R/DAISIE_make_archipelago.R

In xieshu95/Test-Trasie: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

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)
}


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)  
}