MCMC Sampling of Gene Genealogies Conditional on Genetic Data


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Documentation for package ‘Rsampletrees’ version 1.0.2

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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
example_g_pars Genotype data parameters
example_h_2_pars Genotype data parameters
example_h_pars Genotype data parameters
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