R/DAISIE_plot_sims.R
In joshwlambert/DAISIEsim:
#' @title Plot island species-through-time (STT) plots
#' @description Produces STT plots. If only one type of species is present in
#' the simulated islands, STT is plotted for all species. If two types are
#' present, three plots are produced: STT for all, STT for type 1 and STT
#' for type 2.
#'
#' R plots with number of total, endemic and non-endemic STTs for different
#' types of species for the entire time span the islands were simulated.
#' 2.5-97.5th percentiles are plotted in light grey, 25-75th percentiles
#' plotted in dark grey.
#'
#' @param island_replicates Island replicates in DAISIE format (produced in
#' \code{\link{DAISIE_sim}} with \code{format = TRUE} option). Minimally, this must be
#' a list, that has as much elements as replicates. Each element must be a
#' list with the elements \code{island_age}, \code{not_present}
#' and \code{stt_all}. \code{stt_all} must be a data frame with
#' the column names \code{Time}, \code{nI}, \code{nA}, \code{nC}
#' and \code{present}.
#' @param use_dev_new Boolean to indicate to use \code{dev.new} before plotting.
#' Set to \code{TRUE} for default behavior.
#' Set to \code{FALSE} when plotting within a vignette
#' @param plot_plus_one Boolean to indicate to plot all values plus one.
#' Set to \code{TRUE} for default behavior.
#' Set to \code{FALSE} to plot all values without adding one.
#' Only works when there is one type of species
#' @return R plot.
#' @author Luis Valente
#' @seealso \code{\link{DAISIE_sim}} \code{\link{DAISIE_format_CS}}
#' @references Valente, L.M., A.B. Phillimore and R.S. Etienne (2015).
#' Equilibrium and non-equilibrium dynamics simultaneously operate in the
#' Galapagos islands. Ecology Letters 18: 844-852.
#' @keywords models
#' @export
#' @examples
#'
#'
#' ### Plot islands with single process (only one type of species)
#' utils::data(islands_1type_1000reps)
#' DAISIE_plot_sims(
#' island_replicates = islands_1type_1000reps,
#' use_dev_new = FALSE
#' )
#'
#'
#' ### Plot island with type 1 and type 2
#' utils::data(islands_2types_1000reps)
#' DAISIE_plot_sims(
#' island_replicates = islands_2types_1000reps,
#' use_dev_new = FALSE
#' )
#'
#'
#'
DAISIE_plot_sims <- function(
island_replicates,
use_dev_new = TRUE,
plot_plus_one = TRUE
) {
replicates <- length(island_replicates)
time <- max(island_replicates[[1]][[1]]$stt_all[, 1])
### STT ALL species
s_freq <- length(island_replicates[[1]][[1]]$stt_all[, 1])
complete_arr <- array(dim = c(s_freq, 6, replicates))
for (x in 1:replicates) {
sum_endemics <- island_replicates[[x]][[1]]$stt_all[, "nA"] + island_replicates[[x]][[1]]$stt_all[,
"nC"]
total <- island_replicates[[x]][[1]]$stt_all[, "nA"] + island_replicates[[x]][[1]]$stt_all[,
"nC"] + island_replicates[[x]][[1]]$stt_all[, "nI"]
complete_arr[, , x] <- cbind(island_replicates[[x]][[1]]$stt_all[, c("Time", "nI", "nA", "nC")],
sum_endemics, total)
}
stt_average_all <- apply(complete_arr, c(1, 2), stats::median)
testit::assert(stt_average_all == DAISIE_extract_stt_median(island_replicates))
stt_q0.025_all <- apply(complete_arr, c(1, 2), stats::quantile, 0.025)
stt_q0.25_all <- apply(complete_arr, c(1, 2), stats::quantile, 0.25)
stt_q0.75_all <- apply(complete_arr, c(1, 2), stats::quantile, 0.75)
