#' Extract the STT median from the output of DAISIE_sim functions
#'
#' @inheritParams default_params_doc
#'
#' @return a matrix (?)
#' @export
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)
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.