R/load_agebioind.R

In r4atlantis/atlantisom: Generates Data Sets From Atlantis Scenarios

#' @title Load Atlantis \code{[...]AgeBiomIndx.txt} file
#'
#' @description This function loads the Atlantis AgeBiomIndx.txt output file.
#'   Biomass (total annual tonnes) is only available for species that are
#'   turned on in the \code{functionalGroups.csv} file. Function does not
#'   load relative biomass for these species.
#' @template dir
#' @template file_agebioind
#' @template fgs
#' @template verbose
#' @family load functions
#' @return A data frame of total biomass outputs from the \code{AgeBiomIndx.txt} file,
#' formatted similarly to the outputs of run_truth.
#' @author Sarah Gaichas
#' @export
#'
#' @examples
#' \dontrun{
#' d <- system.file("extdata", "SETAS_Example", package = "atlantisom")
#' file <- "outputsAgeBiomIndx.txt"
#' fgs <- load_fgs(dir = d, "Functional_groups.csv")
#' test <- load_agebioind(dir = d, file_bioind = file, fgs = fgs)
#' }

load_agebioind <- function(dir, file_agebioind, fgs, verbose = FALSE) {
  file.bioind <- file.path(dir, file_agebioind)
  truebio <- read.table(file.bioind, header = TRUE)

  truebio <- truebio %>%
    tidyr::pivot_longer(.,cols=contains("."),names_to = "code",values_to = "atoutput") %>%
    dplyr::mutate(age = stringr::str_extract(code,"[^.]+$")) %>%
    dplyr::mutate(code = stringr::str_extract(code,"^[a-z,A-Z]+"))

  groupslookup <- fgs[fgs$IsTurnedOn > 0,] %>%
    dplyr::select(Code,Name)

  out <- truebio %>% dplyr::left_join(.,groupslookup,by = c("code" = "Code")) %>%
    dplyr::rename(species = Name, time=Time) %>%
    dplyr::mutate(agecl=NA,polygon=NA,layer=NA) %>%
    dplyr::select(species,agecl,polygon,layer,time,atoutput,code,age) %>%
    dplyr::arrange(species,time,age,polygon,agecl)

  return(out)
}