readTrace: Read trace

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

Read trace

Description

Reads in MCMC log files

Usage

readTrace(
  paths,
  format = "simple",
  delim = "\t",
  burnin = 0.1,
  check.names = FALSE,
  ...
)

Arguments

paths	(vector of character strings; no default) File path(s) to trace file.
format	(single character string; default = simple) Indicates type of MCMC trace, complex indicates cases where trace contains vectors of vectors/ matrices - mnStochasticVariable monitor will sometimes be of this type.
delim	(single character string; default = "\t") Delimiter of file.
burnin	(single numeric value; default = 0.1) Fraction of generations to discard (if value provided is between 0 and 1) or number of generations (if value provided is greater than 1).
check.names	(logical; default = FALSE) Passed to utils::read.table(); indicates if utils::read.table() should check column names and replace syntactically invalid characters.
...	(various) Additional arguments passed to utils::read.table().

Details

Reads in one or multiple MCMC log files from the same analysis and discards a user-specified burn-in, compatible with multiple monitor types. If the trace contains vectors of vectors and the user does not specify format = "complex", readTrace() will read in those columns as factors rather than as numeric vectors.

Value

List of dataframes (of length 1 if only 1 log file provided).

Examples

# read and process a single trace file


# download the example dataset to working directory
url_gtr <-
   "https://revbayes.github.io/tutorials/intro/data/primates_cytb_GTR.log"
dest_path_gtr <- "primates_cytb_GTR.log"
download.file(url_gtr, dest_path_gtr)

# to run on your own data, change this to the path to your data file
file_single <- dest_path_gtr

one_trace <- readTrace(paths = file_single)

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

# read and process multiple trace files, such as from multiple runs of
# the same analysis

# 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)

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

RevGadgets documentation built on Nov. 17, 2023, 1:07 a.m.