $table[0].ctselect = null; + table.draw(); + } + } + } + instance.ctselectSubscription = instance.ctselectHandle.on("change", applyCrosstalkSelection); + // TODO: This next line doesn't seem to work when renderDataTable is used + applyCrosstalkSelection({value: instance.ctselectHandle.value}); + } + + var inArray = function(val, array) { + return $.inArray(val, $.makeArray(array)) > -1; + }; + + // search the i-th column + var searchColumn = function(i, value) { + var regex = false, ci = true; + if (options.search) { + regex = options.search.regex, + ci = options.search.caseInsensitive !== false; + } + // need to transpose the column index when colReorder is enabled + if (table.colReorder) i = table.colReorder.transpose(i); + return table.column(i).search(value, regex, !regex, ci); + }; + + if (data.filter !== 'none') { + if (!data.hasOwnProperty('filterSettings')) data.filterSettings = {}; + + filterRow.each(function(i, td) { + + var $td = $(td), type = $td.data('type'), filter; + var $input = $td.children('div').first().children('input'); + var disabled = $input.prop('disabled'); + var searchable = table.settings()[0].aoColumns[i].bSearchable; + $input.prop('disabled', !searchable || disabled); + $input.data('searchable', searchable); // for updating later + $input.on('input blur', function() { + $input.next('span').toggle(Boolean($input.val())); + }); + // Bootstrap sets pointer-events to none and we won't be able to click + // the clear button + $input.next('span').css('pointer-events', 'auto').hide().click(function() { + $(this).hide().prev('input').val('').trigger('input').focus(); + }); + var searchCol; // search string for this column + if (searchCols && searchCols[i]) { + searchCol = searchCols[i]; + $input.val(searchCol).trigger('input'); + } + var $x = $td.children('div').last(); + + // remove the overflow: hidden attribute of the scrollHead + // (otherwise the scrolling table body obscures the filters) + // The workaround and the discussion from + // https://github.com/rstudio/DT/issues/554#issuecomment-518007347 + // Otherwise the filter selection will not be anchored to the values + // when the columns number is many and scrollX is enabled. + var scrollHead = $(el).find('.dataTables_scrollHead,.dataTables_scrollFoot'); + var cssOverflowHead = scrollHead.css('overflow'); + var scrollBody = $(el).find('.dataTables_scrollBody'); + var cssOverflowBody = scrollBody.css('overflow'); + var scrollTable = $(el).find('.dataTables_scroll'); + var cssOverflowTable = scrollTable.css('overflow'); + if (cssOverflowHead === 'hidden') { + $x.on('show hide', function(e) { + if (e.type === 'show') { + scrollHead.css('overflow', 'visible'); + scrollBody.css('overflow', 'visible'); + scrollTable.css('overflow-x', 'scroll'); + } else { + scrollHead.css('overflow', cssOverflowHead); + scrollBody.css('overflow', cssOverflowBody); + scrollTable.css('overflow-x', cssOverflowTable); + } + }); + $x.css('z-index', 25); + } + + if (inArray(type, ['factor', 'logical'])) { + $input.on({ + click: function() { + $input.parent().hide(); $x.show().trigger('show'); filter[0].selectize.focus(); + }, + input: function() { + var v1 = JSON.stringify(filter[0].selectize.getValue()), v2 = $input.val(); + if (v1 === '[]') v1 = ''; + if (v1 !== v2) filter[0].selectize.setValue(v2 === '' ? [] : JSON.parse(v2)); + } + }); + var $input2 = $x.children('select'); + filter = $input2.selectize($.extend({ + options: $input2.data('options').map(function(v, i) { + return ({text: v, value: v}); + }), + plugins: ['remove_button'], + hideSelected: true, + onChange: function(value) { + if (value === null) value = []; // compatibility with jQuery 3.0 + $input.val(value.length ? JSON.stringify(value) : ''); + if (value.length) $input.trigger('input'); + $input.attr('title', $input.val()); + if (server) { + searchColumn(i, value.length ? JSON.stringify(value) : '').draw(); + return; + } + // turn off filter if nothing selected + $td.data('filter', value.length > 0); + table.draw(); // redraw table, and filters will be applied + } + }, data.filterSettings.select)); + filter[0].selectize.on('blur', function() { + $x.hide().trigger('hide'); $input.parent().show(); $input.trigger('blur'); + }); + filter.next('div').css('margin-bottom', 'auto'); + } else if (type === 'character') { + var fun = function() { + searchColumn(i, $input.val()).draw(); + }; + // throttle searching for server-side processing + var throttledFun = $.fn.dataTable.util.throttle(fun, options.searchDelay); + $input.on('input', function(e, immediate) { + // always bypass throttling when immediate = true (via the updateSearch method) + (immediate || !server) ? fun() : throttledFun(); + }); + } else if (inArray(type, ['number', 'integer', 'date', 'time'])) { + var $x0 = $x; + $x = $x0.children('div').first(); + $x0.css({ + 'background-color': '#fff', + 'border': '1px #ddd solid', + 'border-radius': '4px', + 'padding': data.vertical ? '35px 20px': '20px 20px 10px 20px' + }); + var $spans = $x0.children('span').css({ + 'margin-top': data.vertical ? '0' : '10px', + 'white-space': 'nowrap' + }); + var $span1 = $spans.first(), $span2 = $spans.last(); + var r1 = +$x.data('min'), r2 = +$x.data('max'); + // when the numbers are too small or have many decimal places, the + // slider may have numeric precision problems (#150) + var scale = Math.pow(10, Math.max(0, +$x.data('scale') || 0)); + r1 = Math.round(r1 * scale); r2 = Math.round(r2 * scale); + var scaleBack = function(x, scale) { + if (scale === 1) return x; + var d = Math.round(Math.log(scale) / Math.log(10)); + // to avoid problems like 3.423/100 -> 0.034230000000000003 + return (x / scale).toFixed(d); + }; + var slider_min = function() { + return filter.noUiSlider('options').range.min; + }; + var slider_max = function() { + return filter.noUiSlider('options').range.max; + }; + $input.on({ + focus: function() { + $x0.show().trigger('show'); + // first, make sure the slider div leaves at least 20px between + // the two (slider value) span's + $x0.width(Math.max(160, $span1.outerWidth() + $span2.outerWidth() + 20)); + // then, if the input is really wide or slider is vertical, + // make the slider the same width as the input + if ($x0.outerWidth() < $input.outerWidth() || data.vertical) { + $x0.outerWidth($input.outerWidth()); + } + // make sure the slider div does not reach beyond the right margin + if ($(window).width() < $x0.offset().left + $x0.width()) { + $x0.offset({ + 'left': $input.offset().left + $input.outerWidth() - $x0.outerWidth() + }); + } + }, + blur: function() { + $x0.hide().trigger('hide'); + }, + input: function() { + if ($input.val() === '') filter.val([slider_min(), slider_max()]); + }, + change: function() { + var v = $input.val().replace(/\s/g, ''); + if (v === '') return; + v = v.split('...'); + if (v.length !== 2) { + $input.parent().addClass('has-error'); + return; + } + if (v[0] === '') v[0] = slider_min(); + if (v[1] === '') v[1] = slider_max(); + $input.parent().removeClass('has-error'); + // treat date as UTC time at midnight + var strTime = function(x) { + var s = type === 'date' ? 'T00:00:00Z' : ''; + var t = new Date(x + s).getTime(); + // add 10 minutes to date since it does not hurt the date, and + // it helps avoid the tricky floating point arithmetic problems, + // e.g. sometimes the date may be a few milliseconds earlier + // than the midnight due to precision problems in noUiSlider + return type === 'date' ? t + 3600000 : t; + }; + if (inArray(type, ['date', 'time'])) { + v[0] = strTime(v[0]); + v[1] = strTime(v[1]); + } + if (v[0] != slider_min()) v[0] *= scale; + if (v[1] != slider_max()) v[1] *= scale; + filter.val(v); + } + }); + var formatDate = function(d) { + d = scaleBack(d, scale); + if (type === 'number') return d; + if (type === 'integer') return parseInt(d); + var x = new Date(+d); + if (type === 'date') { + var pad0 = function(x) { + return ('0' + x).substr(-2, 2); + }; + return x.getUTCFullYear() + '-' + pad0(1 + x.getUTCMonth()) + + '-' + pad0(x.getUTCDate()); + } else { + return x.toISOString(); + } + }; + var opts = type === 'date' ? { step: 60 * 60 * 1000 } : + type === 'integer' ? { step: 1 } : {}; + + opts.orientation = data.vertical ? 'vertical': 'horizontal'; + opts.direction = data.vertical ? 'rtl': 'ltr'; + + filter = $x.noUiSlider($.extend({ + start: [r1, r2], + range: {min: r1, max: r2}, + connect: true + }, opts, data.filterSettings.slider)); + if (scale > 1) (function() { + var t1 = r1, t2 = r2; + var val = filter.val(); + while (val[0] > r1 || val[1] < r2) { + if (val[0] > r1) { + t1 -= val[0] - r1; + } + if (val[1] < r2) { + t2 += r2 - val[1]; + } + filter = $x.noUiSlider($.extend({ + start: [t1, t2], + range: {min: t1, max: t2}, + connect: true + }, opts, data.filterSettings.slider), true); + val = filter.val(); + } + r1 = t1; r2 = t2; + })(); + // format with active column renderer, if defined + var colDef = data.options.columnDefs.find(function(def) { + return (def.targets === i || inArray(i, def.targets)) && 'render' in def; + }); + var updateSliderText = function(v1, v2) { + // we only know how to use function renderers + if (colDef && typeof colDef.render === 'function') { + var restore = function(v) { + v = scaleBack(v, scale); + return inArray(type, ['date', 'time']) ? new Date(+v) : v; + } + $span1.text(colDef.render(restore(v1), 'display')); + $span2.text(colDef.render(restore(v2), 'display')); + } else { + $span1.text(formatDate(v1)); + $span2.text(formatDate(v2)); + } + }; + updateSliderText(r1, r2); + var updateSlider = function(e) { + var val = filter.val(); + // turn off filter if in full range + $td.data('filter', val[0] > slider_min() || val[1] < slider_max()); + var v1 = formatDate(val[0]), v2 = formatDate(val[1]), ival; + if ($td.data('filter')) { + ival = v1 + ' ... ' + v2; + $input.attr('title', ival).val(ival).trigger('input'); + } else { + $input.attr('title', '').val(''); + } + updateSliderText(val[0], val[1]); + if (e.type === 'slide') return; // no searching when sliding only + if (server) { + searchColumn(i, $td.data('filter') ? ival : '').draw(); + return; + } + table.draw(); + }; + filter.on({ + set: updateSlider, + slide: updateSlider + }); + } + + // server-side processing will be handled by R (or whatever server + // language you use); the following code is only needed for client-side + // processing + if (server) { + // if a search string has been pre-set, search now + if (searchCol) $input.trigger('input').trigger('change'); + return; + } + + var customFilter = function(settings, data, dataIndex) { + // there is no way to attach a search function to a specific table, + // and we need to make sure a global search function is not applied to + // all tables (i.e. a range filter in a previous table should not be + // applied to the current table); we use the settings object to + // determine if we want to perform searching on the current table, + // since settings.sTableId will be different to different tables + if (table.settings()[0] !