R/ipni_search.R

In taxize: Taxonomic Information from Around the Web

#' Search for names in the International Plant Names Index (IPNI).
#'
#' Note: This data source is also provided in the Global Names Index (GNI)
#' (http://gni.globalnames.org/data_sources). The interface to the data is
#' different among the two services though.
#'
#' @export
#' @param family Family name to search on (Optional)
#' @param infrafamily Infrafamilial name to search on (Optional)
#' @param genus Genus name to search on (Optional)
#' @param infragenus Infrageneric name to search on (Optional)
#' @param species Species name to search on (Optional) - Note, this is the
#' epithet, not the full genus - epithet name combination.
#' @param infraspecies Infraspecies name to search on (Optional)
#' @param publicationtitle Publication name or abbreviation to search on.
#' Again, replace any spaces with a '+' (e.g. 'J.+Bot.') (Optional)
#' @param authorabbrev Author standard form to search on (publishing author,
#' basionym author or both - see below) (Optional)
#' @param includepublicationauthors TRUE (default) to include the taxon author
#' in the search or FALSE to exclude it
#' @param includebasionymauthors TRUE (default) to include the basionum author
#' in the search or FALSE to exclude it
#' @param geounit Country name or other geographical unit to search on (see
#' the help pages for more information and warnings about the use of this
#' option) (Optional)
#' @param addedsince Date to search on in the format 'yyyy-mm-dd', e.g.
#' 2005-08-01 for all records added since the first of August, 2005. (see the
#' help pages for more information and warnings about the use of this option)
#' (Optional. If supplied must be in format YYYY-MM-DD and must be greater
#' than or equal to 1984-01-01.)
#' @param modifiedsince Date to search on in the format 'yyyy-mm-dd', e.g.
#' 2005-08-01 for all records edited since the first of August, 2005. (See
#' the help pages for more information about the use of this option)
#' (Optional. If supplied must be in format YYYY-MM-DD and must be greater
#' than or equal to 1993-01-01.)
#' @param isapnirecord FALSE (default) to exclude records from the Australian
#' Plant Name Index
#' @param isgcirecord FALSE (default) to exclude records from the Gray Cards
#' Index
#' @param isikrecord FALSE (default) to exclude records from the Index Kewensis
#' @param ranktoreturn One of a few options to choose the ranks returned. See
#' details.
#' @param output One of minimal (default), classic, short, or extended
#' @param ... Curl options passed on to [crul::verb-GET]
#' (Optional). Default: returns all ranks.
#' @references
#' https://web.archive.org/web/20190501132148/http://www.ipni.org/link_to_ipni.html
#' @details
#' `ranktoreturn` options:
#'
#' * "all" - all records
#' * "fam" - family records
#' * "infrafam" - infrafamilial records
#' * "gen" - generic records
#' * "infragen" - infrageneric records
#' * "spec" - species records
#' * "infraspec" - infraspecific records
#'
#' @return a tibble (data.frame)
#' @examples \dontrun{
#' ipni_search(genus='Brintonia', isapnirecord=TRUE, isgcirecord=TRUE,
#'   isikrecord=TRUE)
#' ipni_search(genus='Ceanothus')
#' ipni_search(genus='Pinus', species='contorta')
#'
#' # Different output formats
#' ipni_search(genus='Ceanothus')
#' ipni_search(genus='Ceanothus', output='short')
#' ipni_search(genus='Ceanothus', output='extended')
#' }

ipni_search <- function(family=NULL, infrafamily=NULL, genus=NULL,
  infragenus=NULL, species=NULL, infraspecies=NULL, publicationtitle=NULL,
  authorabbrev=NULL, includepublicationauthors=NULL,
  includebasionymauthors=NULL, geounit=NULL, addedsince=NULL,
  modifiedsince=NULL, isapnirecord=NULL, isgcirecord=NULL, isikrecord=NULL,
  ranktoreturn=NULL, output="minimal", ...) {

  output <- match.arg(output, c('minimal','classic','short','extended'), FALSE)
  output_format <- sprintf('delimited-%s', output)
  url <- "https://www.ipni.org/ipni/advPlantNameSearch.do"
  args <- tc(list(output_format=output_format, find_family=family,
          find_infrafamily=infrafamily, find_genus=genus,
          find_infragenus=infragenus, find_species=species,
          find_infraspecies=infraspecies,
          find_publicationTitle=publicationtitle,
          find_authorAbbrev=authorabbrev,
          find_includePublicationAuthors=l2(includepublicationauthors),
          find_includebasionymauthors=l2(includebasionymauthors),
          find_geounit=geounit,
          find_addedSince=addedsince, find_modifiedSince=modifiedsince,
          find_isAPNIRecord=l2(isapnirecord),
          find_isGCIRecord=l2(isgcirecord),
          find_isIKRecord=l2(isikrecord), find_rankToReturn=ranktoreturn))
  cli <- crul::HttpClient$new(url, headers = tx_ual, opts = list(...))
  tt <- cli$get(query = args)
  if (
    tt$status_code > 200 ||
    tt$response_headers$`content-type` != "text/plain;charset=UTF-8"
  ) {
    stop("No results", call. = FALSE)
  }
  res <- tt$parse("UTF-8")
  df1 <- read.delim(text = res, sep = "%", stringsAsFactors = FALSE)
  if (NROW(df1) == 0) {
    warning("No data found")
    df <- tibble::tibble()
  } else {
    names(df1) <- gsub("\\.", "_", tolower(names(df1)))
    df <- tibble::as_tibble(df1)
  }
  return(df)
}

l2 <- function(x) {
  if (!is.null(x)) {
    if (x) {
      "on"
    } else {
      "off"
    }
  } else{
    NULL
  }
}