processSSE {RevGadgets}

Title

Description

Title

Usage

processSSE(
  path,
  speciation = "speciation",
  extinction = "extinction",
  speciation_hidden = "speciation_hidden",
  rates = c(speciation, extinction, "net-diversification"),
  ...
)

Arguments

path

(vector of character strings; no default) File path(s) to trace file.

speciation

(single character string; "speciation") RevBayes variable name

extinction

(single character string; "extinction") RevBayes variable name

speciation_hidden

(single character string; "speciation_hidden") RevBayes variable name

rates

(vector; c(speciation, extinction, "net-diversification")) names of rates to be included in plot

...

additional arguments passed to readTrace()

Value

a data frame

Examples

# download the example dataset to working directory

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

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

pdata <- processSSE(bisse_file)

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