plotHiSSE {RevGadgets}

plotHiSSE

Description

plotHiSSE

Usage

plotHiSSE(rates)

Arguments

rates

(data.frame; no default) a data frame containing columns "value", "rate", "hidden_state", "observed_state" (such as the output of processSSE())

Value

a ggplot object

Examples

# download the example dataset to working directory

url <- "https://revbayes.github.io/tutorials/intro/data/primates_HiSSE_2.log"
dest_path <- "primates_HiSSE_2.log"
download.file(url, dest_path)

# to run on your own data, change this to the path to your data file
hisse_file <- dest_path

pdata <- processSSE(hisse_file)
p <- plotHiSSE(pdata);p

# change colors:
p + ggplot2::scale_fill_manual(values = c("red","green"))

# change x-axis label
p + ggplot2::xlab("Rate (events/Ma)")

# remove file
# WARNING: only run for example dataset!
# otherwise you might delete your data!
file.remove(dest_path)