addTrees | Read in trees and add them to the tree output object |
addTreeStats | Add tree statistics to a treeoutput 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... |
launch.sampletrees | Launches the c++ sampletrees program using arguments... |
merge.treeoutput | Merge the results from two runs of sampletrees |
newArgs | Create or modify a sampletrees settings object |
pkg-internal | Internal use functions. |
plot.treeoutput | Plot selected output of a sampletrees run |
print.pars | Nice display of tags and values of a sampletrees settings... |
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... |
Rsampletrees-package | MCMC sampling of gene genealogies conditional on genetic data |
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