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Rsampletrees (version 1.0.3)

MCMC Sampling of Gene Genealogies Conditional on Genetic Data

Description

Sample ancestral trees conditional on phased or unphased SNP genotype data. The actual tree sampling is done using a C++ program that is launched within R. The package also contains functions for specifying the tree-sampling settings (pre-processing) and for storing and manipulating the sampled trees (post-processing). More information about 'sampletrees' can be found at .

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Version

Install

install.packages('Rsampletrees')

Monthly Downloads

52

Version

1.0.3

License

GPL (>= 2)

Maintainer

Last Published

March 2nd, 2020

Functions in Rsampletrees (1.0.3)

Set up a settings object for continuing a previous sampletrees run

merge.treeoutput

Merge the results from two runs of sampletrees

plot.treeoutput

Plot selected output of a sampletrees run

Nice display of tags and values of a sampletrees settings object

Read in trees from a run of sampletrees.

Read in sampletrees output

print.treeoutput

Nice display of a treeoutput object

Read arguments for a sampletrees run from a settings file

Read in trees and add them to the tree output object

Add tree statistics to a treeoutput object

launch.sampletrees

Launches the c++ sampletrees program using arguments previously given and checked.

Create or modify a sampletrees settings object

Rsampletrees-package

MCMC sampling of gene genealogies conditional on genetic data

changeArgs.treeoutput

Modify the settings stored in a sampletrees treeoutput object

changeArgs.default

Internal use functions.

Error checking for the arguments to sampletrees

Estimate and write haplotype probabilities and initial values to files