readLog: Read BEAST log files

In laduplessis/beastio: Functions for pre- and post-processing of BEAST and BEAST2 files.

Description

Read a single BEAST log file and return as a coda "mcmc" object. If filenames contains more than one entry each log file is added as a separate chain and a coda "mcmc.list" object is returned.

Usage

readLog(
  filenames,
  burnin = 0.1,
  maxsamples = -1,
  as.mcmc = TRUE,
  burninAsSamples = FALSE
)

Arguments

filenames	The name of the log file to read, or aternatively a vector or list of input log file names.
burnin	Discard this proportion of samples at the start of the chain (if 'burninAsSamples' == FALSE). Otherwise discard this many samples at the start of the chain.
maxsamples	If > 0 stop after reading in this many lines (this option is only for testing and should generally not be used).
as.mcmc	If FALSE then return an object of class "data.frame", else return an "mcmc" object
burninAsSamples	if TRUE burnin is given as the number of samples, if FALSE burnin is a proportion (0 <= burnin < 1) of samples. (default = FALSE).

Value

An "mcmc" object (mcmc) or data frame (data.frame) object containing all of the parameters in the MCMC chain, with the burn-in discarded. If more than one log file was given as input the output will be an "mcmc.list" object (mcmc.list) or a list of data frames (data.frame).

See Also

readSingleLog

laduplessis/beastio documentation built on Dec. 14, 2021, 7:04 p.m.