MCMC Sampling of Gene Genealogies Conditional on Genetic Data

Documentation for package ‘Rsampletrees’ version 1.0.3

Rsampletrees-package	MCMC sampling of gene genealogies conditional on genetic data
addTrees	Read in trees and add them to the tree output object
addTreeStat	Add tree statistics to a treeoutput object
changeArgs	Create or modify a sampletrees settings object
changeArgs.pars	Create or modify a sampletrees settings object
changeArgs.treeoutput	Modify the settings stored in a sampletrees treeoutput object
checkArgs	Error checking for the arguments to sampletrees
estimateHap	Estimate and write haplotype probabilities and initial values to files
launch.sampletrees	Launches the c++ sampletrees program using arguments previously given and checked.
merge.treeoutput	Merge the results from two runs of sampletrees
newArgs	Create or modify a sampletrees settings object
plot.treeoutput	Plot selected output of a sampletrees run
print.pars	Nice display of tags and values of a sampletrees settings object
print.treeoutput	Nice display of a treeoutput object
readArgs	Read arguments for a sampletrees run from a settings file
readOutput	Read in sampletrees output
readTrees	Read in trees from a run of sampletrees.
restartRun	Set up a settings object for continuing a previous sampletrees run
Rsampletrees	MCMC sampling of gene genealogies conditional on genetic data