R/get_spp.R

In nwfsc-assess/VAST_WestCoast: Estimation and simulation with VAST for the US West Coast

#' Get the Species and Survey Name
#'
#' Separate a single character string into three words to 
#' determine the survey and scientific name for the species
#' of interest.
#' 
#' @param input A character value that contains the survey of
#' interest and the scientific name of the species. The three
#' words will be split using the \code{split} argument.
#' @param split A character value specifying how to break up
#' the \code{input} argument. The default is to use \code{"_"}.
#' 
#' @return A vector with two entries, survey specifies the survey
#' name and species provides a normalized scientific name.
#' 
#' @author Kelli F. Johnson
#' @importFrom nwfscSurvey createMatrix
#' @export
#' 
#' @examples
#' get_spp(input = "Triennial_Anoplopoma_fimbria")
#' 
get_spp <- function(input, split = "_") {
  if (length(input) > 1) stop("get_spp only accomadates 1 value.")
  splits <- strsplit(x = input, split = split)

  # Survey name
  availablesurveys <- c("WCGBTS",
    nwfscSurvey::createMatrix()[, 1])
  survey <- sapply(splits, "[[", 1)
  finalsurvey <- switch(survey,
    TRIENNIAL = "Triennial",
    Triennial = "Triennial",
    WCGBT = "WCGBTS",
    NWFSC.Combo = "WCGBTS",
    NWFSC.Shelf = "NWFSC.Shelf",
    NWFSC.Slope = "NWFSC.Slope",
    survey)
  if (!finalsurvey %in% availablesurveys) {
    stop("The survey (specified as ", finalsurvey, 
      ") must be one of the following:\n",
      paste(availablesurveys, collapse = "\n"))
  }

  # Species name
  species <- apply(sapply(splits, "[", 2:3), 2, paste, collapse = " ")
  finalspp <- gsub("(^[[:alpha:]])", "\\U\\1", species, perl = TRUE)
  
  return(c("survey" = finalsurvey, "species" = finalspp))
}