Contains functions that are useful for pre- and post-processing the tree output from the MCMC-based C++ program sampletrees. The program sampletrees is used to sample gene genealogies conditional on either phased or unphased SNP genotype data. More information about sampletrees can be found at http://stat.sfu.ca/statgen/research/sampletrees.html . Pre-processing tasks involve creating the settings file, the haplotype estimation files (if input data is genotype), and error checking the settings. Post-processing involves reading in the MCMC output from a run of sampletrees and computing summary statistics.
|Author||Kelly Burkett, Brad McNeney, Jinko Graham|
|Date of publication||2015-02-02 20:45:11|
|Maintainer||Kelly Burkett <firstname.lastname@example.org>|
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...
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...
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: Pre and Post-Processing of sampletrees output
setWeights: Set weights for the sampletrees proposal distributions
summary.treeoutput: Summary of a tree output object
treeapply: Apply a function to the sampled trees
writeArgs: Write arguments for a sampletrees run to a file in the format...
writeTreeoutput: Write the results of a sampletrees run to file