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

Functions

addTrees Man page
addTreeStat Man page
changeArgs Man page
changeArgs.pars Man page
changeArgs.treeoutput Man page
checkArgs Man page
estimateHap Man page
merge.treeoutput Man page
newArgs Man page
plot.treeoutput Man page
print.pars Man page
print.treeoutput Man page
readArgs Man page
readOutput Man page
readTrees Man page
restartRun Man page
Rsampletrees Man page
Rsampletrees-package Man page
setWeights Man page
summary.treeoutput Man page
treeapply Man page
writeArgs Man page
writeTreeoutput Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.