Rsampletrees: Sampletrees Input/Output Processing

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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 <kburkett@uottawa.ca>
License
GPL-2
Version
0.1

View on CRAN

Man pages

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

Files in this package

Rsampletrees
Rsampletrees/inst
Rsampletrees/inst/Output
Rsampletrees/inst/Output/Example-h-2_firsttree.out
Rsampletrees/inst/Output/Example-h-2_postprob.out
Rsampletrees/inst/Output/Example-g_haplolist.out
Rsampletrees/inst/Output/Example-h_samples.out
Rsampletrees/inst/Output/Example-g_firsttree.out
Rsampletrees/inst/Output/Example-h_trees.out
Rsampletrees/inst/Output/Example-h_lasttree.out
Rsampletrees/inst/Output/Example-h-2_trees.out
Rsampletrees/inst/Output/Example-g_trees.out
Rsampletrees/inst/Output/Example-g_samples.out
Rsampletrees/inst/Output/Example-h_accept.out
Rsampletrees/inst/Output/Example-h-2_samples.out
Rsampletrees/inst/Output/Example-h_firsttree.out
Rsampletrees/inst/Output/Example-g_postprob.out
Rsampletrees/inst/Output/Example-g_accept.out
Rsampletrees/inst/Output/Example-h_postprob.out
Rsampletrees/inst/Output/Example-g_sequences.out
Rsampletrees/inst/Output/Example-g_lasttree.out
Rsampletrees/inst/Output/Example-h-2_lasttree.out
Rsampletrees/inst/Output/Example-h-2_accept.out
Rsampletrees/inst/Examples
Rsampletrees/inst/Examples/example_h_2_pars
Rsampletrees/inst/Examples/EM-known.out
Rsampletrees/inst/Examples/example_g_pars
Rsampletrees/inst/Examples/weights-h.txt
Rsampletrees/inst/Examples/geno_Theta8_Rho8.txt
Rsampletrees/inst/Examples/EM-initial.out
Rsampletrees/inst/Examples/EM-hapfreqs.out
Rsampletrees/inst/Examples/example_h_pars
Rsampletrees/inst/Examples/sequences_Theta8_Rho8.txt
Rsampletrees/inst/Examples/weights-g.txt
Rsampletrees/inst/Examples/locations_Theta8_Rho8.txt
Rsampletrees/NAMESPACE
Rsampletrees/R
Rsampletrees/R/pre_sampletrees.r
Rsampletrees/R/haplo_initialization.r
Rsampletrees/R/post_sampletrees.r
Rsampletrees/MD5
Rsampletrees/DESCRIPTION
Rsampletrees/man
Rsampletrees/man/plot.treeoutput.Rd
Rsampletrees/man/addTrees.Rd
Rsampletrees/man/readArgs.Rd
Rsampletrees/man/estimateHap.Rd
Rsampletrees/man/checkArgs.Rd
Rsampletrees/man/print.treeoutput.Rd
Rsampletrees/man/addTreeStats.Rd
Rsampletrees/man/restartRun.Rd
Rsampletrees/man/newArgs.Rd
Rsampletrees/man/changeArgs.treeoutput.Rd
Rsampletrees/man/summary.treeoutput.Rd
Rsampletrees/man/readTrees.Rd
Rsampletrees/man/readOutput.Rd
Rsampletrees/man/treeapply.Rd
Rsampletrees/man/setWeights.Rd
Rsampletrees/man/print.pars.Rd
Rsampletrees/man/writeTreeoutput.Rd
Rsampletrees/man/merge.treeoutput.Rd
Rsampletrees/man/writeArgs.Rd
Rsampletrees/man/Rsampletrees-package.Rd