R/format_island_mutual_pa.R

In Yangshen0325/specmutual: Evolution of Mutualism Based on Speciation, Immigration and Extinction

#### Format "raw" simulation output into standard DAISIE format, plant and animal are separated ####

# `island_replicates` is the "raw" simulation output

format_island_mutual_pa <- function(island_replicates,
                                 total_time,
                                 sample_freq,
                                 M0,
                                 verbose = verbose) {
  if (is.infinite(sample_freq)) {
    several_islands <- format_full_stt_pa(
      island_replicates = island_replicates,
      total_time = total_time,
      M0 = M0,
      verbose = verbose
    )
  } else {
    several_islands <- format_sampled_stt_pa(
      island_replicates = island_replicates,
      total_time = total_time,
      sample_freq = sample_freq,
      M0 = M0,
      verbose = verbose
    )
  }
  return(several_islands)
}

# For a full table, without `sample_freq` ---------------------------------

# Format plant and animal species separately without `sample_freq`, so it's a
# full table containing all information
format_full_stt_pa <- function(island_replicates,
                            total_time,
                            M0,
                            verbose = verbose) {

  several_islands_plant <- list()
  several_islands_animal <- list()

  for (rep in 1:length(island_replicates)) {
    the_island <- island_replicates[[rep]][["island"]]
    stt_all <- the_island$stt_table

    island_list_plant <- list()
    island_list_animal <- list()

    # deal with plant species
    if (sum(stt_all[nrow(stt_all), 2:4]) == 0) {
      island_list_plant[[1]] <- list(
        island_age = total_time,
        not_present_p = nrow(M0),
        stt_all_plant = stt_all[, 1:4]
      )
    } else {
      plant_size <- length(the_island$clades_info_plant)
      island_list_plant[[1]] <- list(
        island_age = total_time,
        not_present_p = nrow(M0) - plant_size,
        stt_all_plant = stt_all[, 1:4]
      )
      if (plant_size != 0) {
        for (y in seq_len(plant_size)) {
          island_list_plant[[y + 1]] <- the_island$clades_info_plant[[y]]
        }
      }
    }
    island_list_plant <- DAISIE:::add_brt_table(
      island = island_list_plant,
      full_table = FALSE
    )
    several_islands_plant[[rep]] <- island_list_plant

    # deal with animal species
    if (sum(stt_all[nrow(stt_all), 5:7]) == 0) {
      island_list_animal[[1]] <- list(
        island_age = total_time,
        not_present_a = ncol(M0),
        stt_all_animal = stt_all[, c(1, 5:7)]
      )
    } else {
      animal_size <- length(the_island$clades_info_animal)
      island_list_animal[[1]] <- list(
        island_age = total_time,
        not_present_a = ncol(M0) - animal_size,
        stt_all_animal = stt_all[, c(1, 5:7)]
      )
      if (animal_size != 0) {
        for (y in seq_len(animal_size)) {
          island_list_animal[[y + 1]] <- the_island$clades_info_animal[[y]]
        }
      }
    }
    island_list_animal <- DAISIE:::add_brt_table(
      island = island_list_animal,
      full_table = FALSE
    )
    several_islands_animal[[rep]] <- island_list_animal

    if (verbose == TRUE) {
      message(
        "Island being formatted: ", rep, "/", length(island_replicates)
      )
    }
  }
  return(list(
    several_islands_plant = several_islands_plant,
    several_islands_animal = several_islands_animal
  ))
}


# For a sampled table, with `sample_freq`  --------------------------------

# Format plant and animal species separately with `sample_freq`, so it's ready to plot

format_sampled_stt_pa <- function(island_replicates,
                               total_time,
                               sample_freq,
                               M0,
                               verbose) {

  several_islands_plant <- list()
  several_islands_animal <- list()

  for (rep in seq_along(island_replicates)) {

    # Extract one replicate info
    the_island <- island_replicates[[rep]][["island"]]
    the_stt <- the_island$stt_table
    clades_info_plant <- the_island$clades_info_plant
    clades_info_animal <- the_island$clades_info_animal

    # Initialize the formatting stt table
    stt_all <- matrix(ncol = 7, nrow = sample_freq + 1)
    colnames(stt_all) <- c("Time", "nIp", "nAp", "nCp", "nIa", "nAa", "nCa")
    stt_all[, "Time"] <- rev(seq(
      from = 0,
      to = total_time,
      length.out = sample_freq + 1
    ))
    stt_all[1, 2:7] <- c(0, 0, 0, 0, 0, 0)

    # Format the info into the structured table `stt_all`
    for (j in 2:nrow(stt_all)) {
      the_age <- stt_all[j, "Time"]
      stt_all[j, 2:7] <- the_stt[max(which(the_stt[, "Time"] >= the_age)), 2:7]
    }

    # Initialize space for saving info of plant taxon, their branching time,
    # stac, and missing species. The first element will always be the island
    # information: island age, the number of clades not present on the island, the formatted stt table
    island_list_plant <- list()

    if (sum(the_stt[nrow(the_stt), 2:4]) == 0) {
      island_list_plant[[1]] <- list(
        island_age = total_time,
        not_present_p = nrow(M0),
        stt_plant = stt_all[, 1:4]
      )
    } else { # nrow(M0) minus the number of clades of plant species
      island_list_plant[[1]] <- list(
        island_age = total_time,
        not_present_p = nrow(M0) - length(clades_info_plant),
        stt_plant = stt_all[, 1:4]
      )
      for (y in 1:length(clades_info_plant)) {
        island_list_plant[[y + 1]] <- clades_info_plant[[y]]
      }
    }

    # Initialize space for saving info of animal taxon, their branching time,
    # stac, and missing species. The first element will always be the island
    # information: island age, the number of clades not present on the island, the formatted stt table
    island_list_animal <- list()
    if (sum(the_stt[nrow(the_stt), 5:7]) == 0) {
      island_list_animal[[1]] <- list(
        island_age = total_time,
        not_present_a = ncol(M0),
        stt_animal = stt_all[, c(1, 5:7)]
      )
    } else {
      island_list_animal[[1]] <- list(
        island_age = total_time,
        not_present_a = ncol(M0) - length(clades_info_animal),
        stt_animal = stt_all[, c(1, 5:7)]
      )
      for (y in 1:length(clades_info_animal)) {
        island_list_animal[[y + 1]] <- clades_info_animal[[y]]
      }
    }

    island_list_plant <- DAISIE:::add_brt_table(island = island_list_plant)
    island_list_animal <- DAISIE:::add_brt_table(island = island_list_animal)
    several_islands_plant[[rep]] <- island_list_plant
    several_islands_animal[[rep]] <- island_list_animal
    if (verbose == TRUE) {
      message(
        "Island being formatted: ", rep, "/", length(island_replicates)
      )
    }
  }
  return(list(
    several_islands_plant = several_islands_plant,
    several_islands_animal = several_islands_animal
  ))
}