change 'stripauthority' to 'canonical'. Fixes #451

ropensci · Aug 19, 2015 · c999b20 · c999b20
1 parent 34ac66d
commit c999b20
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Showing 3 changed files with 18 additions and 16 deletions.
diff --git a/R/gnr_resolve.R b/R/gnr_resolve.R
@@ -13,8 +13,9 @@
 #'    all supplied names from matches in data sources that have classification
 #'    tree paths. Names out of determined context are penalized during score
 #'    calculation.
-#' @param stripauthority logical; If FALSE (default), gives back names with
-#'    taxonomic authorities. If TRUE, strips author names.
+#' @param canonical logical; If FALSE (default), gives back names with
+#'    taxonomic authorities. If TRUE, returns canocial names 
+#'    (without tax. authorities and abbreviations).
 #' @param highestscore logical; Return those names with the highest score for
 #'    each searched name?
 #' @param best_match_only (logical) If TRUE, best match only returned.
@@ -55,13 +56,13 @@
 #' # Preferred data source
 #' gnr_resolve(names = "Helianthus annuus", preferred_data_sources = c(3,4))
 #'
-#' # Strip taxonomic authorities - default is stripauthority=FALSE
+#' # Return canonical names - default is canonical=FALSE
 #' head(gnr_resolve(names = "Helianthus annuus")$results)
-#' head(gnr_resolve(names = "Helianthus annuus", stripauthority=TRUE)$results)
+#' head(gnr_resolve(names = "Helianthus annuus", canonical=TRUE)$results)
 #' }
 
 gnr_resolve <- function(names, data_source_ids = NULL, resolve_once = FALSE,
-  with_context = FALSE, stripauthority = FALSE, highestscore = TRUE, best_match_only = FALSE,
+  with_context = FALSE, canonical = FALSE, highestscore = TRUE, best_match_only = FALSE,
   preferred_data_sources = NULL, http="get", ...) {
 
   http <- match.arg(http, c("get","post"))
@@ -138,7 +139,7 @@ gnr_resolve <- function(names, data_source_ids = NULL, resolve_once = FALSE,
     data_2$matched_name2 <- as.character(data_2$matched_name2)
     out <- data_2[order(data_2$submitted_name), ]
 
-    if (stripauthority) {
+    if (canonical) {
       out <- out[ , !names(out) %in% "matched_name"]
     } else {
       out <- out[ , !names(out) %in% "matched_name2"]
@@ -169,15 +170,15 @@ gnr_resolve <- function(names, data_source_ids = NULL, resolve_once = FALSE,
     data_2_preferred$matched_name2 <- as.character(data_2_preferred$matched_name2)
     out_preferred <- data_2_preferred[order(data_2_preferred$submitted_name), ]
 
-    if (stripauthority) {
+    if (canonical) {
       out_preferred <- out_preferred[ , !names(out_preferred) %in% "matched_name"]
     } else {
       out_preferred <- out_preferred[ , !names(out_preferred) %in% "matched_name2"]
     }
   } else {
     out_preferred <- NULL
   }
-  # stripauthority = TRUE, may result into duplicates
+  # canonical = TRUE, may result into duplicates
   out <- unique(out)
   list(results = out, preferred = out_preferred, not_known = not_known)
 }

diff --git a/man/gnr_resolve.Rd b/man/gnr_resolve.Rd
@@ -5,7 +5,7 @@
 \title{Resolve names using Global Names Resolver.}
 \usage{
 gnr_resolve(names, data_source_ids = NULL, resolve_once = FALSE,
-  with_context = FALSE, stripauthority = FALSE, highestscore = TRUE,
+  with_context = FALSE, canonical = FALSE, highestscore = TRUE,
   best_match_only = FALSE, preferred_data_sources = NULL, http = "get",
   ...)
 }
@@ -25,8 +25,9 @@ all supplied names from matches in data sources that have classification
 tree paths. Names out of determined context are penalized during score
 calculation.}
 
-\item{stripauthority}{logical; If FALSE (default), gives back names with
-taxonomic authorities. If TRUE, strips author names.}
+\item{canonical}{logical; If FALSE (default), gives back names with
+taxonomic authorities. If TRUE, returns canocial names
+(without tax. authorities and abbreviations).}
 
 \item{highestscore}{logical; Return those names with the highest score for
 each searched name?}
@@ -75,9 +76,9 @@ gnr_resolve(names = "Helianthus annuus", best_match_only = TRUE)
 # Preferred data source
 gnr_resolve(names = "Helianthus annuus", preferred_data_sources = c(3,4))
 
-# Strip taxonomic authorities - default is stripauthority=FALSE
+# Return canonical names - default is canonical=FALSE
 head(gnr_resolve(names = "Helianthus annuus")$results)
-head(gnr_resolve(names = "Helianthus annuus", stripauthority=TRUE)$results)
+head(gnr_resolve(names = "Helianthus annuus", canonical=TRUE)$results)
 }
 }
 \author{

diff --git a/tests/testthat/test-gnr_resolve.R b/tests/testthat/test-gnr_resolve.R
@@ -25,10 +25,10 @@ test_that("best_match_only works correctly", {
   expect_is(b$results, "data.frame")
 })
 
-test_that("stripauthority works correctly", {
+test_that("canonical works correctly", {
   y <- "Helianthus annuus"
-  w <- gnr_resolve(y, stripauthority = TRUE)
-  z <- gnr_resolve(y, stripauthority = FALSE)
+  w <- gnr_resolve(y, canonical = TRUE)
+  z <- gnr_resolve(y, canonical = FALSE)
 
   expect_is(w, "list")
   expect_is(z, "list")