R/ncbi_children.R

In ropensci/taxize: Taxonomic Information from Around the Web

#' @title Search NCBI for children of a taxon
#'
#' @description Search the NCBI Taxonomy database for uids of children of taxa.
#' Taxa can be referenced by name or uid. Referencing by name is faster
#'
#' In a few cases, different taxa have the same name (e.g. Satyrium; see 
#' examples). If one of these are searched for then the children of both taxa 
#' will be returned. This can be avoided by using a uid instead of the name or 
#' specifying an ancestor. If an ancestor is provided, only children of both 
#' the taxon and its ancestor are returned. This will only fail if there are 
#' two taxa with the same name and the same specified ancestor.
#'
#' @export
#' @param name (`character`) The string to search for. Only exact matches 
#' found the name given will be returned. Not compatible with `id`.
#' @param id (`character`/`numeric`) The uid to search for. Not compatible with 
#' `name`.
#' @param start The first record to return. If omitted, the results are 
#' returned from the first record (start=0).
#' @param max_return (`numeric; length=1`) The maximum number of children
#' to return.
#' @param ancestor (`character`) The ancestor of the taxon being searched 
#' for. This is useful if there could be more than one taxon with the same 
#' name. Has no effect if `id` is used.
#' @param out_type (character) Currently either `"summary"` or `"uid"`:
#' * `summary` The output is a list of `data.frame` with children uid, name,
#' and rank.
#' * `uid` A list of character vectors of children uids
#' @param ambiguous `logical; length 1` If `FALSE`, children taxa 
#' with words like "unclassified", "unknown", "uncultured", or "sp." are 
#' removed from the output. NOTE: This option only applies when 
#' `out_type= "summary"`.
#' @param key (character) NCBI Entrez API key. optional. See Details.
#' @param ... Curl options passed on to [crul::HttpClient]
#' @return The output type depends on the value of the `out_type` 
#' parameter. Taxa that cannot be found will result in `NA`s and a lack 
#' of children results in an empty data structure.
#' @seealso [ncbi_get_taxon_summary()], [children()]
#' @author Zachary Foster \email{zacharyfoster1989@@gmail.com}
#' 
#' @section Authentication:
#' See [taxize-authentication()] for help on authentication. 
#' We strongly recommend getting an API key
#' 
#' @section HTTP version:
#' We hard code `http_version = 2L` to use HTTP/1.1 in HTTP requests to
#' the Entrez API. See `curl::curl_symbols('CURL_HTTP_VERSION')` 
#' 
#' @section Rate limits:
#' In case you run into errors due to your rate limit being exceeded, see
#' [taxize_options()], where you can set `ncbi_sleep`.
#'
#' @examples \dontrun{
#' ncbi_children(name="Satyrium") #Satyrium is the name of two different genera
#' ncbi_children(name="Satyrium", ancestor="Eumaeini") # A genus of butterflies
#' ncbi_children(name="Satyrium", ancestor="Orchidaceae") # A genus of orchids
#' ncbi_children(id="266948") #"266948" is the uid for the butterfly genus
#' ncbi_children(id="62858") #"62858" is the uid for the orchid genus
#'
#' # use curl options
#' ncbi_children(name="Satyrium", ancestor="Eumaeini", verbose = TRUE)
#' }
ncbi_children <- function(name = NULL, id = NULL, start = 0, max_return = 1000,
                          ancestor = NULL, out_type = c("summary", "uid"), 
                          ambiguous = FALSE, key = NULL, ...) {

  assert(name, "character")
  assert(id, c("character", "numeric", "uid"))
  key <- getkey(key, "ENTREZ_KEY")

