# MCMC Sampling of Gene Genealogies Conditional on Genetic Data

## Documentation for package ‘Rsampletrees’ version 1.0.2

- DESCRIPTION file.

## Help Pages

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