url fixes

ropensci · Jun 12, 2015 · 6ea6c38 · 6ea6c38
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Showing 3 changed files with 6 additions and 9 deletions.
diff --git a/R/tpl_get.r b/R/tpl_get.r
@@ -1,9 +1,8 @@
 #' Get The Plant List csv files.
 #'
 #' The Plant List \url{http://www.theplantlist.org/}. Note there is a package on
-#' CRAN (taxonstand - \url{http://cran.r-project.org/web/packages/Taxonstand/})
-#' that uses theplantlist.org to search plant names - we have a wrapper around
-#' that function called tpl_search.
+#' CRAN (Taxonstand) that uses theplantlist.org to search plant names - we have
+#' a wrapper around that function called \code{tpl_search}
 #'
 #' @export
 #' @param x Directory to write csv files to.
@@ -12,7 +11,7 @@
 #' @details Throws a warning if you already have a directory of the one
 #' provided, but still works. Writes to your home directory, change dir_ as needed.
 #' @return Returns nothing to console, except a message and progress bar.
-#' Writes csv files to dir_.
+#' Writes csv files to x.
 #' @author John Baumgartner (johnbb@@student.unimelb.edu.au)
 #' @seealso \code{\link{tpl_search}} \code{\link{tpl_families}}
 #' @examples \dontrun{

diff --git a/inst/vign/taxize_vignette.Rmd b/inst/vign/taxize_vignette.Rmd
@@ -38,7 +38,7 @@ temp <- gnr_resolve(names = c("Helianthos annus", "Homo saapiens"))
 head( temp$results )
 ```
 
-The correct spellings are *Helianthus annuus* and *Homo sapiens*. Another approach uses the [Taxonomic Name Resolution Service via the Taxosaurus API][taxosaurus] developed by iPLant and the Phylotastic organization. In this example, we provide a list of species names, some of which are misspelled, and we'll call the API with the *tnrs* function.
+The correct spellings are *Helianthus annuus* and *Homo sapiens*. Another approach uses the Taxonomic Name Resolution Service via the Taxosaurus API developed by iPLant and the Phylotastic organization. In this example, we provide a list of species names, some of which are misspelled, and we'll call the API with the *tnrs* function.
 
 ```{r tnrs, eval=TRUE, cache=FALSE}
 mynames <- c("Helianthus annuus", "Pinus contort", "Poa anua", "Abis magnifica",
@@ -220,7 +220,6 @@ A_clas[[1]]$rank[tolower(A_clas[[1]]$name) %in% B3]
 If we find a direct match (here *Gammarus roeseli*), we are lucky. But we can also match Gammaridae with *Gammarus roeseli*, but on a lower taxonomic level. A more comprehensive and realistic example (matching a trait table with an abundance table) is given in the vignette on matching.
 
 [eol]: http://www.eol.org/
-[taxosaurus]: http://api.phylotastic.org/tnrs
 [ncbi]: http://www.ncbi.nlm.nih.gov/
 [itis]: http://www.itis.gov/
 [phylomatic]: http://phylodiversity.net/phylomatic/

diff --git a/man/tpl_get.Rd b/man/tpl_get.Rd
@@ -18,9 +18,8 @@ Writes csv files to dir_.
 }
 \description{
 The Plant List \url{http://www.theplantlist.org/}. Note there is a package on
-CRAN (taxonstand - \url{http://cran.r-project.org/web/packages/Taxonstand/})
-that uses theplantlist.org to search plant names - we have a wrapper around
-that function called tpl_search.
+CRAN (Taxonstand) that uses theplantlist.org to search plant names - we have
+a wrapper around that function called \code{tpl_search}
 }
 \details{
 Throws a warning if you already have a directory of the one