readSingleLog: Read a single BEAST log file

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.

Usage

readSingleLog(
  filename,
  burnin = 0.1,
  maxsamples = -1,
  as.mcmc = TRUE,
  burninAsSamples = FALSE
)

Arguments

filename	The name of the log file to read.
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.

See Also

readLog

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