== settings) return true; + // no filter on this column or no need to filter this column + if (typeof filter === 'undefined' || !$td.data('filter')) return true; + + var r = filter.val(), v, r0, r1; + var i_data = function(i) { + if (!colReorderEnabled()) return i; + var order = table.colReorder.order(), k; + for (k = 0; k < order.length; ++k) if (order[k] === i) return k; + return i; // in theory it will never be here... + } + v = data[i_data(i)]; + if (type === 'number' || type === 'integer') { + v = parseFloat(v); + // how to handle NaN? currently exclude these rows + if (isNaN(v)) return(false); + r0 = parseFloat(scaleBack(r[0], scale)) + r1 = parseFloat(scaleBack(r[1], scale)); + if (v >= r0 && v <= r1) return true; + } else if (type === 'date' || type === 'time') { + v = new Date(v); + r0 = new Date(r[0] / scale); r1 = new Date(r[1] / scale); + if (v >= r0 && v <= r1) return true; + } else if (type === 'factor') { + if (r.length === 0 || inArray(v, r)) return true; + } else if (type === 'logical') { + if (r.length === 0) return true; + if (inArray(v === '' ? 'na' : v, r)) return true; + } + return false; + }; + + $.fn.dataTable.ext.search.push(customFilter); + + // search for the preset search strings if it is non-empty + if (searchCol) $input.trigger('input').trigger('change'); + + }); + + } + + // highlight search keywords + var highlight = function() { + var body = $(table.table().body()); + // removing the old highlighting first + body.unhighlight(); + + // don't highlight the "not found" row, so we get the rows using the api + if (table.rows({ filter: 'applied' }).data().length === 0) return; + // highlight global search keywords + body.highlight($.trim(table.search()).split(/\s+/)); + // then highlight keywords from individual column filters + if (filterRow) filterRow.each(function(i, td) { + var $td = $(td), type = $td.data('type'); + if (type !== 'character') return; + var $input = $td.children('div').first().children('input'); + var column = table.column(i).nodes().to$(), + val = $.trim($input.val()); + if (type !== 'character' || val === '') return; + column.highlight(val.split(/\s+/)); + }); + }; + + if (options.searchHighlight) { + table + .on('draw.dt.dth column-visibility.dt.dth column-reorder.dt.dth', highlight) + .on('destroy', function() { + // remove event handler + table.off('draw.dt.dth column-visibility.dt.dth column-reorder.dt.dth'); + }); + + // Set the option for escaping regex characters in our search string. This will be used + // for all future matching. + jQuery.fn.highlight.options.escapeRegex = (!options.search || !options.search.regex); + + // initial highlight for state saved conditions and initial states + highlight(); + } + + // run the callback function on the table instance + if (typeof data.callback === 'function') data.callback(table); + + // double click to edit the cell, row, column, or all cells + if (data.editable) table.on('dblclick.dt', 'tbody td', function(e) { + // only bring up the editor when the cell itself is dbclicked, and ignore + // other dbclick events bubbled up (e.g. from the ) + if (e.target !== this) return; + var target = [], immediate = false; + switch (data.editable.target) { + case 'cell': + target = [this]; + immediate = true; // edit will take effect immediately + break; + case 'row': + target = table.cells(table.cell(this).index().row, '*').nodes(); + break; + case 'column': + target = table.cells('*', table.cell(this).index().column).nodes(); + break; + case 'all': + target = table.cells().nodes(); + break; + default: + throw 'The editable parameter must be "cell", "row", "column", or "all"'; + } + var disableCols = data.editable.disable ? data.editable.disable.columns : null; + var numericCols = data.editable.numeric; + var areaCols = data.editable.area; + var dateCols = data.editable.date; + for (var i = 0; i < target.length; i++) { + (function(cell, current) { + var $cell = $(cell), html = $cell.html(); + var _cell = table.cell(cell), value = _cell.data(), index = _cell.index().column; + var $input; + if (inArray(index, numericCols)) { + $input = $(''); + } else if (inArray(index, areaCols)) { + $input = $(''); + } else if (inArray(index, dateCols)) { + $input = $(''); + } else { + $input = $(''); + } + if (!immediate) { + $cell.data('input', $input).data('html', html); + $input.attr('title', 'Hit Ctrl+Enter to finish editing, or Esc to cancel'); + } + $input.val(value); + if (inArray(index, disableCols)) { + $input.attr('readonly', '').css('filter', 'invert(25%)'); + } + $cell.empty().append($input); + if (cell === current) $input.focus(); + $input.css('width', '100%'); + + if (immediate) $input.on('blur', function(e) { + var valueNew = $input.val(); + if (valueNew !