#' @title Load Atlantis \code{[...]BiomIndx.txt} file
#'
#' @description This function loads the Atlantis BiomIndx.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. Also loads ecosystem
#' indicators (PelDemRatio, PiscivPlankRatio, DivCount, InfEpiRatio,
#' BSSslope, HabitCover) available in the BiomInx.txt file.
#' @template dir
#' @template file_bioind
#' @template fgs
#' @template verbose
#' @family load functions
#' @return A data frame of total biomass outputs from the \code{BiomIndx.txt} file,
#' formatted similarly to the outputs of run_truth.
#' @author Sarah Gaichas
#' @export
#'
#' @examples
#' d <- system.file("extdata", "SETAS_Example", package = "atlantisom")
#' file <- "outputsBiomIndx.txt"
#' fgs <- load_fgs(dir = d, "Functional_groups.csv")
#' test <- load_bioind(dir = d, file_bioind = file, fgs = fgs)
load_bioind <- function(dir, file_bioind, fgs, verbose = FALSE) {
file.bioind <- file.path(dir, file_bioind)
truebio <- read.table(file.bioind, header = TRUE)
truebio <- truebio[, -grep("Rel", colnames(truebio))]
groupslookup <- fgs[fgs$IsTurnedOn > 0,]
names(truebio)[match(groupslookup$Code,names(truebio))] <- groupslookup$Name
truebio <- truebio %>%
tidyr::gather(species, truebio, -Time) %>%
dplyr::left_join(.,groupslookup %>% dplyr::select(Name,Code),by = c("species"= "Name"))
out <- data.frame(species = truebio$species,
agecl = NA,
polygon = NA,
layer = NA,
time = truebio$Time,
atoutput = truebio$truebio,
code = truebio$Code)
out <- out[order(out$species,out$time,out$polygon,out$agecl),]
return(out)
}
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