stt_q0.975_all <- apply(complete_arr, c(1, 2), stats::quantile, 0.975)
colnames(stt_average_all) <- c("Time", "nI", "nA", "nC", "Endemic", "Total")
colnames(stt_q0.025_all) <- c("Time", "nI", "nA", "nC", "Endemic", "Total")
colnames(stt_q0.25_all) <- c("Time", "nI", "nA", "nC", "Endemic", "Total")
colnames(stt_q0.75_all) <- c("Time", "nI", "nA", "nC", "Endemic", "Total")
colnames(stt_q0.975_all) <- c("Time", "nI", "nA", "nC", "Endemic", "Total")
if (is.null(island_replicates[[1]][[1]]$stt_type1) == FALSE) {
### STT TYPE1
s_freq <- length(island_replicates[[1]][[1]]$stt_type1[, 1])
complete_arr <- array(dim = c(s_freq, 7, replicates))
for (x in 1:replicates) {
sum_endemics <- island_replicates[[x]][[1]]$stt_type1[, "nA"] + island_replicates[[x]][[1]]$stt_type1[,
"nC"]
total <- island_replicates[[x]][[1]]$stt_type1[, "nA"] + island_replicates[[x]][[1]]$stt_type1[,
"nC"] + island_replicates[[x]][[1]]$stt_type1[, "nI"]
complete_arr[, , x] <- cbind(island_replicates[[x]][[1]]$stt_type1, sum_endemics, total)
}
stt_average_type1 <- apply(complete_arr, c(1, 2), stats::median)
stt_q0.025_type1 <- apply(complete_arr, c(1, 2), stats::quantile, 0.025)
stt_q0.25_type1 <- apply(complete_arr, c(1, 2), stats::quantile, 0.25)
stt_q0.75_type1 <- apply(complete_arr, c(1, 2), stats::quantile, 0.75)
stt_q0.975_type1 <- apply(complete_arr, c(1, 2), stats::quantile, 0.975)
colnames(stt_average_type1) <- c("Time", "nI", "nA", "nC", "present", "Endemic", "Total")
colnames(stt_q0.025_type1) <- c("Time", "nI", "nA", "nC", "present", "Endemic", "Total")
colnames(stt_q0.25_type1) <- c("Time", "nI", "nA", "nC", "present", "Endemic", "Total")
colnames(stt_q0.75_type1) <- c("Time", "nI", "nA", "nC", "present", "Endemic", "Total")
colnames(stt_q0.975_type1) <- c("Time", "nI", "nA", "nC", "present", "Endemic", "Total")
### STT TYPE2
s_freq <- length(island_replicates[[1]][[1]]$stt_type2[, 1])
complete_arr <- array(dim = c(s_freq, 7, replicates))
for (x in 1:replicates) {
sum_endemics <- island_replicates[[x]][[1]]$stt_type2[, "nA"] + island_replicates[[x]][[1]]$stt_type2[,
"nC"]
total <- island_replicates[[x]][[1]]$stt_type2[, "nA"] + island_replicates[[x]][[1]]$stt_type2[,
"nC"] + island_replicates[[x]][[1]]$stt_type2[, "nI"]
complete_arr[, , x] <- cbind(island_replicates[[x]][[1]]$stt_type2, sum_endemics, total)
}
stt_average_type2 <- apply(complete_arr, c(1, 2), stats::median)
stt_q0.025_type2 <- apply(complete_arr, c(1, 2), stats::quantile, 0.025)
stt_q0.25_type2 <- apply(complete_arr, c(1, 2), stats::quantile, 0.25)
stt_q0.75_type2 <- apply(complete_arr, c(1, 2), stats::quantile, 0.75)
stt_q0.975_type2 <- apply(complete_arr, c(1, 2), stats::quantile, 0.975)
colnames(stt_average_type2) <- c("Time", "nI", "nA", "nC", "present", "Endemic", "Total")
colnames(stt_q0.025_type2) <- c("Time", "nI", "nA", "nC", "present", "Endemic", "Total")
colnames(stt_q0.25_type2) <- c("Time", "nI", "nA", "nC", "present", "Endemic", "Total")
colnames(stt_q0.75_type2) <- c("Time", "nI", "nA", "nC", "present", "Endemic", "Total")
colnames(stt_q0.975_type2) <- c("Time", "nI", "nA", "nC", "present", "Endemic", "Total")
if (use_dev_new == TRUE) {
grDevices::dev.new(width = 12, height = 4)
}
graphics::par(mfrow = c(1, 3))
