readOBDP: Read OBDP Outputs

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

Read OBDP Outputs

Description

Reads and formats the outputs of an analysis with the Occurrence Birth Death Process (MCMC parameter inference + diversity estimation)

Usage

readOBDP(
  start_time_trace_file,
  popSize_distribution_matrices_file,
  trees_trace_file
)

Arguments

start_time_trace_file	(character; no default) Trace of the starting times along the MCMC chain.
popSize_distribution_matrices_file	(character; no default) Kt matrices computed with 'fnInferAncestralPopSize' in RevBayes.
trees_trace_file	(character; no default) Trace of the trees.

Value

A data.frame

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.