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#' Formats island-wide simulation output into standard
#' DAISIE list output
#'
#' @inheritParams default_params_doc
#'
#' @return List with IW DAISIE simulation output
#' @keywords internal
DAISIE_format_IW_sampled_stt <- function(island_replicates,
total_time,
M,
sample_freq,
verbose) {
several_islands <- list()
for (rep in 1:length(island_replicates)) {
the_island <- island_replicates[[rep]]
stt_all <- matrix(ncol = 4, nrow = sample_freq + 1)
colnames(stt_all) <- c("Time", "nI", "nA", "nC")
stt_all[, "Time"] <- rev(seq(from = 0,
to = total_time,
length.out = sample_freq + 1))
immig_spec <- the_island$stt_table[1, 2]
ana_spec <- the_island$stt_table[1, 3]
stt_all[1, 2:4] <- c(immig_spec,
ana_spec,
0)
the_stt <- the_island$stt_table
for (i in 2:nrow(stt_all)) {
the_age <- stt_all[i, "Time"]
stt_all[i, 2:4] <- the_stt[max(which(the_stt[, "Time"] >= the_age)), 2:4]
}
island_list <- list()
if (sum(the_stt[nrow(the_stt), 2:4]) == 0) {
island_list[[1]] <- list(
island_age = total_time,
not_present = M,
stt_all = stt_all
)
} else {
taxon_list_size <- length(the_island$taxon_list)
island_list[[1]] <- list(
island_age = total_time,
not_present = M - taxon_list_size,
stt_all = stt_all
)
if (taxon_list_size != 0) {
for (y in seq_len(taxon_list_size)) {
island_list[[y + 1]] <- the_island$taxon_list[[y]]
}
}
}
island_list <- add_brt_table(island_list)
several_islands[[rep]] <- island_list
if (verbose == TRUE) {
message(
"Island being formatted: ", rep, "/", length(island_replicates)
)
}
}
return(several_islands)
}
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