Rsampletrees-package    MCMC sampling of gene genealogies conditional
                        on genetic data
addTreeStat             Add tree statistics to a treeoutput object
addTrees                Read in trees and add them to the tree output
                        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
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
