plotDiversityOBDP: Plot Diversity Distribution from OBDP Analysis

In RevGadgets: Visualization and Post-Processing of 'RevBayes' Analyses

Plot Diversity Distribution from OBDP Analysis

Description

Plots the probability distribution of the number of lineages through time inferred with the Occurrence Birth Death Process #'

Usage

plotDiversityOBDP(
  Kt_mean,
  xlab = "Time",
  ylab = "Number of lineages",
  xticks_n_breaks = 5,
  col_Hidden = "dodgerblue3",
  col_LTT = "gray25",
  col_Total = "forestgreen",
  col_Hidden_interval = "dodgerblue2",
  col_Total_interval = "darkolivegreen4",
  palette_Hidden = c("transparent", "dodgerblue2", "dodgerblue3", "dodgerblue4", "black"),
  palette_Total = c("transparent", "green4", "forestgreen", "black"),
  line_size = 0.7,
  interval_line_size = 0.5,
  show_Hidden = TRUE,
  show_LTT = TRUE,
  show_Total = TRUE,
  show_intervals = TRUE,
  show_densities = TRUE,
  show_expectations = TRUE,
  use_interpolate = TRUE
)

Arguments

Kt_mean	(data.frame; no default) The processed data.frame (output of readOBDP()).
xlab	(character; "Time") The label of the x-axis.
ylab	(character; "Number of lineages") The label of the y-axis.
xticks_n_breaks	(numeric; 5) An integer guiding the number of major breaks.
col_Hidden	(character; "dodgerblue3") The color of the hidden lineages plot line.
col_LTT	(character; "gray25") The color of the LTT plot line.
col_Total	(character; "forestgreen") The color of the total lineages plot line.
col_Hidden_interval	(character; "dodgerblue2") The color of the credible interval lines around the hidden lineages plot.
col_Total_interval	(character; "darkolivegreen4") The color of the credible interval lines around the total lineages plot.
palette_Hidden	(character; c("transparent", "dodgerblue2", "dodgerblue3", "dodgerblue4", "black")) The palette of the hidden lineages plot distribution.
palette_Total	(character; c("transparent", "green4", "forestgreen", "black")) The palette of the total lineages plot distribution.
line_size	(numeric; 0.7) The width of the lineage plot line.
interval_line_size	(numeric; 0.5) The width of the credible interval.
show_Hidden	(boolean; TRUE) Whether to show the plot for hidden lineages.
show_LTT	(boolean; TRUE) Whether to show the plot for observed lineages.
show_Total	(boolean; TRUE) Whether to show the plot for total lineages.
show_intervals	(boolean; TRUE) Whether to show the credible intervals.
show_densities	(boolean; TRUE) Whether to show the diversity densities.
show_expectations	(boolean; TRUE) Whether to show the diversity expectations.
use_interpolate	(boolean; TRUE) Whether to interpolate densities.

Value

A ggplot object

Examples

## Not run: 
# first run readOBDP()
start_time_trace_file <- 
     system.file("extdata", "obdp/start_time_trace.p", package="RevGadgets")
popSize_distribution_matrices_file <- 
     system.file("extdata", "obdp/Kt_trace.p", package="RevGadgets")
trees_trace_file <- 
     system.file("extdata", "obdp/mcmc_OBDP_trees.p", package="RevGadgets")
    
Kt_mean <- readOBDP( start_time_trace_file=start_time_trace_file, 
                     popSize_distribution_matrices_file=popSize_distribution_matrices_file, 
                     trees_trace_file=trees_trace_file )

# then get the customized ggplot object with plotDiversityOBDP()
p <- plotDiversityOBDP( Kt_mean,
                        xlab="Time (My)",
                        ylab="Number of lineages",
                        xticks_n_breaks=21,
                        col_Hidden="dodgerblue3",
                        col_LTT="gray25",
                        col_Total="forestgreen",
                        col_Hidden_interval="dodgerblue2",
                        col_Total_interval="darkolivegreen4",
                        palette_Hidden=c("transparent", "dodgerblue2", "dodgerblue3", 
                                         "dodgerblue4", "black"),
                        palette_Total=c("transparent", "green4", "forestgreen", "black"),
                        line_size=0.7,
                        interval_line_size=0.5,
                        show_Hidden=TRUE,
                        show_LTT=TRUE,
                        show_Total=TRUE,
                        show_intervals=TRUE,
                        show_densities=TRUE,
                        show_expectations=TRUE,
                        use_interpolate=TRUE )

# basic plot
p

# option: add a stratigraphic scale
library(deeptime)
library(ggplot2)
q <- gggeo_scale(p, dat="periods", height=unit(1.3, "line"), abbrv=F, size=4.5, neg=T)
r <- gggeo_scale(q, dat="epochs", height=unit(1.1, "line"), abbrv=F, size=3.5, neg=T, 
                    skip=c("Paleocene", "Pliocene", "Pleistocene", "Holocene"))
s <- gggeo_scale(r, dat="stages", height=unit(1, "line"), abbrv=T, size=2.5, neg=T)
s

## End(Not run)

RevGadgets documentation built on May 29, 2024, 10:03 a.m.