== value) { + _cell.data(valueNew); + if (HTMLWidgets.shinyMode) { + changeInput('cell_edit', [cellInfo(cell)], 'DT.cellInfo', null, {priority: 'event'}); + } + // for server-side processing, users have to call replaceData() to update the table + if (!server) table.draw(false); + } else { + $cell.html(html); + } + }).on('keyup', function(e) { + // hit Escape to cancel editing + if (e.keyCode === 27) $input.trigger('blur'); + }); + + // bulk edit (row, column, or all) + if (!immediate) $input.on('keyup', function(e) { + var removeInput = function($cell, restore) { + $cell.data('input').remove(); + if (restore) $cell.html($cell.data('html')); + } + if (e.keyCode === 27) { + for (var i = 0; i < target.length; i++) { + removeInput($(target[i]), true); + } + } else if (e.keyCode === 13 && e.ctrlKey) { + // Ctrl + Enter + var cell, $cell, _cell, cellData = []; + for (var i = 0; i < target.length; i++) { + cell = target[i]; $cell = $(cell); _cell = table.cell(cell); + _cell.data($cell.data('input').val()); + HTMLWidgets.shinyMode && cellData.push(cellInfo(cell)); + removeInput($cell, false); + } + if (HTMLWidgets.shinyMode) { + changeInput('cell_edit', cellData, 'DT.cellInfo', null, {priority: "event"}); + } + if (!server) table.draw(false); + } + }); + })(target[i], this); + } + }); + + // interaction with shiny + if (!HTMLWidgets.shinyMode && !crosstalkOptions.group) return; + + var methods = {}; + var shinyData = {}; + + methods.updateCaption = function(caption) { + if (!caption) return; + $table.children('caption').replaceWith(caption); + } + + // register clear functions to remove input values when the table is removed + instance.clearInputs = {}; + + var changeInput = function(id, value, type, noCrosstalk, opts) { + var event = id; + id = el.id + '_' + id; + if (type) id = id + ':' + type; + // do not update if the new value is the same as old value + if (event !== 'cell_edit' && !/_clicked$/.test(event) && shinyData.hasOwnProperty(id) && shinyData[id] === JSON.stringify(value)) + return; + shinyData[id] = JSON.stringify(value); + if (HTMLWidgets.shinyMode && Shiny.setInputValue) { + Shiny.setInputValue(id, value, opts); + if (!instance.clearInputs[id]) instance.clearInputs[id] = function() { + Shiny.setInputValue(id, null); + } + } + + // HACK + if (event === "rows_selected" && !noCrosstalk) { + if (crosstalkOptions.group) { + var keys = crosstalkOptions.key; + var selectedKeys = null; + if (value) { + selectedKeys = []; + for (var i = 0; i < value.length; i++) { + // The value array's contents use 1-based row numbers, so we must + // convert to 0-based before indexing into the keys array. + selectedKeys.push(keys[value[i] - 1]); + } + } + instance.ctselectHandle.set(selectedKeys); + } + } + }; + + var addOne = function(x) { + return x.map(function(i) { return 1 + i; }); + }; + + var unique = function(x) { + var ux = []; + $.each(x, function(i, el){ + if ($.inArray(el, ux) === -1) ux.push(el); + }); + return ux; + } + + // change the row index of a cell + var tweakCellIndex = function(cell) { + var info = cell.index(); + // some cell may not be valid. e.g, #759 + // when using the RowGroup extension, datatables will + // generate the row label and the cells are not part of + // the data thus contain no row/col info + if (info === undefined) + return {row: null, col: null}; + if (server) { + info.row = DT_rows_current[info.row]; + } else { + info.row += 1; + } + return {row: info.row, col: info.column}; + } + + var cleanSelectedValues = function() { + changeInput('rows_selected', []); + changeInput('columns_selected', []); + changeInput('cells_selected', transposeArray2D([]), 'shiny.matrix'); + } + // #828 we should clean the selection on the server-side when the table reloads + cleanSelectedValues(); + + // a flag to indicates if select extension is initialized or not + var flagSelectExt = table.settings()[0]._select !== undefined; + // the Select extension should only be used in the client mode and + // when the selection.mode is set to none + if (data.selection.mode === 'none' && !server && flagSelectExt) { + var updateRowsSelected = function() { + var rows = table.rows({selected: true}); + var selected = []; + $.each(rows.indexes().toArray(), function(i, v) { + selected.push(v + 1); + }); + changeInput('rows_selected', selected); + } + var updateColsSelected = function() { + var columns = table.columns({selected: true}); + changeInput('columns_selected', columns.indexes().toArray()); + } + var updateCellsSelected = function() { + var cells = table.cells({selected: true}); + var selected = []; + cells.every(function() { + var row = this.index().row; + var col = this.index().column; + selected = selected.concat([[row + 1, col]]); + }); + changeInput('cells_selected', transposeArray2D(selected), 'shiny.matrix'); + } + table.on('select deselect', function(e, dt, type, indexes) { + updateRowsSelected(); + updateColsSelected(); + updateCellsSelected(); + }) + updateRowsSelected(); + updateColsSelected(); + updateCellsSelected(); + } + + var selMode = data.selection.mode, selTarget = data.selection.target; + var selDisable = data.selection.selectable === false; + if (inArray(selMode, ['single', 'multiple'])) { + var selClass = inArray(data.style, ['bootstrap', 'bootstrap4']) ? 