R/DAISIE_extract_stt_median.R

In DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

#' Extract the STT median from the output of DAISIE_sim functions
#'
#' @inheritParams default_params_doc
#'
#' @return a matrix (?)
#' @keywords internal
DAISIE_extract_stt_median <- function(
  island_replicates,
  trait_pars = NULL) {

  replicates <- length(island_replicates)
  time <- max(island_replicates[[1]][[1]]$stt_all[, 1])
  ### STT ALL species
  s_freq <- length(island_replicates[[1]][[1]]$stt_all[, 1])
  complete_arr <- array(dim = c(s_freq, 6, replicates))
  for (x in 1:replicates) {

    if(is.null(trait_pars)){
      sum_endemics <- island_replicates[[x]][[1]]$stt_all[, "nA"] +
        island_replicates[[x]][[1]]$stt_all[, "nC"]
      total <- island_replicates[[x]][[1]]$stt_all[, "nA"] +
        island_replicates[[x]][[1]]$stt_all[, "nC"] +
        island_replicates[[x]][[1]]$stt_all[, "nI"]
      complete_arr[, , x] <- cbind(
        island_replicates[[x]][[1]]$stt_all[, c("Time", "nI", "nA", "nC")],
        sum_endemics,
        total)
    }else{
      sum_endemics <- island_replicates[[x]][[1]]$stt_all[, "nA"] +
        island_replicates[[x]][[1]]$stt_all[, "nC"] +
        island_replicates[[x]][[1]]$stt_all[, "nA2"] +
        island_replicates[[x]][[1]]$stt_all[, "nC2"]
      total <- island_replicates[[x]][[1]]$stt_all[, "nA"] +
        island_replicates[[x]][[1]]$stt_all[, "nC"] +
        island_replicates[[x]][[1]]$stt_all[, "nI"] +
        island_replicates[[x]][[1]]$stt_all[, "nA2"] +
        island_replicates[[x]][[1]]$stt_all[, "nC2"] +
        island_replicates[[x]][[1]]$stt_all[, "nI2"]
      nI <- island_replicates[[x]][[1]]$stt_all[, "nI"] +
        island_replicates[[x]][[1]]$stt_all[, "nI2"]
      nA <- island_replicates[[x]][[1]]$stt_all[, "nA"] +
        island_replicates[[x]][[1]]$stt_all[, "nA2"]
      nC <- island_replicates[[x]][[1]]$stt_all[, "nC"] +
        island_replicates[[x]][[1]]$stt_all[, "nC2"]
      complete_arr[,,x]<-cbind(island_replicates[[x]][[1]]$stt_all[, 'Time'],
                               nI,
                               nA,
                               nC,
                               sum_endemics,
                               total)
    }
  }
  stt_average_all <- apply(complete_arr, c(1, 2), stats::median)
  colnames(stt_average_all) <- c("Time", "nI", "nA", "nC", "Endemic", "Total")
  return(stt_average_all)
}