ran through all egs, fixed any not working

ropensci · Jun 13, 2015 · 8885e5c · 8885e5c
1 parent 54bc65d
commit 8885e5c
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diff --git a/NAMESPACE b/NAMESPACE
@@ -214,6 +214,7 @@ export(itis_name)
 export(itis_native)
 export(itis_ping)
 export(itis_refs)
+export(itis_searchcommon)
 export(itis_taxrank)
 export(itis_terms)
 export(iucn_getname)

diff --git a/R/children.R b/R/children.R
@@ -51,6 +51,7 @@
 #' children("Poa", db = 'col', rows=1)
 #'
 #' # use curl options
+#' library("httr")
 #' res <- children("Poa", db = 'col', rows=1, config=verbose())
 #' res <- children("Salmo", db = 'itis', config=verbose())
 #' res <- children("Salmo", db = 'ncbi', config=verbose())

diff --git a/R/col_classification.R b/R/col_classification.R
@@ -27,26 +27,6 @@
 #' @export
 #' @rdname col_classification-defunct
 #' @keywords internal
-#' @examples \dontrun{
-#' # A basic example
-#' col_classification(name="Apis")
-#'
-#' # An example where there is no classification
-#' col_classification(id=11935941)
-#'
-#' # Use a specific year's checklist
-#' col_classification(name="Apis", checklist="2012")
-#' col_classification(name="Apis", checklist="2009")
-#'
-#' # Pass in many names or many id's
-#' out <- col_classification(name=c("Buteo","Apis","Accipiter","asdf"),
-#'    checklist="2012")
-#' out$Apis # get just the output you want
-#' ldply(out) # or combine to one data.frame
-#'
-#' # Use get_colid to pass in ID directly
-#' col_classification(id=get_colid(sciname='Puma concolor'))
-#' }
 col_classification <- function(name=NULL, id=NULL, format=NULL, start=NULL, checklist=NULL)
 {
   .Defunct(msg="This function is defunct. See classification().")

diff --git a/R/col_search.R b/R/col_search.R
@@ -1,6 +1,6 @@
 #' Search Catalogue of Life for taxonomic IDs
 #'
-#' @import RCurl XML plyr
+#' @import XML plyr
 #' @export
 #' @param name The string to search for. Only exact matches found the name given
 #'   	will be returned, unless one or wildcards are included in the search
@@ -77,11 +77,17 @@ parse_full <- function(x) {
   taxize_ldfast(lapply(tmp, function(z) {
     switch(xpathSApply(z, "name_status", xmlValue),
            `accepted name` = {
-             h_vals <- xpathSApply(z, "classification//name", xmlValue)
-             h_nms <- xpathSApply(z, "classification//rank", xmlValue)
-             h <- setNames(rbind.data.frame(h_vals), h_nms)
-             rank <- xpathSApply(z, "rank", xmlValue)
-             id <- xpathSApply(z, "id", xmlValue)
+             if (xpathSApply(z, "classification", xmlValue) == "") {
+                h <- parse_terse(z)
+                rank <- xpathSApply(z, "rank", xmlValue)
+                id <- xpathSApply(z, "id", xmlValue)
+             } else {
+               h_vals <- xpathSApply(z, "classification//name", xmlValue)
+               h_nms <- xpathSApply(z, "classification//rank", xmlValue)
+               h <- setNames(rbind.data.frame(h_vals), h_nms)
+               rank <- xpathSApply(z, "rank", xmlValue)
+               id <- xpathSApply(z, "id", xmlValue)
+             }
            },
            `common name` = {
              h_vals <- xpathSApply(z, "accepted_name//classification//name", xmlValue)
@@ -91,11 +97,17 @@ parse_full <- function(x) {
              id <- xpathSApply(z, "accepted_name/id", xmlValue)
            },
            synonym = {
-             h_vals <- xpathSApply(z, "accepted_name//classification//name", xmlValue)
-             h_nms <- xpathSApply(z, "accepted_name//classification//rank", xmlValue)
-             h <- setNames(rbind.data.frame(h_vals), h_nms)
-             rank <- xpathSApply(z, "accepted_name/rank", xmlValue)
-             id <- xpathSApply(z, "accepted_name/id", xmlValue)
+             if (length(xpathSApply(z, "classification")) == 0) {
+               h <- parse_terse(z)
+               rank <- xpathSApply(z, "rank", xmlValue)
+               id <- xpathSApply(z, "id", xmlValue)
+             } else {
+               h_vals <- xpathSApply(z, "accepted_name//classification//name", xmlValue)
+               h_nms <- xpathSApply(z, "accepted_name//classification//rank", xmlValue)
+               h <- setNames(rbind.data.frame(h_vals), h_nms)
+               rank <- xpathSApply(z, "accepted_name/rank", xmlValue)
+               id <- xpathSApply(z, "accepted_name/id", xmlValue)
+             }
            }
     )
     target <- setNames(rbind.data.frame(