# Could use DAISIE_plot_stt here one day...
suppressWarnings(graphics::plot(NULL, NULL, xlim = rev(c(0, time)), ylim = c(1, max(stt_q0.975_all)), ylab = "No of species + 1",
bty = "l", xaxs = "i", xlab = "Time before present", main = "Species-through-time - All species",
log = "y", cex.lab = 1.5, cex.main = 1.2, cex.axis = 1.2))
graphics::polygon(c(stt_average_all[, "Time"], rev(stt_average_all[, "Time"])), c(stt_q0.025_all[, "Total"] +
1, rev(stt_q0.975_all[, "Total"] + 1)), col = "light grey", border = NA)
graphics::polygon(c(stt_average_all[, "Time"], rev(stt_average_all[, "Time"])), c(stt_q0.25_all[, "Total"] +
1, rev(stt_q0.75_all[, "Total"] + 1)), col = "dark grey", border = NA)
graphics::lines(stt_average_all[, "Time"], stt_average_all[, "Total"] + 1, lwd = 2)
graphics::lines(stt_average_all[, "Time"], stt_average_all[, "nI"] + 1, lwd = 2, col = "cyan3")
graphics::lines(stt_average_all[, "Time"], stt_average_all[, "Endemic"] + 1, lwd = 2, col = "dodgerblue1")
graphics::legend(time, max(stt_q0.975_all), c("Total", "Non-endemic", "Endemic"), lty = 1, lwd = 2, col = c("black",
"cyan3", "dodgerblue1"), cex = 1.2, border = NA, bty = "n")
suppressWarnings(graphics::plot(NULL, NULL, xlim = rev(c(0, time)), ylim = c(1, max(stt_q0.975_type1)),
ylab = "No of species + 1", bty = "l", xaxs = "i", xlab = "Time before present", main = "STT Type 1 species",
log = "y", cex.lab = 1.5, cex.main = 1.2, cex.axis = 1.2))
graphics::polygon(c(stt_average_type1[, "Time"], rev(stt_average_type1[, "Time"])), c(stt_q0.025_type1[,
"Total"] + 1, rev(stt_q0.975_type1[, "Total"] + 1)), col = "light grey", border = NA)
graphics::polygon(c(stt_average_type1[, "Time"], rev(stt_average_type1[, "Time"])), c(stt_q0.25_type1[,
"Total"] + 1, rev(stt_q0.75_type1[, "Total"] + 1)), col = "dark grey", border = NA)
graphics::lines(stt_average_type1[, "Time"], stt_average_type1[, "Total"] + 1, lwd = 2)
graphics::lines(stt_average_type1[, "Time"], stt_average_type1[, "nI"] + 1, lwd = 2, col = "cyan3")
graphics::lines(stt_average_type1[, "Time"], stt_average_type1[, "Endemic"] + 1, lwd = 2, col = "dodgerblue1")
suppressWarnings(graphics::plot(NULL, NULL, xlim = rev(c(0, time)), ylim = c(1, max(stt_q0.975_type2)),
ylab = "No of species + 1", bty = "l", xaxs = "i", xlab = "Time before present", main = "STT Type 2 species",
log = "y", cex.lab = 1.5, cex.main = 1.2, cex.axis = 1.2))
graphics::polygon(c(stt_average_type2[, "Time"], rev(stt_average_type2[, "Time"])), c(stt_q0.025_type2[,
"Total"] + 1, rev(stt_q0.975_type2[, "Total"] + 1)), col = "light grey", border = NA)
graphics::polygon(c(stt_average_type2[, "Time"], rev(stt_average_type2[, "Time"])), c(stt_q0.25_type2[,
"Total"] + 1, rev(stt_q0.75_type2[, "Total"] + 1)), col = "dark grey", border = NA)
graphics::lines(stt_average_type2[, "Time"], stt_average_type2[, "Total"] + 1, lwd = 2)
graphics::lines(stt_average_type2[, "Time"], stt_average_type2[, "nI"] + 1, lwd = 2, col = "cyan3")
graphics::lines(stt_average_type2[, "Time"], stt_average_type2[, "Endemic"] + 1, lwd = 2, col = "dodgerblue1")
graphics::par(mfrow = c(1, 3))
suppressWarnings(graphics::plot(NULL, NULL, xlim = rev(c(0, time)), ylim = c(1, max(stt_q0.975_all)), ylab = "No of species + 1",
bty = "l", xaxs = "i", xlab = "Time before present", main = "Species-through-time - All species",
log = "y", cex.lab = 1.5, cex.main = 1.2, cex.axis = 1.2))
