#' Does somethings
#'
#' @inheritParams default_params_doc
#'
#' @return something
#' @export
DAISIE_make_archipelago <- function(archipelago,
M,
phylo_data,
archipelago_data) {
the_row <- which(archipelago_data[, "Archipelago"] == archipelago)
island_age <- archipelago_data[the_row, "Age_oldest.Myr."]
area <- archipelago_data[the_row, "Area.km2."]
distance_continent <- archipelago_data[the_row, "Distance_continent"]
distance_nearest_big <- archipelago_data[the_row, "Distance_nearest_big"]
if (archipelago_data[the_row, "Total_species"] == 0) {
archipelago_daisie <- list()
archipelago_daisie[[1]] <- list(island_age = island_age, not_present = M)
} else {
archi_subset <- phylo_data[which(phylo_data[, "Archipelago"] == archipelago), ]
da <- paste(archi_subset[, "Genus"], archi_subset[, "Species"], archi_subset[, "Subspecies"], sep = " ")
db <- as.character(archi_subset[, "DAISIE_STATUS"])
dc <- as.numeric(archi_subset[, "Missing_spec"])
de <- as.character(archi_subset[, "BRANCHING_TIMES"])
de[is.na(de)] <- island_age
archi_daisie <- data.frame(da, db, dc, de)
colnames(archi_daisie) <- c("Clade_name", "Status", "Missing_species", "Branching_times")
archi_daisie <- archi_daisie[rev(order(archi_daisie[, "Branching_times"])), ]
archipelago_daisie <- DAISIE_dataprep(archi_daisie, island_age, M = M)
}
archipelago_daisie[[1]]$area <- area
archipelago_daisie[[1]]$distance_continent <- distance_continent
archipelago_daisie[[1]]$distance_nearest_big <- distance_nearest_big
archipelago_daisie[[1]]$name <- archipelago
archipelago_daisie <- Add_brt_table(archipelago_daisie)
archipelago_daisie[[1]]$brts_table <- NULL
return(archipelago_daisie)
}
#' Does something
#'
#' @param archipelago_list something
#' @param M something
#' @param phylo_data something
#' @param archipelago_data something
#'
#' @return something
#' @export
DAISIE_make_global <- function(archipelago_list, M, phylo_data, archipelago_data) {
global_object <- list()
for (i in 1:length(archipelago_list)) {
the_archipelago <- as.character(archipelago_list[i])
print(the_archipelago)
global_object[[i]] <- DAISIE_make_archipelago(the_archipelago, M, phylo_data, archipelago_data)
}
return(global_object)
}
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