Make package citation optional

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
 Version: 0.5.7
-Date: 2024-06-23 13:30:32 UTC
-SHA: 547f788a4430979117ed5e5aea803b043c9921ba
+Date: 2024-06-23 14:07:20 UTC
+SHA: b4fd865c3f391ceffb6f62e409cafb50737bfa0b

NEWS.md

@@ -4,6 +4,7 @@
 * Updated date formatting using `format()` instead of `as.character()`
 * Updated test files to incorporate rgbif 3.8.0 output changes, make more efficient
 * In occResults, renamed "Dataset", "DatasetKey", and "DataService" to "datasetName", "datasetKey", "dataService", respectively.
+* Made an option for removing package citations
 
 # occCite 0.5.6
 

R/occCitePrint.R

@@ -33,6 +33,12 @@ print.occCiteCitation <- function(x, ...) {
     bySpecies <- FALSE
   }
 
+  if ("skipPackages" %in% names(args)) {
+    skipPackages <- args$skipPackages
+  } else {
+    skipPackages <- FALSE
+  }
+
   stopifnot(is(x, "occCiteCitation"))
 
   if (!requireNamespace("RefManageR", quietly = TRUE)) {
@@ -173,7 +179,11 @@ print.occCiteCitation <- function(x, ...) {
       packages <- unique(x$occCitationResults[[i]]$occSearch)
       if ("GBIF" %in% packages) packCit <- c(packCit, "rgbif")
       if ("BIEN" %in% packages) packCit <- c(packCit, "BIEN")
-      packCit <- packageCitations(packCit)
+      if(skipPackages){
+        packCit <- NULL
+      } else {
+        packCit <- packageCitations(packCit)
+      }
 
       # Print results
       cat(paste("Species:", names(x$occCitationResults)[[i]], "\n\n"))
@@ -202,7 +212,11 @@ print.occCiteCitation <- function(x, ...) {
     packages <- unique(recordCitations$occSearch)
     if ("GBIF" %in% packages) packCit <- c(packCit, "rgbif")
     if ("BIEN" %in% packages) packCit <- c(packCit, "BIEN")
-    packCit <- packageCitations(packCit)
+    if(skipPackages){
+      packCit <- NULL
+    } else {
+      packCit <- packageCitations(packCit)
+    }
 
     # Print results
     recordCitations <- recordCitations[order(recordCitations$Citation), ]

R/studyTaxonList.R

@@ -9,13 +9,13 @@
 #' containing the names of taxa of interest
 #'
 #' @param datasources A vector of taxonomic data sources implemented in
-#' \code{\link{gnr_resolve}}. You can see the list using
+#' \code{\link[taxize]{gnr_resolve}}. You can see the list using
 #' \code{taxize::gnr_datasources()}.
 #'
 #' @return An object of class \code{\link{occCiteData}} containing the type
 #' of inquiry the user has made --a phylogeny or a vector of names-- and a
 #' data frame containing input taxa names, the closest match according to
-#' \code{\link{gnr_resolve}}, and a list of taxonomic data sources that
+#' \code{\link[taxize]{gnr_resolve}}, and a list of taxonomic data sources that
 #' contain the matching name.
 #'
 #' @examples

cran-comments.md

@@ -5,6 +5,7 @@ This is a package update. In this version, I have:
 * Updated date formatting using `format()` instead of `as.character()`
 * Updated test files to incorporate rgbif 3.8.0 output changes, make more efficient
 * In occResults, renamed "Dataset", "DatasetKey", and "DataService" to "datasetName", "datasetKey", "dataService", respectively.
+* Made an option for removing package citations.
 
 ## Test environments
 * local OS X 14.5 install, R 4.3.2 (with and without internet connection)

docs/pkgdown.yml

@@ -4,5 +4,5 @@ pkgdown_sha: ~
 articles:
   a_Simple: a_Simple.html
   b_Advanced: b_Advanced.html
-last_built: 2024-06-23T14:01Z
+last_built: 2024-06-23T14:32Z