graphics::polygon(c(stt_average_all[, "Time"], rev(stt_average_all[, "Time"])), c(stt_q0.025_all[, "Total"] +
1, rev(stt_q0.975_all[, "Total"] + 1)), col = "light grey", border = NA)
graphics::polygon(c(stt_average_all[, "Time"], rev(stt_average_all[, "Time"])), c(stt_q0.25_all[, "Total"] +
1, rev(stt_q0.75_all[, "Total"] + 1)), col = "dark grey", border = NA)
graphics::lines(stt_average_all[, "Time"], stt_average_all[, "Total"] + 1, lwd = 2)
graphics::lines(stt_average_all[, "Time"], stt_average_all[, "nI"] + 1, lwd = 2, col = "cyan3")
graphics::lines(stt_average_all[, "Time"], stt_average_all[, "Endemic"] + 1, lwd = 2, col = "dodgerblue1")
graphics::legend(time, max(stt_q0.975_all), c("Total", "Non-endemic", "Endemic"), lty = 1, lwd = 2, col = c("black",
"cyan3", "dodgerblue1"), cex = 1.2, border = NA, bty = "n")
suppressWarnings(graphics::plot(NULL, NULL, xlim = rev(c(0, time)), ylim = c(1, max(stt_q0.975_type1)),
ylab = "No of species + 1", bty = "l", xaxs = "i", xlab = "Time before present", main = "STT Type 1 species",
log = "y", cex.lab = 1.5, cex.main = 1.2, cex.axis = 1.2))
graphics::polygon(c(stt_average_type1[, "Time"], rev(stt_average_type1[, "Time"])), c(stt_q0.025_type1[,
"Total"] + 1, rev(stt_q0.975_type1[, "Total"] + 1)), col = "light grey", border = NA)
graphics::polygon(c(stt_average_type1[, "Time"], rev(stt_average_type1[, "Time"])), c(stt_q0.25_type1[,
"Total"] + 1, rev(stt_q0.75_type1[, "Total"] + 1)), col = "dark grey", border = NA)
graphics::lines(stt_average_type1[, "Time"], stt_average_type1[, "Total"] + 1, lwd = 2)
graphics::lines(stt_average_type1[, "Time"], stt_average_type1[, "nI"] + 1, lwd = 2, col = "cyan3")
graphics::lines(stt_average_type1[, "Time"], stt_average_type1[, "Endemic"] + 1, lwd = 2, col = "dodgerblue1")
suppressWarnings(graphics::plot(NULL, NULL, xlim = rev(c(0, time)), ylim = c(1, max(stt_q0.975_type2)),
ylab = "No of species + 1", bty = "l", xaxs = "i", xlab = "Time before present", main = "STT Type 2 species",
log = "y", cex.lab = 1.5, cex.main = 1.2, cex.axis = 1.2))
graphics::polygon(c(stt_average_type2[, "Time"], rev(stt_average_type2[, "Time"])), c(stt_q0.025_type2[,
"Total"] + 1, rev(stt_q0.975_type2[, "Total"] + 1)), col = "light grey", border = NA)
graphics::polygon(c(stt_average_type2[, "Time"], rev(stt_average_type2[, "Time"])), c(stt_q0.25_type2[,
"Total"] + 1, rev(stt_q0.75_type2[, "Total"] + 1)), col = "dark grey", border = NA)
graphics::lines(stt_average_type2[, "Time"], stt_average_type2[, "Total"] + 1, lwd = 2)
graphics::lines(stt_average_type2[, "Time"], stt_average_type2[, "nI"] + 1, lwd = 2, col = "cyan3")
graphics::lines(stt_average_type2[, "Time"], stt_average_type2[, "Endemic"] + 1, lwd = 2, col = "dodgerblue1")
} else {
# Default behavior to open a new device, which hurts vignettes
if (use_dev_new == TRUE) {
grDevices::dev.new(width = 6, height = 6)
}
graphics::par(mfrow = c(1, 1))
DAISIE_plot_stt(
plot_plus_one = plot_plus_one,
time = time,
stt_q0.025_all = stt_q0.025_all,
stt_q0.25_all = stt_q0.25_all,
stt_average_all = stt_average_all,
stt_q0.75_all = stt_q0.75_all,
stt_q0.975_all = stt_q0.975_all
)
}
}
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#' @title Plot island species-through-time (STT) plots
#' @description Produces STT plots. If only one type of species is present in
#' the simulated islands, STT is plotted for all species. If two types are
#' present, three plots are produced: STT for all, STT for type 1 and STT
#' for type 2.
