R/ncbiSpecies.R

In ropensci/rusda: Interface to USDA Databases

##                       ncbiSpecies                 ##
##      This code is part of the rusda package       ##
##     F.-S. Krah 2016 (last update: 2016-03-18)     ##


# ncbiSpecies <- function(sciname, clean, sub){
#   uid <- get_uid(sciname, check = TRUE)[[1]]
#   url <- paste("http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=",uid, sep="")
#   parse <- htmlTreeParse(url, useInternal = TRUE)
#   parse <- xpathApply(parse, "//strong", xmlValue)
#   sp <- unlist(parse)
#   sp <- sp[grep(sciname, sp)]
#   if(clean == TRUE)
#   {
#     nowant <- c("f\\.|sp\\.|var\\.|subsp\\.|ssp\\.|x|unclassified")
#     if(length(grep(nowant, sp))>0)
#     {sp <- sp[-grep(nowant, sp)]}
#   }
#   if(!sub == TRUE)
#   {
#     sp <- sp[vapply(strsplit(sp, "\\W+"), length, integer(1))==2]
#   }
#   return(sp)
# }


ncbiSpecies <- function(sciname, clean, sub, db = "ncbi"){

  sp <- downstream(sciname, downto = "species", db = db)
  sp <- sp[[1]]$childtaxa_name

  if(clean == TRUE)
  {
    nowant <- c("f\\.|sp\\.|var\\.|subsp\\.|ssp\\.|x|unclassified|sensu")
    if(length(grep(nowant, sp))>0)
    { sp <- sp[-grep(nowant, sp)] }
  }
  if(!sub == TRUE)
  {
    sp <- sp[vapply(strsplit(sp, "\\W+"), length, integer(1))==2]
  }
  sp <- unique(sp)
  return(sp)
}