R/plots.R

In Neves-P/utilSIE: Utility Functions for DAISIE

# ran_sims <- run_simulations_from_MLE(res, replicates = 100, time = 7, M = 1000)


# plot_n_colonist_distribution <- function(standard_model_simulations_name,
#                                          tested_model_simulations_name) {
#
#   ran_sims <- get_simulations_to_run(res, lac_treshold = 10)
#
#   standard_model_simulations <- load_DAISIE_data(
#     standard_model_simulations_name,
#     "no_ont"
#   )
#
#   tested_model_simulations <- load_DAISIE_data(
#     tested_model_simulations_name,
#     "ont"
#   )
#
#
#
#
# }

# tested_model_simulations <- load_DAISIE_data(
#   "sim-DAISIE-1-7-1000-7.48223e-05-1-0.00740740740740741-0.001-1-1000-0.1-0.11-13500-0.1-1-9-1.RData"
# )
#
# standard_model_simulations_name <- "sim-DAISIE-1-7-1000-1.4108982460293-0.423651701021359-17.0772220259305-0.000798977094655427-17005.1057607595-100-1.RData"
#
# useable_replicates_ontogeny <- tested_model_simulations[[1]]$out[ran_sims$id]
# useable_replicates_ontogeny <- tested_model_simulations[[1]]$out[103]
# useable_simulations_standard <- standard_model_simulations


#' Plot number of colonists
#'
#' @param useable_replicates_ontogeny something
#' @param useable_simulations_standard something
#'
#' @return Plots of number of colonizations
#' @export
plot_ncolonist_distribution <- function(useable_replicates_ontogeny,
                                        useable_simulations_standard) {
  time <- rev(useable_simulations_standard[[1]][[1]][[1]][[1]]$stt_all[, 1])

  suppressWarnings(
    graphics::plot(
      x = NULL,
      y = NULL,
      xlim = c(0, max(1, time)),
      ylim = c(0, max(useable_replicates_ontogeny[[1]][[1]]$stt_all[, 5])),
      type = "l",
      main = "Number of colonizations",
      xlab = "Time",
      ylab = "Number of colonizations",
      col = "red"
    )
  )
  for (i in seq_along(useable_simulations_standard[[1]][[1]])) {
    lines(
      x = rev(useable_simulations_standard[[1]][[1]][[i]][[1]]$stt_all[, 1]),
      y = useable_simulations_standard[[1]][[1]][[i]][[1]]$stt_all[, 5],
      col = "green"
    )
    lines(
      x = rev(useable_replicates_ontogeny[[1]][[1]]$stt_all[, 1]),
      y = useable_replicates_ontogeny[[1]][[1]]$stt_all[, 5],
      col = "red"
    )
  }
}

#' Plot number of species
#'
#' @param useable_replicates_ontogeny something
#' @param useable_simulations_standard somthing
#'
#' @return Plots of number of species
#' @export
plot_nspecies_distribution <- function(useable_replicates_ontogeny,
                                       useable_simulations_standard) {
  time <- rev(useable_simulations_standard[[1]][[1]][[1]][[1]]$stt_all[, 1])

  cumulative_ontogeny_richness <- c()
  list_cumulative_standard_richness <- list()

  for (i in seq_along(useable_simulations_standard[[1]][[1]])) {
  cumulative_standard_richness <- c()
    for (t in seq_along(time)) {
      cumulative_standard_richness <- c(
        cumulative_standard_richness,
        sum(useable_simulations_standard[[1]][[1]][[i]][[1]]$stt_all[t, 2],
            useable_simulations_standard[[1]][[1]][[i]][[1]]$stt_all[t, 3],
            useable_simulations_standard[[1]][[1]][[i]][[1]]$stt_all[t, 4]
        )
      )
    }
    list_cumulative_standard_richness[[i]] <- cumulative_standard_richness
  }

  for (t in seq_along(time)) {
    cumulative_ontogeny_richness <- c(
      cumulative_ontogeny_richness,
      sum(useable_replicates_ontogeny[[1]][[1]]$stt_all[t, 2],
          useable_replicates_ontogeny[[1]][[1]]$stt_all[t, 3],
          useable_replicates_ontogeny[[1]][[1]]$stt_all[t, 4]
      )
    )
  }

  suppressWarnings(
    graphics::plot(
      x = NULL,
      y = NULL,
      xlim = c(0, max(1, time)),
      ylim = c(0, max(cumulative_ontogeny_richness)),
      main = "Species richness",
      xlab = "Time",
      ylab = "Number of species on island"
    )
  )
  for (i in seq_along(cumulative_standard_richness)) {
    lines(
      x = time,
      y = list_cumulative_standard_richness[[i]],
      col = "green"
    )

  }
    lines(
      x = time,
      y = cumulative_ontogeny_richness,
      col = "red"
    )
}