  # Constants -----------------------------------------------------------------
  ambiguous_regex <- paste(
     sep = "|", "unclassified", "environmental", "uncultured", "unknown",
     "unidentified", "candidate", "\\ssp\\.", "s\\.l\\.", "sensu lato", "clone",
     "miscellaneous", "candidatus", "affinis", "aff\\.", "incertae sedis",
     "mixed", "samples", "libaries")
  # Argument validation -------------------------------------------------------
  if (sum(c(is.null(name), is.null(id))) != 1) {
    stop("Either name or id must be specified, but not both")
  }
  out_type <- match.arg(out_type)
  # Get name from id ----------------------------------------------------------
  if (is.null(name)) {
    if (!inherits(id, 'uid')) attr(id, 'class') <- 'uid'
    id_taxonomy <- classification(id, db = 'ncbi')
    id_taxonomy <- lapply(id_taxonomy, function(z) {
      if (!(inherits(z, "data.frame"))) data.frame(NULL) else z
    })
    name <- vapply(id_taxonomy,
                   function(x) ifelse(nrow(x) > 0, x$name[nrow(x)], 
                    as.character(NA)), character(1))
    ancestor <- vapply(id_taxonomy,
                       function(x) ifelse(nrow(x) > 1, x$name[nrow(x) - 1], 
                        as.character(NA)), character(1))
    # set id to NULL because we're using name now
    id <- NULL
  } else if (is.null(ancestor)) {
    ancestor <- rep(NA, length(name))
  }
  # Function to search for queries one at a time ------------------------------
  single_search <- function(name, ancestor, ...) {
    if (is.na(name)) return(NA)
    # Make eutils esearch query  - - - - - - - - - - - - - - - - - - - - - - - 
    if (is.na(ancestor)) {
      ancestor_query <- NULL
    } else {
      ancestor_query <- paste0("+AND+", ancestor, "[subtree]")
    }
    
    if (is.null(id)) {
      args <- tc(list(
        db = 'taxonomy', 
        term = paste0(name, "[Next+Level]", ancestor_query),
        RetMax = max_return,
        RetStart = start,
        api_key = key
      ))
      args$term <- gsub("\\+", " ", args$term)
      
      # Search ncbi for children - - - - - - - - - - - - - - - - - - - - - - - 
      cli <- crul::HttpClient$new(ncbi_base(), headers = tx_ual,
        opts = list(http_version = 2L, ...))
      rr <- cli$get('entrez/eutils/esearch.fcgi', query = args)
      rr$raise_for_status()
      raw_results <- rr$parse("UTF-8")
      
      # Parse results  - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
      results <- xml2::read_xml(raw_results)
      children_uid <- xml_text_all(results, "//eSearchResult/IdList/Id")
      
    } else {
      args <- tc(list(
        dbfrom = 'taxonomy',
        db = 'taxonomy',
        id = id,
        term = paste0(name, "[Next+Level]"),
        RetMax = max_return,
        RetStart = start,
        api_key = key
      ))
      args$term <- gsub("\\+", " ", args$term)
      
      # Search ncbi for children - - - - - - - - - - - - - - - - - - - - - - - 
      cli <- crul::HttpClient$new(ncbi_base(), headers = tx_ual,
        opts = list(http_version = 2L, ...))
      rr <- cli$get('entrez/eutils/elink.fcgi', query = args)
      rr$raise_for_status()
      raw_results <- rr$parse("UTF-8")
      
      # Parse results  - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
      results <- xml2::read_xml(raw_results)
      children_uid <- xml_text_all(results, 
        "//eLinkResult/LinkSet/LinkSetDb/Link/Id")
    }
    if (length(children_uid) == 0) {
      if (out_type == "summary") {
        output <- data.frame(
          childtaxa_id     = character(),
          childtaxa_name   = character(),
          childtaxa_rank   = character(),
          stringsAsFactors = FALSE
        )
      } else {
        output <- numeric()
      }
    } else {
      if (out_type == "summary") {
        output <- ncbi_get_taxon_summary(children_uid, key = key, ...)
        names(output) <- c("childtaxa_id", "childtaxa_name", "childtaxa_rank")
        # Remove ambiguous results  -  -  -  -  -  -  -  -  -  -  -  -  -  -  -
        if (!ambiguous) {
          output <- output[!grepl(ambiguous_regex, output$childtaxa_name, 
            ignore.case = TRUE), ]
        }
      } else {
        output <- children_uid
      }
      # numeric row names can be misleading after filtering
      rownames(output) <- NULL 
    }
    # NCBI limits requests to three per second
    ncbi_rate_limit_pause(key)
    return(output)
  }
  # Combine the result of multiple searches -----------------------------------
  # output <- Map(single_search, name, ancestor)
  output <- list()
  for (i in seq_along(name)) {
    output[[i]] <- single_search(name[[i]], ancestor[[i]], ...)
  }
  if (is.null(id)) names(output) <- name else names(output) <- id
  return(output)
}