diff --git a/R/eol_hierarchy.R b/R/eol_hierarchy.R
@@ -16,10 +16,6 @@
 #' @export
 #' @rdname eol_hierarchy-defunct
 #' @keywords internal
-#' @examples \dontrun{
-#' # Using get_eolid
-#' eol_hierarchy(get_eolid(sciname='Poa annua'))
-#' }
 eol_hierarchy <- function(taxonid, common_names = NULL, synonyms = NULL,
                           key = NULL, callopts=list())
 {

diff --git a/R/eol_invasive.R b/R/eol_invasive.R
@@ -62,24 +62,6 @@
 #' @references See info for each data source at \url{http://eol.org/collections/55367/taxa}
 #' @rdname eol_invasive-defunct
 #' @keywords internal
-#'
-#' @examples \dontrun{
-#' eol_invasive(name='Brassica oleracea', dataset='gisd')
-#' eol_invasive(name=c('Lymantria dispar','Cygnus olor','Hydrilla verticillata','Pinus concolor'),
-#'    dataset='gisd')
-#' eol_invasive(name='Sargassum', dataset='gisd')
-#' eol_invasive(name='Ciona intestinalis', dataset='mineps')
-#' eol_invasive(name=c('Lymantria dispar','Cygnus olor','Hydrilla verticillata','Pinus concolor'),
-#'    dataset='i3n')
-#' eol_invasive(name=c('Branta canadensis','Gallus gallus','Myiopsitta monachus'),
-#'    dataset='daisie')
-#' eol_invasive(name=c('Branta canadensis','Gallus gallus','Myiopsitta monachus'), dataset='isc')
-#'
-#' # Count
-#' eol_invasive(name=c('Lymantria dispar','Cygnus olor','Hydrilla verticillata','Pinus concolor'),
-#'    dataset='gisd', count = TRUE)
-#' }
-
 eol_invasive <- function(name = NULL, dataset="all", searchby = grep, page=NULL,
   per_page=NULL, key = NULL, verbose=TRUE, count=FALSE, ...) {
 

diff --git a/R/get_ubioid.R b/R/get_ubioid.R
@@ -129,9 +129,15 @@ get_ubioid <- function(searchterm, searchtype = "scientific", ask = TRUE, verbos
       ubio_df <- switch(searchtype,
                         scientific = ubio_df[,c("namebankid","namestring","packagename","rankname")],
                         vernacular = ubio_df[,c("namebankid","namestring","packagename")])
-      ubio_df <- rename(ubio_df, c('packagename' = 'family', 'rankname' = 'rank',
-                                   'namebankid' = 'ubioid'))
-      ubio_df <- fix_ranks(ubio_df)
+      if (searchtype == "scientific") {
+        ubio_df <- rename(ubio_df, c('packagename' = 'family',
+                                     'rankname' = 'rank',
+                                     'namebankid' = 'ubioid'))
+      } else {
+        ubio_df <- rename(ubio_df, c('packagename' = 'family',
+                                     'namebankid' = 'ubioid'))
+      }
+      if (searchtype == "scientific") ubio_df <- fix_ranks(ubio_df)
 
       direct <- NA
       # should return NA if spec not found
@@ -176,10 +182,9 @@ get_ubioid <- function(searchterm, searchtype = "scientific", ask = TRUE, verbos
 
           if (!is.null(family) || !is.null(rank)) {
             ubio_df <- filt(ubio_df, "family", family)
-            ubio_df <- filt(ubio_df, "rank", rank)
+            if (searchtype == "scientific") ubio_df <- filt(ubio_df, "rank", rank)
             ubioid <- id <- ubio_df$ubioid
             if (length(id) == 1) {
-              rank_taken <- as.character(ubio_df$rank)
               att <- "found"
             }
           }

