incorpporatd get_nbnid into get_ids, #332

ropensci · Oct 1, 2014 · fa85ba7 · fa85ba7
1 parent 9529b86
commit fa85ba7
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diff --git a/R/get_ids.R b/R/get_ids.R
@@ -7,19 +7,20 @@
 #' @export
 #' @param names character; Taxonomic name to query.
 #' @param db character; database to query. One or  more of \code{ncbi}, \code{itis},
-#'    \code{eol}, \code{col}, \code{tropicos}, \code{gbif}, or \code{ubio}. By
+#'    \code{eol}, \code{col}, \code{tropicos}, \code{gbif}, \code{ubio}, or \code{nbn}. By
 #'    default db is set to search all data sources. 
 #' @param ... Other arguments passed to \code{\link[taxize]{get_tsn}},
 #'    \code{\link[taxize]{get_uid}}, \code{\link[taxize]{get_eolid}},
 #'    \code{\link[taxize]{get_colid}}, \code{\link[taxize]{get_tpsid}},
-#'    \code{\link[taxize]{get_gbifid}}, or \code{\link[taxize]{get_ubioid}}.
+#'    \code{\link[taxize]{get_gbifid}}, \code{\link[taxize]{get_ubioid}},
+#'    \code{\link[taxize]{get_nbnid}}.
 #' @return A vector of taxonomic identifiers, each retaining their respective S3
 #'    classes so that each element can be passed on to another function (see e.g.'s).
 #' @note There is a timeout of 1/3 seconds between queries to NCBI.
 #' @seealso \code{\link[taxize]{get_tsn}}, \code{\link[taxize]{get_uid}},
 #'    \code{\link[taxize]{get_eolid}}, \code{\link[taxize]{get_colid}},
-#'    \code{\link[taxize]{get_tpsid}}, \code{\link[taxize]{get_gbifid}}, or
-#'    \code{\link[taxize]{get_ubioid}}.
+#'    \code{\link[taxize]{get_tpsid}}, \code{\link[taxize]{get_gbifid}},
+#'    \code{\link[taxize]{get_ubioid}}, or \code{\link[taxize]{get_nbnid}}.
 #' @examples \donttest{
 #' # Plug in taxon names directly
 #' ## By default you get ids for all data sources
@@ -28,6 +29,9 @@
 #' ## Or you can specify which source you want via the db parameter
 #' get_ids(names="Chironomus riparius", db = 'ncbi')
 #' get_ids(names="Salvelinus fontinalis", db = 'ubio')
+#' 
+#' get_ids(names="Salvelinus fontinalis", db = 'nbn')
+#' 
 #' get_ids(names=c("Chironomus riparius", "Pinus contorta"), db = 'ncbi')
 #' get_ids(names=c("Chironomus riparius", "Pinus contorta"), db = c('ncbi','itis'))
 #' get_ids(names=c("Chironomus riparius", "Pinus contorta"), db = c('ncbi','itis','col'))
@@ -41,11 +45,12 @@
 #' synonyms(out$tropicos)
 #' }
 
-get_ids <- function(names, db = c('itis','ncbi','eol','col','tropicos','gbif','ubio'), ...)
+get_ids <- function(names, db = c('itis','ncbi','eol','col','tropicos','gbif','ubio','nbn'), ...)
 {
   if(is.null(db))
     stop("Must specify on or more values for db!")
-  db <- match.arg(db, choices = c('itis','ncbi','eol','col','tropicos','gbif','ubio'), several.ok = TRUE)
+  db <- match.arg(db, choices = c('itis','ncbi','eol','col','tropicos','gbif','ubio','nbn'), 
+                  several.ok = TRUE)
 
   foo <- function(x, names, ...){
     ids <- switch(x,
@@ -55,7 +60,8 @@ get_ids <- function(names, db = c('itis','ncbi','eol','col','tropicos','gbif','u
                   col = get_colid(names, ...),
                   tropicos = get_tpsid(names, ...),
                   gbif = get_gbifid(names, ...),
-                  ubio = get_ubioid(names, ...))
+                  ubio = get_ubioid(names, ...),
+                  nbn = get_nbnid(names, ...))
     names(ids) <- names
     return( ids )
   }

diff --git a/man/get_ids.Rd b/man/get_ids.Rd
@@ -4,19 +4,20 @@
 \title{Retrieve taxonomic identifiers for a given taxon name.}
 \usage{
 get_ids(names, db = c("itis", "ncbi", "eol", "col", "tropicos", "gbif",
-  "ubio"), ...)
+  "ubio", "nbn"), ...)
 }
 \arguments{
 \item{names}{character; Taxonomic name to query.}
 
 \item{db}{character; database to query. One or  more of \code{ncbi}, \code{itis},
-\code{eol}, \code{col}, \code{tropicos}, \code{gbif}, or \code{ubio}. By
+\code{eol}, \code{col}, \code{tropicos}, \code{gbif}, \code{ubio}, or \code{nbn}. By
 default db is set to search all data sources.}
 
 \item{...}{Other arguments passed to \code{\link[taxize]{get_tsn}},
 \code{\link[taxize]{get_uid}}, \code{\link[taxize]{get_eolid}},
 \code{\link[taxize]{get_colid}}, \code{\link[taxize]{get_tpsid}},
-\code{\link[taxize]{get_gbifid}}, or \code{\link[taxize]{get_ubioid}}.}
+\code{\link[taxize]{get_gbifid}}, \code{\link[taxize]{get_ubioid}},
+\code{\link[taxize]{get_nbnid}}.}
 }
 \value{
 A vector of taxonomic identifiers, each retaining their respective S3
@@ -39,6 +40,9 @@ get_ids(names="Chironomus riparius")
 ## Or you can specify which source you want via the db parameter
 get_ids(names="Chironomus riparius", db = 'ncbi')
 get_ids(names="Salvelinus fontinalis", db = 'ubio')
+
+get_ids(names="Salvelinus fontinalis", db = 'nbn')
+
 get_ids(names=c("Chironomus riparius", "Pinus contorta"), db = 'ncbi')
 get_ids(names=c("Chironomus riparius", "Pinus contorta"), db = c('ncbi','itis'))
 get_ids(names=c("Chironomus riparius", "Pinus contorta"), db = c('ncbi','itis','col'))
@@ -55,7 +59,7 @@ synonyms(out$tropicos)
 \seealso{
 \code{\link[taxize]{get_tsn}}, \code{\link[taxize]{get_uid}},
    \code{\link[taxize]{get_eolid}}, \code{\link[taxize]{get_colid}},
-   \code{\link[taxize]{get_tpsid}}, \code{\link[taxize]{get_gbifid}}, or
-   \code{\link[taxize]{get_ubioid}}.
+   \code{\link[taxize]{get_tpsid}}, \code{\link[taxize]{get_gbifid}},
+   \code{\link[taxize]{get_ubioid}}, or \code{\link[taxize]{get_nbnid}}.
 }