loadTrees: Modified from RWTY

In lfabreti/convenience: Convergence assessment for phylogenetic inference

Modified from RWTY

Description

Loads trees, looks for a log file of tree likelihoods and parameter values, returns an rwty.chain object containing both

Usage

loadTrees(
  file,
  type = NA,
  format = "mb",
  gens.per.tree = NA,
  trim = 1,
  logfile = NA,
  skip = NA
)

Arguments

file	The tree file
type	The type of tree file
format	The format of the phylogenetic output. Current supported formats are: "revbayes", "mb", "beast", "*beast", "phylobayes"
gens.per.tree	Number of generations between sampled trees
trim	Increment for the sequence of trees to read
logfile	The log files from the MCMC
skip	Number of lines to skip before reading the data from the log file

Value

output A list of rwty.chain objects containing the multiPhylos and the tables of values from the log files if available

lfabreti/convenience documentation built on June 17, 2022, 8:12 a.m.