R/DAISIE_format_IW.R

In xieshu95/DAISIE_new: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

#' Formats island-wide simulation output into
#' standard DAISIE list output
#'
#' @inheritParams default_params_doc
#'
#' @return List with CS DAISIE simulation output
#' @examples
#' island_replicates <- list()
#' island_replicates[[1]] <- DAISIE:::DAISIE_sim_core_constant_rate(
#'   time = 5,
#'   mainland_n = 1000,
#'   pars = c(2, 2, 40, 0.1, 1),
#'   nonoceanic_pars = c(0, 0)
#')
#' formated_island <- DAISIE:::DAISIE_format_IW(
#'   island_replicates = island_replicates,
#'   time = 5,
#'   M = 1000,
#'   sample_freq = 25,
#'   verbose = FALSE
#')
DAISIE_format_IW <- function(island_replicates,
                             time,
                             M,
                             sample_freq,
                             verbose = TRUE,
                             trait_pars = NULL) {
  
  if(!is.null(trait_pars)){
    return(
      DAISIE_format_IW_trait(
        island_replicates = island_replicates,
        time = time,
        M = M,
        sample_freq = sample_freq,
        verbose = verbose,
        trait_pars = trait_pars
      )
    )
  }
  totaltime <- time
  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 = totaltime,
                                 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$stt_table
    for (i in 2:nrow(stt_all)) {
      the_age <- stt_all[i, "Time"]
      stt_all[i, 2:4] <- the_stt[max(which(the_stt[, "Time"] >= the_age)), 2:4]
    }
    island_list <- list()
    if (sum(the_stt[nrow(the_stt), 2:4]) == 0) {
      island_list[[1]] <- list(
        island_age = totaltime,
        not_present = M,
        stt_all = stt_all
      )
    } else {
      island_list[[1]] <- list(
        island_age = totaltime,
        not_present = length(the_island$taxon_list),
        stt_all = stt_all
      )
      for (y in 1:length(the_island$taxon_list)) {
        island_list[[y + 1]] <- the_island$taxon_list[[y]]
      }
    }
    island_list <- Add_brt_table(island_list)
    several_islands[[rep]] <- island_list

    if (verbose == TRUE) {
      print(paste(
        "Island being formatted: ",
        rep,
        "/",
        length(island_replicates),
        sep = "")
      )
    }
  }
  return(several_islands)
}

DAISIE_format_IW_trait <- function(island_replicates,
                                   time,
                                   M,
                                   sample_freq,
                                   verbose = FALSE,
                                   trait_pars = NULL)
{
  
  totaltime <- time
  several_islands = list()
  for(rep in 1:length(island_replicates))
  {
    the_island = island_replicates[[rep]]
    M1 <- M
    M2 <- trait_pars$M2
    Mtotal <- M1 + M2
    stt_all = matrix(ncol = 7,nrow = sample_freq + 1)
    colnames(stt_all) = c("Time","nI","nA","nC","nI2","nA2","nC2")
    stt_all[,"Time"] = rev(seq(from = 0,to = totaltime,length.out = sample_freq + 1))
    stt_all[1,2:7] = c(0,0,0,0,0,0)
    
    the_stt = the_island$stt_table
    
    for(i in 2:nrow(stt_all))
    {
      the_age = stt_all[i,"Time"]
      stt_all[i,2:7] = the_stt[max(which(the_stt[,"Time"] >= the_age)),2:7]
    }
    island_list = list()
    
    if(sum(the_stt[nrow(the_stt),2:7]) == 0)
    {
      
      island_list[[1]] = list(
        island_age = totaltime,
        not_present = Mtotal,
        stt_all = stt_all
      )
      # island_list[[2]] = list(branching_times = totaltime, stac = 0, missing_species = 0)
      
    } else {
      
      island_list[[1]] = list(island_age = totaltime,
                              not_present =Mtotal - length(the_island$taxon_list),
                              stt_all = stt_all)
      
      for(y in 1:length(the_island$taxon_list))
      {
        island_list[[y + 1]] = the_island$taxon_list[[y]]
      }
    }
    
    island_list = Add_brt_table(island_list)
    
    several_islands[[rep]] = island_list
    if (verbose) {
      print(paste(
        "Island being formatted: ",
        rep,
        "/",
        length(island_replicates),
        sep = "")
      )
    }
  }
  return(several_islands)
}
Add_brt_table <- function(island) {
  island_age <- island[[1]]$island_age
  island_top <- island[[1]]
  if (length(island) == 1) {
    brts_table <- matrix(ncol = 4, nrow = 1)
    brts_table[1, ] <-  c(island_age, 0, 0, NA)
    island[[1]]$brts_table <- brts_table
  } else {
    island_top <- island[[1]]
    island[[1]] <- NULL
    btimes <- list()
    for (i in 1:length(island)) {
      btimes[[i]] <- island[[i]]$branching_times[-1]
    }
    island <- island[rev(order(sapply(btimes, "[", 1)))]
    il <- unlist(island)
    stac1s <- which(il[which(names(il) == "stac")] == "1")
    stac5s <- which(il[which(names(il) == "stac")] == "5")
    stac1_5s <- sort(c(stac1s, stac5s))
    if (length(stac1_5s) != 0) {
      if (length(stac1_5s) == length(island)) {
        brts_table <- matrix(ncol = 4, nrow = 1)
        brts_table[1, ] <- c(island_age, 0, 0, NA)
        island_no_stac1or5 <- NULL
      } else {
        island_no_stac1or5 <- island[-stac1_5s]
      }
    }
    if (length(stac1_5s) == 0) {
      island_no_stac1or5 <- island
    }
    if (length(island_no_stac1or5) != 0) {
      btimes <- list()
      for (i in 1:length(island_no_stac1or5)) {
        btimes[[i]] <- island_no_stac1or5[[i]]$branching_times[-1]
      }
      brts <- rev(sort(unlist(btimes)))
      brts_IWK <- matrix(ncol = 4, nrow = length(brts))
      pos1 <- 0
      for (i in 1:length(btimes)) {
        the_brts <- btimes[[i]]
        the_stac <- island_no_stac1or5[[i]]$stac
        pos2 <- pos1 + length(the_brts)
        brts_IWK[(pos1 + 1):pos2, 1] <- the_brts
        brts_IWK[(pos1 + 1):pos2, 2] <- i
        brts_IWK[(pos1 + 1):pos2, 3] <- seq(1, length(the_brts))
        brts_IWK[(pos1 + 1):pos2, 4] <- (the_stac == 2) +
          (the_stac == 3) + (the_stac == 4) * 0
        pos1 <- pos2
      }
      brts_table <- brts_IWK[rev(order(brts_IWK[, 1])), ]
      brts_table <- rbind(c(island_age, 0, 0, NA), brts_table)
    }
    island_top$brts_table <- brts_table
    if (length(stac1_5s) != 0) {
      for (i in 1:length(stac1_5s)) {
        island[[length(island) + 1]] <- island[[stac1_5s[i]]]
        island[[stac1_5s[i]]] <- NULL
        stac1_5s <- stac1_5s - 1
      }
    }
    island <- append(list(island_top), island)
  }
  colnames(island[[1]]$brts_table) <- c("brt", "clade", "event", "endemic")
  return(island)
}