diff --git a/R/gisd_isinvasive.R b/R/gisd_isinvasive.R
@@ -38,14 +38,6 @@
 #' @seealso \code{eol_invasive}
 #' @rdname gisd_invasive-defunct
 #' @keywords internal
-#' @examples \dontrun{
-#' sp <- c("Carpobrotus edulis", "Rosmarinus officinalis")
-#' ## first species is invasive, second one is not.
-#' gisd_isinvasive(sp)
-#' gisd_isinvasive(sp, simplify = TRUE)
-#' }
-#'
-
 gisd_isinvasive <- function(x, simplify = FALSE, verbose=TRUE)
 {
   .Defunct("g_invasive", "traits", msg = "This function is defunct. See traits::g_invasive()")

diff --git a/R/itis.R b/R/itis.R
@@ -861,6 +861,7 @@ searchbycommonname <- function(x, ...) {
 
 #' Searches common name and acts as thin wrapper around \code{searchbycommonnamebeginswith} and \code{searchbycommonnameendswith}
 #'
+#' @export
 #' @param x Search terms
 #' @param from Default is to search from beginning. Use \code{end} to serch from end.
 #' @param ... Curl options passed on to \code{\link[httr]{GET}}

diff --git a/R/nbn_search.R b/R/nbn_search.R
@@ -18,7 +18,7 @@
 #'
 #' @examples \dontrun{
 #' nbn_search(q = "blackbird")
-#' nbn_search(q = "blackbird", start = TRUE)
+#' nbn_search(q = "blackbird", start = 4)
 #' nbn_search(q = "blackbird", all = TRUE)
 #' nbn_search(q = "blackbird", taxonOutputGroupKey = "NHMSYS0000080039")
 #'

diff --git a/R/ncbi_getbyid.R b/R/ncbi_getbyid.R
@@ -15,13 +15,6 @@
 #' @author Scott Chamberlain \email{myrmecocystus@@gmail.com}
 #' @rdname ncbi_getbyid-defunct
 #' @keywords internal
-#' @examples \dontrun{
-#' # A single gene
-#' ncbi_getbyid(ids="360040093", format="fasta")
-#'
-#' # Many genes (with different accession numbers)
-#' ncbi_getbyid(ids=c("360040093","347448433"), format="fasta")
-#' }
 ncbi_getbyid <- function(ids, format="fasta", verbose=TRUE)
 {
   .Defunct("ncbi_byid", "traits", msg="This function is defunct. See traits::ncbi_byid()")

diff --git a/R/ncbi_getbyname.R b/R/ncbi_getbyname.R
@@ -14,14 +14,6 @@
 #' @author Scott Chamberlain \email{myrmecocystus@@gmail.com}
 #' @rdname ncbi_getbyname-defunct
 #' @keywords internal
-#' @examples \dontrun{
-#' # A single species
-#' ncbi_getbyname(taxa="Acipenser brevirostrum")
-#'
-#' # Many species
-#' species <- c("Colletes similis","Halictus ligatus","Perdita trisignata")
-#' ncbi_getbyname(taxa=species, gene = c("coi", "co1"), seqrange = "1:2000")
-#' }
 ncbi_getbyname <- function(taxa, gene="COI", seqrange="1:3000", getrelated=FALSE,
                            verbose=TRUE)
 {

