combineTraces: Combine traces

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

Combine traces

Description

Combine traces into one trace file

Usage

combineTraces(traces, burnin = 0)

Arguments

traces	(list of data frames; no default) Name of a list of data frames, such as produced by readTrace().
burnin	(single numeric value; default = 0.0) Fraction of generations to discard (if value provided is between 0 and 1) or number of generations to discard (if value provided is greater than 1) before combining the samples.

Details

Combines multiple traces from independent MCMC replicates into one trace file.

Value

combineTraces() returns a list of data frames of length 1, corresponding to the combination of the provided samples.

Examples

#' # download the example dataset to working directory
url_1 <-
"https://revbayes.github.io/tutorials/intro/data/primates_cytb_GTR_run_1.log"
dest_path_1 <- "primates_cytb_GTR_run_1.log"
download.file(url_1, dest_path_1)

url_2 <-
"https://revbayes.github.io/tutorials/intro/data/primates_cytb_GTR_run_2.log"
dest_path_2 <- "primates_cytb_GTR_run_2.log"
download.file(url_2, dest_path_2)

# to run on your own data, change this to the path to your data file
file_1 <- dest_path_1
file_2 <- dest_path_2

# read in the multiple trace files
multi_trace <- readTrace(path = c(file_1, file_2), burnin = 0.0)

# combine samples after discarding 10% burnin
combined_trace <- combineTraces(trace = multi_trace,
                                burnin = 0.1)

# remove files
# WARNING: only run for example dataset!
# otherwise you might delete your data!
file.remove(dest_path_1, dest_path_2)

revbayes/RevGadgets documentation built on Jan. 19, 2024, 3:29 p.m.