R/get_traits.R

In DanOvando/sraplus: Run sraplus Assessments

#' Get Traits
#'
#' Retrieves life history traits from FishLife
#'
#' This function returns the mean un-logged life history traits for the closest match to the
#' supplied taxonomic information.
#'
#' @param Class Character input for taxonomic class
#' @param Order Character input for taxonomic class
#' @param Family Character input for taxonomic class
#' @param Genus Character input for taxonomic class
#' @param Species Character input for taxonomic class
#' @param verbose logical where TRUE prints closest match, FALSE does not
#'
#' @return a dataframe of mean trait values
#' @export
#'
#' @examples
#' \dontrun{
#' life_traits <- Get_traits(Genus = "Lutjanus", Species = "campechanus")
#' }
get_traits <- function( Class="predictive", Order="predictive", Family="predictive", Genus="predictive", Species="predictive",verbose = FALSE) {
  
  
  closest_match <- sraplus::search_species(Class = Class, Order = Order, Family = Family, Genus = Genus, Species = Species)
  
  trait_table <- as.data.frame(t(sraplus::FishBase_and_RAM$ParHat$beta_gj[closest_match$GroupNum[[1]],]))
  
  trait_table[colnames(trait_table) != 'Temperature'] <-
    exp(trait_table[colnames(trait_table) != 'Temperature'])
  
  return(trait_table)
}