Rsampletrees: Sampletrees Input/Output Processing

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.

AuthorKelly Burkett, Brad McNeney, Jinko Graham
Date of publication2015-02-02 20:45:11
MaintainerKelly Burkett <kburkett@uottawa.ca>
LicenseGPL-2
Version0.1

View on CRAN

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

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