#'
#' R plots with number of total, endemic and non-endemic STTs for different
#' types of species for the entire time span the islands were simulated.
#' 2.5-97.5th percentiles are plotted in light grey, 25-75th percentiles
#' plotted in dark grey.
#'
#' @param island_replicates Island replicates in DAISIE format (produced in
#' \code{\link{DAISIE_sim}} with \code{format = TRUE} option). Minimally, this must be
#' a list, that has as much elements as replicates. Each element must be a
#' list with the elements \code{island_age}, \code{not_present}
#' and \code{stt_all}. \code{stt_all} must be a data frame with
#' the column names \code{Time}, \code{nI}, \code{nA}, \code{nC}
#' and \code{present}.
#' @param use_dev_new Boolean to indicate to use \code{dev.new} before plotting.
#' Set to \code{TRUE} for default behavior.
#' Set to \code{FALSE} when plotting within a vignette
#' @param plot_plus_one Boolean to indicate to plot all values plus one.
#' Set to \code{TRUE} for default behavior.
#' Set to \code{FALSE} to plot all values without adding one.
#' Only works when there is one type of species
#' @return R plot.
#' @author Luis Valente
#' @seealso \code{\link{DAISIE_sim}} \code{\link{DAISIE_format_CS}}
#' @references Valente, L.M., A.B. Phillimore and R.S. Etienne (2015).
#' Equilibrium and non-equilibrium dynamics simultaneously operate in the
#' Galapagos islands. Ecology Letters 18: 844-852.
#' @keywords models
#' @export
#' @examples
#'
#'
#' ### Plot islands with single process (only one type of species)
#' utils::data(islands_1type_1000reps)
#' DAISIE_plot_sims(
#' island_replicates = islands_1type_1000reps,
#' use_dev_new = FALSE
#' )
#'
#'
#' ### Plot island with type 1 and type 2
#' utils::data(islands_2types_1000reps)
#' DAISIE_plot_sims(
#' island_replicates = islands_2types_1000reps,
#' use_dev_new = FALSE
#' )
#'
#'
#'
DAISIE_plot_sims <- function(
island_replicates,
use_dev_new = TRUE,
plot_plus_one = TRUE
) {
replicates <- length(island_replicates)
time <- max(island_replicates[[1]][[1]]$stt_all[, 1])
### STT ALL species
s_freq <- length(island_replicates[[1]][[1]]$stt_all[, 1])
complete_arr <- array(dim = c(s_freq, 6, replicates))
for (x in 1:replicates) {
sum_endemics <- island_replicates[[x]][[1]]$stt_all[, "nA"] + island_replicates[[x]][[1]]$stt_all[,
"nC"]
total <- island_replicates[[x]][[1]]$stt_all[, "nA"] + island_replicates[[x]][[1]]$stt_all[,
"nC"] + island_replicates[[x]][[1]]$stt_all[, "nI"]
complete_arr[, , x] <- cbind(island_replicates[[x]][[1]]$stt_all[, c("Time", "nI", "nA", "nC")],
sum_endemics, total)
}
stt_average_all <- apply(complete_arr, c(1, 2), stats::median)
testit::assert(stt_average_all == DAISIE_extract_stt_median(island_replicates))
stt_q0.025_all <- apply(complete_arr, c(1, 2), stats::quantile, 0.025)
stt_q0.25_all <- apply(complete_arr, c(1, 2), stats::quantile, 0.25)
stt_q0.75_all <- apply(complete_arr, c(1, 2), stats::quantile, 0.75)
stt_q0.975_all <- apply(complete_arr, c(1, 2), stats::quantile, 0.975)
colnames(stt_average_all) <- c("Time", "nI", "nA", "nC", "Endemic", "Total")