'active' : 'selected'; + // selected1: row indices; selected2: column indices + var initSel = function(x) { + if (x === null || typeof x === 'boolean' || selTarget === 'cell') { + return {rows: [], cols: []}; + } else if (selTarget === 'row') { + return {rows: $.makeArray(x), cols: []}; + } else if (selTarget === 'column') { + return {rows: [], cols: $.makeArray(x)}; + } else if (selTarget === 'row+column') { + return {rows: $.makeArray(x.rows), cols: $.makeArray(x.cols)}; + } + } + var selected = data.selection.selected; + var selected1 = initSel(selected).rows, selected2 = initSel(selected).cols; + // selectable should contain either all positive or all non-positive values, not both + // positive values indicate "selectable" while non-positive values means "nonselectable" + // the assertion is performed on R side. (only column indicides could be zero which indicates + // the row name) + var selectable = data.selection.selectable; + var selectable1 = initSel(selectable).rows, selectable2 = initSel(selectable).cols; + + // After users reorder the rows or filter the table, we cannot use the table index + // directly. Instead, we need this function to find out the rows between the two clicks. + // If user filter the table again between the start click and the end click, the behavior + // would be undefined, but it should not be a problem. + var shiftSelRowsIndex = function(start, end) { + var indexes = server ? DT_rows_all : table.rows({ search: 'applied' }).indexes().toArray(); + start = indexes.indexOf(start); end = indexes.indexOf(end); + // if start is larger than end, we need to swap + if (start > end) { + var tmp = end; end = start; start = tmp; + } + return indexes.slice(start, end + 1); + } + + var serverRowIndex = function(clientRowIndex) { + return server ? DT_rows_current[clientRowIndex] : clientRowIndex + 1; + } + + // row, column, or cell selection + var lastClickedRow; + if (inArray(selTarget, ['row', 'row+column'])) { + // Get the current selected rows. It will also + // update the selected1's value based on the current row selection state + // Note we can't put this function inside selectRows() directly, + // the reason is method.selectRows() will override selected1's value but this + // function will add rows to selected1 (keep the existing selection), which is + // inconsistent with column and cell selection. + var selectedRows = function() { + var rows = table.rows('.' + selClass); + var idx = rows.indexes().toArray(); + if (!server) { + selected1 = addOne(idx); + return selected1; + } + idx = idx.map(function(i) { + return DT_rows_current[i]; + }); + selected1 = selMode === 'multiple' ? unique(selected1.concat(idx)) : idx; + return selected1; + } + // Change selected1's value based on selectable1, then refresh the row state + var onlyKeepSelectableRows = function() { + if (selDisable) { // users can't select; useful when only want backend select + selected1 = []; + return; + } + if (selectable1.length === 0) return; + var nonselectable = selectable1[0] <= 0; + if (nonselectable) { + // should make selectable1 positive + selected1 = $(selected1).not(selectable1.map(function(i) { return -i; })).get(); + } else { + selected1 = $(selected1).filter(selectable1).get(); + } + } + // Change selected1's value based on selectable1, then + // refresh the row selection state according to values in selected1 + var selectRows = function(ignoreSelectable) { + if (!ignoreSelectable) onlyKeepSelectableRows(); + table.$('tr.' + selClass).removeClass(selClass); + if (selected1.length === 0) return; + if (server) { + table.rows({page: 'current'}).every(function() { + if (inArray(DT_rows_current[this.index()], selected1)) { + $(this.node()).addClass(selClass); + } + }); + } else { + var selected0 = selected1.map(function(i) { return i - 1; }); + $(table.rows(selected0).nodes()).addClass(selClass); + } + } + table.on('mousedown.dt', 'tbody tr', function(e) { + var $this = $(this), thisRow = table.row(this); + if (selMode === 'multiple') { + if (e.shiftKey && lastClickedRow !== undefined) { + // select or de-select depends on the last clicked row's status + var flagSel = !$this.hasClass(selClass); + var crtClickedRow = serverRowIndex(thisRow.index()); + if (server) { + var rowsIndex = shiftSelRowsIndex(lastClickedRow, crtClickedRow); + // update current page's selClass + rowsIndex.map(function(i) { + var rowIndex = DT_rows_current.indexOf(i); + if (rowIndex >= 0) { + var row = table.row(rowIndex).nodes().to$(); + var flagRowSel = !row.hasClass(selClass); + if (flagSel === flagRowSel) row.toggleClass(selClass); + } + }); + // update selected1 + if (flagSel) { + selected1 = unique(selected1.concat(rowsIndex)); + } else { + selected1 = selected1.filter(function(index) { + return !inArray(index, rowsIndex); + }); + } + } else { + // js starts from 0 + shiftSelRowsIndex(lastClickedRow - 1, crtClickedRow - 1).map(function(value) { + var row = table.row(value).nodes().to$(); + var flagRowSel = !row.hasClass(selClass); + if (flagSel === flagRowSel) row.toggleClass(selClass); + }); + } + e.preventDefault(); + } else { + $this.toggleClass(selClass); + } + } else { + if ($this.hasClass(selClass)) { + $this.removeClass(selClass); + } else { + table.