diff --git a/R/ncbi_search.R b/R/ncbi_search.R
@@ -22,38 +22,6 @@
 #'   \email{zacharyfoster1989@@gmail.com}
 #' @rdname ncbi_search-defunct
 #' @keywords internal
-#' @examples \dontrun{
-#' # A single species
-#' out <- ncbi_search(taxa="Umbra limi", seqrange = "1:2000")
-#' # Get the same species information using a taxonomy id
-#' out <- ncbi_search(id = "75935", seqrange = "1:2000")
-#' # If the taxon name is unique, using the taxon name and id are equivalent
-#' all(ncbi_search(id = "75935") ==  ncbi_search(taxa="Umbra limi"))
-#' # If the taxon name is not unique, use taxon id
-#' #  "266948" is the uid for the butterfly genus, but there is also a genus of orchids with the
-#' #  same name
-#' nrow(ncbi_search(id = "266948")) ==  nrow(ncbi_search(taxa="Satyrium"))
-#' # get list of genes available, removing non-unique
-#' unique(out$gene_desc)
-#' # does the string 'RAG1' exist in any of the gene names
-#' out[grep("RAG1", out$gene_desc, ignore.case=TRUE),]
-#'
-#' # A single species without records in NCBI
-#' out <- ncbi_search(taxa="Sequoia wellingtonia", seqrange="1:2000", getrelated=TRUE)
-#'
-#' # Many species, can run in parallel or not using plyr
-#' species <- c("Salvelinus alpinus","Ictalurus nebulosus","Carassius auratus")
-#' out2 <- ncbi_search(taxa=species, seqrange = "1:2000")
-#' lapply(out2, head) # see heads of all
-#' library("plyr")
-#' out2df <- ldply(out2) # make data.frame of all
-#' unique(out2df$gene_desc) # get list of genes available, removing non-unique
-#' out2df[grep("60S ribosomal protein", out2df$gene_desc, ignore.case=TRUE),] # search across all
-#'
-#' # Using the getrelated and entrez_query options
-#' ncbi_search(taxa = "Olpidiopsidales", limit = 5, getrelated = TRUE,
-#'             entrez_query = "18S[title] AND 28S[title]")
-#' }
 #' @export
 ncbi_search <- function(taxa = NULL, id = NULL, seqrange="1:3000", getrelated=FALSE, limit = 500,
                         entrez_query = NULL, hypothetical = FALSE, verbose=TRUE)

diff --git a/R/phylomatic_tree.R b/R/phylomatic_tree.R
@@ -50,13 +50,15 @@
 #' # names, so there's no per se rule), you will get an error when using \code{get='GET'},
 #' # when that happens use \code{get='POST'}
 #' spp <- names_list("species", 200)
-#' (out <- phylomatic_tree(taxa = spp, get = "GET"))
+#' # (out <- phylomatic_tree(taxa = spp, get = "GET"))
 #' (out <- phylomatic_tree(taxa = spp, get = "POST"))
 #' plot(out)
 #'
 #' # Pass in a tree from a URL on the web
 #' spp <- c('Abies amabilis','Abies balsamea','Abies bracteata','Abies concolor','Abies fraseri',
 #'    'Abies grandis','Abies lasiocarpa','Abies magnifica','Abies procera','Acacia berlandieri')
+#' spp <- c('Pinus koraiensis', 'Pinus sibirica', 'Pinus albicaulis', 'Pinus lambertiana',
+#'          'Pinus bungeana', 'Pinus strobus', 'Pinus_cembra')
 #' url <- "http://datadryad.org/bitstream/handle/10255/dryad.8791/final_tree.tre?sequence=1"
 #' phylomatic_tree(taxa=spp, treeuri=url)
 #'

diff --git a/R/tnrs.R b/R/tnrs.R
@@ -27,11 +27,8 @@
 #' @details If there is no match in the Taxosaurus database, nothing is
 #'    returned, so youwill not get anything back for non matches.
 #' @examples \dontrun{
-#' # Default, uses GET curl method, you can't specify any other parameters when
-#' using GET
-#' mynames <- c("Panthera tigris", "Neotamias minimus", "Magnifera indica")
-#' tnrs(query = mynames)
-#'
+#' # Default, uses GET curl method, you can't specify any other
+#' # parameters when using GET
 #' # Specifying the source to match against
 #' mynames <- c("Helianthus annuus", "Poa annua")
 #' tnrs(query = mynames, source = "iPlant_TNRS")

diff --git a/R/tp_classification.R b/R/tp_classification.R
@@ -10,11 +10,6 @@
 #' @export
 #' @rdname tp_classification-defunct
 #' @keywords internal
-#' @examples \dontrun{
-#' tp_classification(id = 25509881)
-#' tp_classification(id = c(25509881,2700851))
-#' tp_classification(id = c(25509881,2700851), callopts=verbose())
-#' }
 tp_classification <- function(id=NULL, key=NULL, callopts=list())
 {
   .Defunct(msg="This function is defunct. See classification().")

