authority -> provider (#32)

.gitignore

@@ -20,3 +20,6 @@ data/*
 taxadb
 inst/doc
 taxizedb
+*.spl
+*.tex
+paper/manuscript.pdf

R/classification.R

@@ -5,7 +5,7 @@
 #' @param species a character vector of species names, typically
 #'  specified as (`Genus species` or `Genus species epithet`)
 #' @param id alternately users can provide a vector of species ids.
-#'  IDs must be prefixed matching the requested authority.  See `id`
+#'  IDs must be prefixed matching the requested provider.  See `id`
 #'  column returned by most `taxadb` functions for examples.
 #' @inheritParams ids
 #' @return a data.frame with one row for each requested species,
@@ -26,12 +26,12 @@
 #'
 classification <- function(species = NULL,
                            id = NULL,
-                           authority = KNOWN_AUTHORITIES,
+                           provider = KNOWN_AUTHORITIES,
                            collect = TRUE,
                            db = td_connect()){
 
   suppress_msg({
-  out <- dplyr::right_join(taxa_tbl(authority = authority,
+  out <- dplyr::right_join(taxa_tbl(provider = provider,
                                    schema = "dwc",
                                    db = db),
                           null_tibble(id, scientificName = species),

R/descendants.R

@@ -12,7 +12,7 @@
 descendants <- function(name = NULL,
                         rank = NULL,
                         id = NULL,
-                        authority = KNOWN_AUTHORITIES,
+                        provider = KNOWN_AUTHORITIES,
                         collect = TRUE,
                         db = td_connect()){
 
@@ -22,7 +22,7 @@ descendants <- function(name = NULL,
     df <- data.frame(setNames(list(name), rank), stringsAsFactors = FALSE)
     df$id <- id
 
-    taxa <- taxa_tbl(authority = authority,
+    taxa <- taxa_tbl(provider = provider,
                      schema = "dwc",
                      db = db)
 

R/fuzzy.R

@@ -2,23 +2,23 @@
 
 
 search <- function(name = NULL,
-                   authority = KNOWN_AUTHORITIES,
+                   provider = KNOWN_AUTHORITIES,
                    match = c("exact", "starts_with", "contains"),
                    format = c("bare", "prefix", "uri"),
                    db = td_connect()){
   match <- match.arg(match)
   switch(match,
          exact = get_ids(names = name,
-                         authority = authority,
+                         provider = provider,
                          format = format,
                          db = db),
          starts_with = fuzzy_ids(name = name,
-                                 authority = authority,
+                                 provider = provider,
                                  match = match,
                                  format = format,
                                  db = db),
          contains = fuzzy_ids(name = name,
-                              authority = authority,
+                              provider = provider,
                               match = match,
                               format = format,
                               db = db),
@@ -29,7 +29,7 @@ search <- function(name = NULL,
 
 #' @importFrom dplyr bind_rows filter collect mutate
 fuzzy_ids <- function(name = NULL,
-                      authority = KNOWN_AUTHORITIES,
+                      provider = KNOWN_AUTHORITIES,
                       match = c("starts_with", "contains"),
                       format = c("bare", "prefix", "uri"),
                       db = td_connect()){
@@ -44,7 +44,7 @@ fuzzy_ids <- function(name = NULL,
     lapply(name_pattern,
           function(pattern){
 
-            taxa_tbl(authority, "dwc", db) %>%
+            taxa_tbl(provider, "dwc", db) %>%
             dplyr::filter(name %like% pattern) %>%
             dplyr::collect() %>%
             dplyr::mutate(input_name = gsub("%", "", pattern))

R/get_ids.R

@@ -5,7 +5,7 @@
 #' A drop-in replacement for `[taxize::get_ids()]`
 #' @param names a list of scientific names (which may
 #'   include higher-order ranks in most authorities).
-#' @param db abbreviation code for the authority.  See details.
+#' @param db abbreviation code for the provider.  See details.
 #' @param format Format for the returned: bare identifier, one of
 #'   - `bare` (e.g. `9606`, default, matching `taxize::get_ids()`),
 #'   - `prefix` (e.g. `NCBI:9606`), or
@@ -19,7 +19,7 @@
 #' Both include `itis`, `ncbi`, `col`, and `gbif`.
 #'
 #' Like all taxadb functions, this function will run
-#' fastest if a local copy of the authority is installed in advance
+#' fastest if a local copy of the provider is installed in advance
 #' using `[td_create()]`.
 #' @examples \dontrun{
 #' get_ids("Homo sapiens")
@@ -38,7 +38,7 @@ get_ids <- function(names,
   # be compatible with common space delimiters
   names <- gsub("[_|-|\\.]", " ", names)
   df <- ids(name = names,
-             authority = db,
+             provider = db,
              collect = TRUE,
              db = taxadb_db)
 

R/ids.R

@@ -4,7 +4,7 @@
 #' @param name a character vector of species names, e.g. "Homo sapiens"
 #' (Most but not all authorities can also return ids for higher-level
 #'  taxonomic names).
-#' @param authority from which authority should the hierachy be returned?
+#' @param provider from which provider should the hierachy be returned?
 #'  Default is 'itis'.
 #' @param collect logical, default `TRUE`. Should we return an in-memory
 #' data.frame (default, usually the most convenient), or a reference to
@@ -29,7 +29,7 @@
 #' @importFrom rlang !!
 #' @importFrom magrittr %>%
 ids <- function(name = NULL,
-                authority = KNOWN_AUTHORITIES,
+                provider = KNOWN_AUTHORITIES,
                 collect = TRUE,
                 db = td_connect()){
 