colnames(stt_q0.025_all) <- c("Time", "nI", "nA", "nC", "Endemic", "Total")
colnames(stt_q0.25_all) <- c("Time", "nI", "nA", "nC", "Endemic", "Total")
colnames(stt_q0.75_all) <- c("Time", "nI", "nA", "nC", "Endemic", "Total")
colnames(stt_q0.975_all) <- c("Time", "nI", "nA", "nC", "Endemic", "Total")
if (is.null(island_replicates[[1]][[1]]$stt_type1) == FALSE) {
### STT TYPE1
s_freq <- length(island_replicates[[1]][[1]]$stt_type1[, 1])
complete_arr <- array(dim = c(s_freq, 7, replicates))
for (x in 1:replicates) {
sum_endemics <- island_replicates[[x]][[1]]$stt_type1[, "nA"] + island_replicates[[x]][[1]]$stt_type1[,
"nC"]
total <- island_replicates[[x]][[1]]$stt_type1[, "nA"] + island_replicates[[x]][[1]]$stt_type1[,
"nC"] + island_replicates[[x]][[1]]$stt_type1[, "nI"]
complete_arr[, , x] <- cbind(island_replicates[[x]][[1]]$stt_type1, sum_endemics, total)
}
stt_average_type1 <- apply(complete_arr, c(1, 2), stats::median)
stt_q0.025_type1 <- apply(complete_arr, c(1, 2), stats::quantile, 0.025)
stt_q0.25_type1 <- apply(complete_arr, c(1, 2), stats::quantile, 0.25)
stt_q0.75_type1 <- apply(complete_arr, c(1, 2), stats::quantile, 0.75)
stt_q0.975_type1 <- apply(complete_arr, c(1, 2), stats::quantile, 0.975)
colnames(stt_average_type1) <- c("Time", "nI", "nA", "nC", "present", "Endemic", "Total")
colnames(stt_q0.025_type1) <- c("Time", "nI", "nA", "nC", "present", "Endemic", "Total")
colnames(stt_q0.25_type1) <- c("Time", "nI", "nA", "nC", "present", "Endemic", "Total")
colnames(stt_q0.75_type1) <- c("Time", "nI", "nA", "nC", "present", "Endemic", "Total")
colnames(stt_q0.975_type1) <- c("Time", "nI", "nA", "nC", "present", "Endemic", "Total")
### STT TYPE2
s_freq <- length(island_replicates[[1]][[1]]$stt_type2[, 1])
complete_arr <- array(dim = c(s_freq, 7, replicates))
for (x in 1:replicates) {
sum_endemics <- island_replicates[[x]][[1]]$stt_type2[, "nA"] + island_replicates[[x]][[1]]$stt_type2[,
"nC"]
total <- island_replicates[[x]][[1]]$stt_type2[, "nA"] + island_replicates[[x]][[1]]$stt_type2[,
"nC"] + island_replicates[[x]][[1]]$stt_type2[, "nI"]
complete_arr[, , x] <- cbind(island_replicates[[x]][[1]]$stt_type2, sum_endemics, total)
}
stt_average_type2 <- apply(complete_arr, c(1, 2), stats::median)
stt_q0.025_type2 <- apply(complete_arr, c(1, 2), stats::quantile, 0.025)
stt_q0.25_type2 <- apply(complete_arr, c(1, 2), stats::quantile, 0.25)
stt_q0.75_type2 <- apply(complete_arr, c(1, 2), stats::quantile, 0.75)
stt_q0.975_type2 <- apply(complete_arr, c(1, 2), stats::quantile, 0.975)
colnames(stt_average_type2) <- c("Time", "nI", "nA", "nC", "present", "Endemic", "Total")
colnames(stt_q0.025_type2) <- c("Time", "nI", "nA", "nC", "present", "Endemic", "Total")
colnames(stt_q0.25_type2) <- c("Time", "nI", "nA", "nC", "present", "Endemic", "Total")
colnames(stt_q0.75_type2) <- c("Time", "nI", "nA", "nC", "present", "Endemic", "Total")
colnames(stt_q0.975_type2) <- c("Time", "nI", "nA", "nC", "present", "Endemic", "Total")
if (use_dev_new == TRUE) {
grDevices::dev.new(width = 12, height = 4)
}
graphics::par(mfrow = c(1, 3))