diff --git a/R/tpl_search.r b/R/tpl_search.r
@@ -16,17 +16,6 @@
 #' @param ... Further arguments passed on to the TPL or TPLck function of Taxonstand.
 #' 		See \code{TPL} and \code{TPLck} for arguments.
 #' @seealso \code{\link[taxize]{tpl_get}}, \code{\link[taxize]{tpl_families}}
-#' @examples \dontrun{
-#' # Regular non-parallel
-#' splist <- c("Heliathus annuus","Abies procera","Poa annua",
-#'    "Platanus occidentalis","Carex abrupta","Arctostaphylos canescens",
-#'    "Ocimum basilicum","Vicia faba","Quercus kelloggii","Lactuca serriola")
-#' tpl_search(taxon = splist)
-#'
-#' # Use more arguments within TPLck
-#' tpl_search(taxon = "Microbryum curvicollum", corr = TRUE)
-#' tpl_search(taxon = "Microbryum curvicollum", corr = TRUE, max.distance=5)
-#' }
 #' @export
 #' @rdname tpl_search-defunct
 tpl_search <- function(taxon, paral = FALSE, ...) {

diff --git a/man/children.Rd b/man/children.Rd
@@ -77,6 +77,7 @@ children("Poa", db = 'col')
 children("Poa", db = 'col', rows=1)
 
 # use curl options
+library("httr")
 res <- children("Poa", db = 'col', rows=1, config=verbose())
 res <- children("Salmo", db = 'itis', config=verbose())
 res <- children("Salmo", db = 'ncbi', config=verbose())

diff --git a/man/col_classification-defunct.Rd b/man/col_classification-defunct.Rd
@@ -42,27 +42,5 @@ THIS FUNCTION IS DEFUNCT.
 You must provide one of name or id. The other parameters (format
 		and start) are optional.
 }
-\examples{
-\dontrun{
-# A basic example
-col_classification(name="Apis")
-
-# An example where there is no classification
-col_classification(id=11935941)
-
-# Use a specific year's checklist
-col_classification(name="Apis", checklist="2012")
-col_classification(name="Apis", checklist="2009")
-
-# Pass in many names or many id's
-out <- col_classification(name=c("Buteo","Apis","Accipiter","asdf"),
-   checklist="2012")
-out$Apis # get just the output you want
-ldply(out) # or combine to one data.frame
-
-# Use get_colid to pass in ID directly
-col_classification(id=get_colid(sciname='Puma concolor'))
-}
-}
 \keyword{internal}
 
diff --git a/man/eol_hierarchy-defunct.Rd b/man/eol_hierarchy-defunct.Rd
@@ -30,11 +30,5 @@ THIS FUNCTION IS DEFUNCT.
 It's possible to return JSON or XML with the EOL API. However,
 		this function only returns JSON for now.
 }
-\examples{
-\dontrun{
-# Using get_eolid
-eol_hierarchy(get_eolid(sciname='Poa annua'))
-}
-}
 \keyword{internal}
 
diff --git a/man/eol_invasive-defunct.Rd b/man/eol_invasive-defunct.Rd
@@ -77,24 +77,6 @@ Datasets are not updated that often. Here's last updated dates for some of the d
  \item mineps updated 1 yr ago
 }
 }
-\examples{
-\dontrun{
-eol_invasive(name='Brassica oleracea', dataset='gisd')
-eol_invasive(name=c('Lymantria dispar','Cygnus olor','Hydrilla verticillata','Pinus concolor'),
-   dataset='gisd')
-eol_invasive(name='Sargassum', dataset='gisd')
-eol_invasive(name='Ciona intestinalis', dataset='mineps')
-eol_invasive(name=c('Lymantria dispar','Cygnus olor','Hydrilla verticillata','Pinus concolor'),
-   dataset='i3n')
-eol_invasive(name=c('Branta canadensis','Gallus gallus','Myiopsitta monachus'),
-   dataset='daisie')
-eol_invasive(name=c('Branta canadensis','Gallus gallus','Myiopsitta monachus'), dataset='isc')
-
-# Count
-eol_invasive(name=c('Lymantria dispar','Cygnus olor','Hydrilla verticillata','Pinus concolor'),
-   dataset='gisd', count = TRUE)
-}
-}
 \references{
 See info for each data source at \url{http://eol.org/collections/55367/taxa}
 }