@@ -48,13 +48,13 @@ ids <- function(name = NULL,
 
   ## Could be pre-computed to avoid the performance hit here.
   db_table <-
-    taxa_tbl(authority, "dwc", db) %>%
+    taxa_tbl(provider, "dwc", db) %>%
   ## Could consider other cleaning
   ## when run in backend DB, uses the DB's built-in lowercase SQL command:
     mutate(input = tolower(scientificName))
 
   ## Use right_join, so unmatched names are kept, with NA
-  ## Using right join, names appear in order of authority!
+  ## Using right join, names appear in order of provider!
 
   suppress_msg({   # bc MonetDBLite whines about upper-case characters
   out <-
@@ -86,18 +86,18 @@ ids <- function(name = NULL,
 
 ## FIXME abstract this to filter on id / name / generic column?
 accepted_name <- function(id = NULL,
-                authority = KNOWN_AUTHORITIES,
+                provider = KNOWN_AUTHORITIES,
                 collect = TRUE,
                 db = td_connect()){
   sort <- TRUE # dummy name
   input_table <- dplyr::tibble(taxonID = id, sort = 1:length(id))
 
   ## Use right_join, so unmatched names are kept, with NA
-  ## Means names appear in order of authority, so we must arrange
+  ## Means names appear in order of provider, so we must arrange
   ## after-the-fact to match the query order
   out <-
     dplyr::right_join(
-      taxa_tbl(authority, "dwc", db),
+      taxa_tbl(provider, "dwc", db),
       input_table,
       by = "taxonID",
       copy = TRUE) %>%

R/synonyms.R

@@ -30,10 +30,10 @@ syn_table <- function(taxon, accepted = "accepted"){
 #' @inheritParams ids
 #' @export
 synonyms <- function(name = NULL,
-                     authority = KNOWN_AUTHORITIES,
+                     provider = KNOWN_AUTHORITIES,
                      collect = TRUE,
                      db = td_connect()){
-  ids(name, authority, collect, db) %>%
+  ids(name, provider, collect, db) %>%
     syn_table()
 
 }

R/taxa_tbl.R

@@ -10,12 +10,12 @@ KNOWN_AUTHORITIES <- c("itis", "ncbi", "col", "tpl",
 #' @inheritParams classification
 #' @export
 taxa_tbl <- function(
-  authority = KNOWN_AUTHORITIES,
+  provider = KNOWN_AUTHORITIES,
   schema = "dwc",
   db = td_connect()){
 
-  authority <- match.arg(authority)
-  tbl_name <- authority
+  provider <- match.arg(provider)
+  tbl_name <- provider
   if (is.null(db)) return(quick_db(tbl_name))
   if (!has_table(tbl_name, db)) return(quick_db(tbl_name))
 

README.Rmd

@@ -43,7 +43,7 @@ library(taxadb)
 td_create()
 ```
 
-The default behavior installs only the ITIS database.  You can also specify a list of authorities to install, or install every authority using `td_create("all")`.  
+The default behavior installs only the ITIS database.  You can also specify a list of authorities to install, or install every provider using `td_create("all")`.  
 
 
 ## Test drive

README.md

@@ -52,7 +52,7 @@ td_create()
 ```
 
 The default behavior installs only the ITIS database. You can also
-specify a list of authorities to install, or install every authority
+specify a list of authorities to install, or install every provider
 using `td_create("all")`.
 
 ## Test drive

tests/testthat/test-all-dbs.R

@@ -27,7 +27,7 @@ test_that("we can set up a db and call basic functions", {
 
 
 
-  df <- taxa_tbl(authority = "col")
+  df <- taxa_tbl(provider = "col")
   chameleons <- df %>% filter(family == "Chamaeleonidae") %>% collect()
 
   df <- descendants(name = "Aves", rank = "class")

tests/testthat/test-connections.R

@@ -28,7 +28,7 @@ test_that("we can use alternative DBs, such as SQLite", {
 
   ## and here we go.
   td_create(schema = "hierarchy", db = db)
-  itis <- taxa_tbl(authority = "itis",
+  itis <- taxa_tbl(provider = "itis",
                    schema = "hierarchy",
                    db = db)
   DBI::dbDisconnect(db)

tests/testthat/test-fast.R

@@ -7,7 +7,7 @@ library(dplyr)
 
 test_that("setup-free calls to basic functions", {
 
-  df <- taxa_tbl(authority = "itis", db = NULL)
+  df <- taxa_tbl(provider = "itis", db = NULL)
   chameleons <- filter(df, family == "Chamaeleonidae")
 
   df <- descendants(name = "Aves", rank = "class", db = NULL)

tests/testthat/test-taxald.R

@@ -12,7 +12,7 @@ test_that("we can set up a db and call basic functions", {
   td_create(dbdir = test_db)
   db <- td_connect(test_db)
 
-  df <- taxa_tbl(authority = "itis",
+  df <- taxa_tbl(provider = "itis",
                  db = db)
 
   chameleons <- df %>%

vignettes/intro.Rmd

@@ -43,7 +43,7 @@ library(taxadb)
 td_create()
 ```
 
-The default behavior installs only the ITIS database.  You can also specify a list of authorities to install, or install every authority using `td_create("all")`.  
+The default behavior installs only the ITIS database.  You can also specify a list of authorities to install, or install every provider using `td_create("all")`.  
 
 
 ## Test drive