# Could use DAISIE_plot_stt here one day...
suppressWarnings(graphics::plot(NULL, NULL, xlim = rev(c(0, time)), ylim = c(1, max(stt_q0.975_all)), ylab = "No of species + 1",
bty = "l", xaxs = "i", xlab = "Time before present", main = "Species-through-time - All species",
log = "y", cex.lab = 1.5, cex.main = 1.2, cex.axis = 1.2))
graphics::polygon(c(stt_average_all[, "Time"], rev(stt_average_all[, "Time"])), c(stt_q0.025_all[, "Total"] +
1, rev(stt_q0.975_all[, "Total"] + 1)), col = "light grey", border = NA)
graphics::polygon(c(stt_average_all[, "Time"], rev(stt_average_all[, "Time"])), c(stt_q0.25_all[, "Total"] +
1, rev(stt_q0.75_all[, "Total"] + 1)), col = "dark grey", border = NA)
graphics::lines(stt_average_all[, "Time"], stt_average_all[, "Total"] + 1, lwd = 2)
graphics::lines(stt_average_all[, "Time"], stt_average_all[, "nI"] + 1, lwd = 2, col = "cyan3")
graphics::lines(stt_average_all[, "Time"], stt_average_all[, "Endemic"] + 1, lwd = 2, col = "dodgerblue1")
graphics::legend(time, max(stt_q0.975_all), c("Total", "Non-endemic", "Endemic"), lty = 1, lwd = 2, col = c("black",
"cyan3", "dodgerblue1"), cex = 1.2, border = NA, bty = "n")
suppressWarnings(graphics::plot(NULL, NULL, xlim = rev(c(0, time)), ylim = c(1, max(stt_q0.975_type1)),
ylab = "No of species + 1", bty = "l", xaxs = "i", xlab = "Time before present", main = "STT Type 1 species",
log = "y", cex.lab = 1.5, cex.main = 1.2, cex.axis = 1.2))
graphics::polygon(c(stt_average_type1[, "Time"], rev(stt_average_type1[, "Time"])), c(stt_q0.025_type1[,
"Total"] + 1, rev(stt_q0.975_type1[, "Total"] + 1)), col = "light grey", border = NA)
graphics::polygon(c(stt_average_type1[, "Time"], rev(stt_average_type1[, "Time"])), c(stt_q0.25_type1[,
"Total"] + 1, rev(stt_q0.75_type1[, "Total"] + 1)), col = "dark grey", border = NA)
graphics::lines(stt_average_type1[, "Time"], stt_average_type1[, "Total"] + 1, lwd = 2)
graphics::lines(stt_average_type1[, "Time"], stt_average_type1[, "nI"] + 1, lwd = 2, col = "cyan3")
graphics::lines(stt_average_type1[, "Time"], stt_average_type1[, "Endemic"] + 1, lwd = 2, col = "dodgerblue1")
suppressWarnings(graphics::plot(NULL, NULL, xlim = rev(c(0, time)), ylim = c(1, max(stt_q0.975_type2)),
ylab = "No of species + 1", bty = "l", xaxs = "i", xlab = "Time before present", main = "STT Type 2 species",
log = "y", cex.lab = 1.5, cex.main = 1.2, cex.axis = 1.2))
graphics::polygon(c(stt_average_type2[, "Time"], rev(stt_average_type2[, "Time"])), c(stt_q0.025_type2[,
"Total"] + 1, rev(stt_q0.975_type2[, "Total"] + 1)), col = "light grey", border = NA)
graphics::polygon(c(stt_average_type2[, "Time"], rev(stt_average_type2[, "Time"])), c(stt_q0.25_type2[,
"Total"] + 1, rev(stt_q0.75_type2[, "Total"] + 1)), col = "dark grey", border = NA)
graphics::lines(stt_average_type2[, "Time"], stt_average_type2[, "Total"] + 1, lwd = 2)
graphics::lines(stt_average_type2[, "Time"], stt_average_type2[, "nI"] + 1, lwd = 2, col = "cyan3")
graphics::lines(stt_average_type2[, "Time"], stt_average_type2[, "Endemic"] + 1, lwd = 2, col = "dodgerblue1")
graphics::par(mfrow = c(1, 3))
suppressWarnings(graphics::plot(NULL, NULL, xlim = rev(c(0, time)), ylim = c(1, max(stt_q0.975_all)), ylab = "No of species + 1",
bty = "l", xaxs = "i", xlab = "Time before present", main = "Species-through-time - All species",