$('tr.' + selClass).removeClass(selClass); + $this.addClass(selClass); + } + } + if (server && !$this.hasClass(selClass)) { + var id = DT_rows_current[thisRow.index()]; + // remove id from selected1 since its class .selected has been removed + if (inArray(id, selected1)) selected1.splice($.inArray(id, selected1), 1); + } + selectedRows(); // update selected1's value based on selClass + selectRows(false); // only keep the selectable rows + changeInput('rows_selected', selected1); + changeInput('row_last_clicked', serverRowIndex(thisRow.index()), null, null, {priority: 'event'}); + lastClickedRow = serverRowIndex(thisRow.index()); + }); + selectRows(false); // in case users have specified pre-selected rows + // restore selected rows after the table is redrawn (e.g. sort/search/page); + // client-side tables will preserve the selections automatically; for + // server-side tables, we have to *real* row indices are in `selected1` + changeInput('rows_selected', selected1); + if (server) table.on('draw.dt', function(e) { selectRows(false); }); + methods.selectRows = function(selected, ignoreSelectable) { + selected1 = $.makeArray(selected); + selectRows(ignoreSelectable); + changeInput('rows_selected', selected1); + } + } + + if (inArray(selTarget, ['column', 'row+column'])) { + if (selTarget === 'row+column') { + $(table.columns().footer()).css('cursor', 'pointer'); + } + // update selected2's value based on selectable2 + var onlyKeepSelectableCols = function() { + if (selDisable) { // users can't select; useful when only want backend select + selected2 = []; + return; + } + if (selectable2.length === 0) return; + var nonselectable = selectable2[0] <= 0; + if (nonselectable) { + // need to make selectable2 positive + selected2 = $(selected2).not(selectable2.map(function(i) { return -i; })).get(); + } else { + selected2 = $(selected2).filter(selectable2).get(); + } + } + // update selected2 and then + // refresh the col selection state according to values in selected2 + var selectCols = function(ignoreSelectable) { + if (!ignoreSelectable) onlyKeepSelectableCols(); + // if selected2 is not a valide index (e.g., larger than the column number) + // table.columns(selected2) will fail and result in a blank table + // this is different from the table.rows(), where the out-of-range indexes + // doesn't affect at all + selected2 = $(selected2).filter(table.columns().indexes()).get(); + table.columns().nodes().flatten().to$().removeClass(selClass); + if (selected2.length > 0) + table.columns(selected2).nodes().flatten().to$().addClass(selClass); + } + var callback = function() { + var colIdx = selTarget === 'column' ? table.cell(this).index().column : + $.inArray(this, table.columns().footer()), + thisCol = $(table.column(colIdx).nodes()); + if (colIdx === -1) return; + if (thisCol.hasClass(selClass)) { + thisCol.removeClass(selClass); + selected2.splice($.inArray(colIdx, selected2), 1); + } else { + if (selMode === 'single') $(table.cells().nodes()).removeClass(selClass); + thisCol.addClass(selClass); + selected2 = selMode === 'single' ? [colIdx] : unique(selected2.concat([colIdx])); + } + selectCols(false); // update selected2 based on selectable + changeInput('columns_selected', selected2); + } + if (selTarget === 'column') { + $(table.table().body()).on('click.dt', 'td', callback); + } else { + $(table.table().footer()).on('click.dt', 'tr th', callback); + } + selectCols(false); // in case users have specified pre-selected columns + changeInput('columns_selected', selected2); + if (server) table.on('draw.dt', function(e) { selectCols(false); }); + methods.selectColumns = function(selected, ignoreSelectable) { + selected2 = $.makeArray(selected); + selectCols(ignoreSelectable); + changeInput('columns_selected', selected2); + } + } + + if (selTarget === 'cell') { + var selected3 = [], selectable3 = []; + if (selected !== null) selected3 = selected; + if (selectable !== null && typeof selectable !== 'boolean') selectable3 = selectable; + var findIndex = function(ij, sel) { + for (var i = 0; i < sel.length; i++) { + if (ij[0] === sel[i][0] && ij[1] === sel[i][1]) return i; + } + return -1; + } + // Change selected3's value based on selectable3, then refresh the cell state + var onlyKeepSelectableCells = function() { + if (selDisable) { // users can't select; useful when only want backend select + selected3 = []; + return; + } + if (selectable3.length === 0) return; + var nonselectable = selectable3[0][0] <= 0; + var out = []; + if (nonselectable) { + selected3.map(function(ij) { + // should make selectable3 positive + if (findIndex([-ij[0], -ij[1]], selectable3) === -1) { out.push(ij); } + }); + } else { + selected3.map(function(ij) { + if (findIndex(ij, selectable3) > -1) { out.push(ij); } + }); + } + selected3 = out; + } + // Change selected3's value based on selectable3, then + // refresh the cell selection state according to values in selected3 + var selectCells = function(ignoreSelectable) { + if (!ignoreSelectable) onlyKeepSelectableCells(); + table.