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Rsampletrees (version 0.1)

Sampletrees Input/Output Processing

Description

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.

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Version

Install

install.packages('Rsampletrees')

Monthly Downloads

4

Version

0.1

License

GPL-2

Maintainer

Kelly Burkett

Last Published

February 2nd, 2015

Functions in Rsampletrees (0.1)

print.treeoutput

Nice display of a treeoutput object
readOutput

Read in sampletrees output
plot.treeoutput

Plot selected output of a sampletrees run
setWeights

Set weights for the sampletrees proposal distributions
checkArgs

Error checking for the arguments to sampletrees
newArgs

Create or modify a sampletrees settings object
addTrees

Read in trees and add them to the tree output object
Rsampletrees-package

Pre and Post-Processing of sampletrees output
addTreeStat

Add tree statistics to a treeoutput object
readArgs

Read arguments for a sampletrees run from a settings file
merge.treeoutput

Merge the results from two runs of sampletrees
print.pars

Nice display of tags and values of a sampletrees settings object
changeArgs.treeoutput

Modify the settings stored in a sampletrees treeoutput object
writeArgs

Write arguments for a sampletrees run to a file in the format required for sampletrees
estimateHap

Estimate and write haplotype probabilities and initial values to files
restartRun

Set up a settings object for continuing a previous sampletrees run
readTrees

Read in trees from a run of sampletrees.
writeTreeoutput

Write the results of a sampletrees run to file
treeapply

Apply a function to the sampled trees
summary.treeoutput

Summary of a tree output object