log = "y", cex.lab = 1.5, cex.main = 1.2, cex.axis = 1.2))
graphics::polygon(c(stt_average_all[, "Time"], rev(stt_average_all[, "Time"])), c(stt_q0.025_all[, "Total"] +
1, rev(stt_q0.975_all[, "Total"] + 1)), col = "light grey", border = NA)
graphics::polygon(c(stt_average_all[, "Time"], rev(stt_average_all[, "Time"])), c(stt_q0.25_all[, "Total"] +
1, rev(stt_q0.75_all[, "Total"] + 1)), col = "dark grey", border = NA)
graphics::lines(stt_average_all[, "Time"], stt_average_all[, "Total"] + 1, lwd = 2)
graphics::lines(stt_average_all[, "Time"], stt_average_all[, "nI"] + 1, lwd = 2, col = "cyan3")
graphics::lines(stt_average_all[, "Time"], stt_average_all[, "Endemic"] + 1, lwd = 2, col = "dodgerblue1")
graphics::legend(time, max(stt_q0.975_all), c("Total", "Non-endemic", "Endemic"), lty = 1, lwd = 2, col = c("black",
"cyan3", "dodgerblue1"), cex = 1.2, border = NA, bty = "n")
suppressWarnings(graphics::plot(NULL, NULL, xlim = rev(c(0, time)), ylim = c(1, max(stt_q0.975_type1)),
ylab = "No of species + 1", bty = "l", xaxs = "i", xlab = "Time before present", main = "STT Type 1 species",
log = "y", cex.lab = 1.5, cex.main = 1.2, cex.axis = 1.2))
graphics::polygon(c(stt_average_type1[, "Time"], rev(stt_average_type1[, "Time"])), c(stt_q0.025_type1[,
"Total"] + 1, rev(stt_q0.975_type1[, "Total"] + 1)), col = "light grey", border = NA)
graphics::polygon(c(stt_average_type1[, "Time"], rev(stt_average_type1[, "Time"])), c(stt_q0.25_type1[,
"Total"] + 1, rev(stt_q0.75_type1[, "Total"] + 1)), col = "dark grey", border = NA)
graphics::lines(stt_average_type1[, "Time"], stt_average_type1[, "Total"] + 1, lwd = 2)
graphics::lines(stt_average_type1[, "Time"], stt_average_type1[, "nI"] + 1, lwd = 2, col = "cyan3")
graphics::lines(stt_average_type1[, "Time"], stt_average_type1[, "Endemic"] + 1, lwd = 2, col = "dodgerblue1")
suppressWarnings(graphics::plot(NULL, NULL, xlim = rev(c(0, time)), ylim = c(1, max(stt_q0.975_type2)),
ylab = "No of species + 1", bty = "l", xaxs = "i", xlab = "Time before present", main = "STT Type 2 species",
log = "y", cex.lab = 1.5, cex.main = 1.2, cex.axis = 1.2))
graphics::polygon(c(stt_average_type2[, "Time"], rev(stt_average_type2[, "Time"])), c(stt_q0.025_type2[,
"Total"] + 1, rev(stt_q0.975_type2[, "Total"] + 1)), col = "light grey", border = NA)
graphics::polygon(c(stt_average_type2[, "Time"], rev(stt_average_type2[, "Time"])), c(stt_q0.25_type2[,
"Total"] + 1, rev(stt_q0.75_type2[, "Total"] + 1)), col = "dark grey", border = NA)
graphics::lines(stt_average_type2[, "Time"], stt_average_type2[, "Total"] + 1, lwd = 2)
graphics::lines(stt_average_type2[, "Time"], stt_average_type2[, "nI"] + 1, lwd = 2, col = "cyan3")
graphics::lines(stt_average_type2[, "Time"], stt_average_type2[, "Endemic"] + 1, lwd = 2, col = "dodgerblue1")
} else {
# Default behavior to open a new device, which hurts vignettes
if (use_dev_new == TRUE) {
grDevices::dev.new(width = 6, height = 6)
}
graphics::par(mfrow = c(1, 1))
DAISIE_plot_stt(
plot_plus_one = plot_plus_one,
time = time,
stt_q0.025_all = stt_q0.025_all,
stt_q0.25_all = stt_q0.25_all,
stt_average_all = stt_average_all,
stt_q0.75_all = stt_q0.75_all,
stt_q0.975_all = stt_q0.975_all
)
}
}
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