$('td.' + selClass).removeClass(selClass); + if (selected3.length === 0) return; + if (server) { + table.cells({page: 'current'}).every(function() { + var info = tweakCellIndex(this); + if (findIndex([info.row, info.col], selected3) > -1) + $(this.node()).addClass(selClass); + }); + } else { + selected3.map(function(ij) { + $(table.cell(ij[0] - 1, ij[1]).node()).addClass(selClass); + }); + } + }; + table.on('click.dt', 'tbody td', function() { + var $this = $(this), info = tweakCellIndex(table.cell(this)); + if ($this.hasClass(selClass)) { + $this.removeClass(selClass); + selected3.splice(findIndex([info.row, info.col], selected3), 1); + } else { + if (selMode === 'single') $(table.cells().nodes()).removeClass(selClass); + $this.addClass(selClass); + selected3 = selMode === 'single' ? [[info.row, info.col]] : + unique(selected3.concat([[info.row, info.col]])); + } + selectCells(false); // must call this to update selected3 based on selectable3 + changeInput('cells_selected', transposeArray2D(selected3), 'shiny.matrix'); + }); + selectCells(false); // in case users have specified pre-selected columns + changeInput('cells_selected', transposeArray2D(selected3), 'shiny.matrix'); + + if (server) table.on('draw.dt', function(e) { selectCells(false); }); + methods.selectCells = function(selected, ignoreSelectable) { + selected3 = selected ? selected : []; + selectCells(ignoreSelectable); + changeInput('cells_selected', transposeArray2D(selected3), 'shiny.matrix'); + } + } + } + + // expose some table info to Shiny + var updateTableInfo = function(e, settings) { + // TODO: is anyone interested in the page info? + // changeInput('page_info', table.page.info()); + var updateRowInfo = function(id, modifier) { + var idx; + if (server) { + idx = modifier.page === 'current' ? DT_rows_current : DT_rows_all; + } else { + var rows = table.rows($.extend({ + search: 'applied', + page: 'all' + }, modifier)); + idx = addOne(rows.indexes().toArray()); + } + changeInput('rows' + '_' + id, idx); + }; + updateRowInfo('current', {page: 'current'}); + updateRowInfo('all', {}); + } + table.on('draw.dt', updateTableInfo); + updateTableInfo(); + + // state info + table.on('draw.dt column-visibility.dt', function() { + changeInput('state', table.state()); + }); + changeInput('state', table.state()); + + // search info + var updateSearchInfo = function() { + changeInput('search', table.search()); + if (filterRow) changeInput('search_columns', filterRow.toArray().map(function(td) { + return $(td).find('input').first().val(); + })); + } + table.on('draw.dt', updateSearchInfo); + updateSearchInfo(); + + var cellInfo = function(thiz) { + var info = tweakCellIndex(table.cell(thiz)); + info.value = table.cell(thiz).data(); + return info; + } + // the current cell clicked on + table.on('click.dt', 'tbody td', function() { + changeInput('cell_clicked', cellInfo(this), null, null, {priority: 'event'}); + }) + changeInput('cell_clicked', {}); + + // do not trigger table selection when clicking on links unless they have classes + table.on('mousedown.dt', 'tbody td a', function(e) { + if (this.className === '') e.stopPropagation(); + }); + + methods.addRow = function(data, rowname, resetPaging) { + var n = table.columns().indexes().length, d = n - data.length; + if (d === 1) { + data = rowname.concat(data) + } else if (d !== 0) { + console.log(data); + console.log(table.columns().indexes()); + throw 'New data must be of the same length as current data (' + n + ')'; + }; + table.row.add(data).draw(resetPaging); + } + + methods.updateSearch = function(keywords) { + if (keywords.global !== null) + $(table.table().container()).find('input[type=search]').first() + .val(keywords.global).trigger('input'); + var columns = keywords.columns; + if (!filterRow || columns === null) return; + filterRow.toArray().map(function(td, i) { + var v = typeof columns === 'string' ? columns : columns[i]; + if (typeof v === 'undefined') { + console.log('The search keyword for column ' + i + ' is undefined') + return; + } + // Update column search string and values on linked filter widgets. + // 'input' for factor and char filters, 'change' for numeric filters. + $(td).find('input').first().val(v).trigger('input', [true]).trigger('change'); + }); + table.draw(); + } + + methods.hideCols = function(hide, reset) { + if (reset) table.columns().visible(true, false); + table.columns(hide).visible(false); + } + + methods.showCols = function(show, reset) { + if (reset) table.columns().visible(false, false); + table.columns(show).visible(true); + } + + methods.colReorder = function(order, origOrder) { + table.colReorder.order(order, origOrder); + } + + methods.selectPage = function(page) { + if (table.page.info().pages < page || page < 1) { + throw 'Selected page is out of range'; + }; + table.page(page - 1).draw(false); + } + + methods.reloadData = function(resetPaging, clearSelection) { + // empty selections first if necessary + if (methods.selectRows && inArray('row', clearSelection)) methods.selectRows([]); + if (methods.selectColumns && inArray('column', clearSelection)) methods.selectColumns([]); + if (methods.selectCells && inArray('cell', clearSelection)) methods.selectCells([]); + table.ajax.reload(null, resetPaging); + } + + // update table filters (set new limits of sliders) + methods.updateFilters = function(newProps) { + // loop through each filter in the filter row + filterRow.each(function(i, td) { + var k = i; + if (filterRow.length > newProps.length) { + if (i === 0) return; // first column is row names + k = i - 1; + } + // Update the filters to reflect the updated data. + // Allow "falsy" (e.g. NULL) to signify a no-op. + if (newProps[k]) { + setFilterProps(td, newProps[k]); + } + }); + }; + + table.shinyMethods = methods; + }, + resize: function(el, width, height, instance) { + if (instance.data) this.renderValue(el, instance.data, instance); + + // dynamically adjust height if fillContainer = TRUE + if (instance.fillContainer) + this.fillAvailableHeight(el, height); + + this.adjustWidth(el); + }, + + // dynamically set the scroll body to fill available height + // (used with fillContainer = TRUE) + fillAvailableHeight: function(el, availableHeight) { + + // see how much of the table is occupied by header/footer elements + // and use that to compute a target scroll body height + var dtWrapper = $(el).find('div.dataTables_wrapper'); + var dtScrollBody = $(el).find($('div.dataTables_scrollBody')); + var framingHeight = dtWrapper.innerHeight() - dtScrollBody.innerHeight(); + var scrollBodyHeight = availableHeight - framingHeight; + + // we need to set `max-height` to none as datatables library now sets this + // to a fixed height, disabling the ability to resize to fill the window, + // as it will be set to a fixed 100px under such circumstances, e.g., RStudio IDE, + // or FlexDashboard + // see https://github.com/rstudio/DT/issues/951#issuecomment-1026464509 + dtScrollBody.css('max-height', 'none'); + // set the height + dtScrollBody.height(scrollBodyHeight + 'px'); + }, + + // adjust the width of columns; remove the hard-coded widths on table and the + // scroll header when scrollX/Y are enabled + adjustWidth: function(el) { + var $el = $(el), table = $el.data('datatable'); + if (table) table.columns.adjust(); + $el.find('.dataTables_scrollHeadInner').css('width', '') + .children('table').css('margin-left', ''); + } +}); + + if (!HTMLWidgets.shinyMode) return; + + Shiny.addCustomMessageHandler('datatable-calls', function(data) { + var id = data.id; + var el = document.getElementById(id); + var table = el ? $(el).data('datatable') : null; + if (!table) { + console.log("Couldn't find table with id " + id); + return; + } + + var methods = table.shinyMethods, call = data.call; + if (methods[call.method]) { + methods[call.method].apply(table, call.args); + } else { + console.log("Unknown method " + call.method); + } + }); + +})(); diff --git a/docs/articles/PareReportBranches_files/dt-core-1.13.6/css/jquery.dataTables.extra.css b/docs/articles/PareReportBranches_files/dt-core-1.13.6/css/jquery.dataTables.extra.css new file mode 100644 index 0000000..b2dd141 --- /dev/null +++ b/docs/articles/PareReportBranches_files/dt-core-1.13.6/css/jquery.dataTables.extra.css @@ -0,0 +1,28 @@ +/* Selected rows/cells */ +table.dataTable tr.selected td, table.dataTable td.selected { + background-color: #b0bed9 !important; +} +/* In case of scrollX/Y or FixedHeader */ +.dataTables_scrollBody .dataTables_sizing { + visibility: hidden; +} + +/* The datatables' theme CSS file doesn't define +the color but with white background. It leads to an issue that +when the HTML's body color is set to 'white', the user can't +see the text since the background is white. One case happens in the +RStudio's IDE when inline viewing the DT table inside an Rmd file, +if the IDE theme is set to "Cobalt". + +See https://github.com/rstudio/DT/issues/447 for more info + +This fixes should have little side-effects because all the other elements +of the default theme use the #333 font color. + +TODO: The upstream may use relative colors for both the table background +and the color. It means the table can display well without this patch +then. At that time, we need to remove the below CSS attributes. +*/ +div.datatables { + color: #333; +} diff --git a/docs/articles/PareReportBranches_files/dt-core-1.13.6/css/jquery.dataTables.min.css b/docs/articles/PareReportBranches_files/dt-core-1.13.6/css/jquery.dataTables.min.css new file mode 100644 index 0000000..ad59f84 --- /dev/null +++ b/docs/articles/PareReportBranches_files/dt-core-1.13.6/css/jquery.dataTables.min.css @@ -0,0 +1 @@ +:root{--dt-row-selected: 13, 110, 253;--dt-row-selected-text: 255, 255, 255;--dt-row-selected-link: 9, 10, 11;--dt-row-stripe: 0, 0, 0;--dt-row-hover: 0, 0, 0;--dt-column-ordering: 0, 0, 0;--dt-html-background: white}:root.dark{--dt-html-background: rgb(33, 37, 41)}table.dataTable td.dt-control{text-align:center;cursor:pointer}table.dataTable td.dt-control:before{display:inline-block;color:rgba(0, 0, 0, 0.5);content:"►"}table.dataTable tr.dt-hasChild td.dt-control:before{content:"▼"}html.dark table.dataTable td.dt-control:before{color:rgba(255, 255, 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