Rsampletrees: MCMC Sampling of Gene Genealogies Conditional on Genetic Data
Version 1.0

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 .

Browse man pages Browse package API and functions Browse package files

AuthorKelly Burkett, Brad McNeney, Jinko Graham, Jean-Francois Lefebvre
Date of publication2017-04-18 16:02:36 UTC
MaintainerJean-Francois Lefebvre <jflefebvre27@gmail.com>
LicenseGPL (>= 2)
Version1.0
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("Rsampletrees")

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...
example_g_pars: Genotype data parameters
launch.sampletrees: Launches the c++ sampletrees program using arguments...
merge.treeoutput: Merge the results from two runs of sampletrees
newArgs: Create or modify a sampletrees settings object
pkg-internal: Internal use functions.
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: MCMC sampling of gene genealogies conditional on genetic data

Functions

Rsampletrees Man page
Rsampletrees-package Man page
addTreeStat Man page Source code
addTrees Man page Source code
changeArgs Man page Source code
changeArgs.default Man page Source code
changeArgs.pars Man page Source code
changeArgs.treeoutput Man page Source code
checkArgs Man page Source code
checkfile Man page Source code
defaultArgs Man page Source code
estimateHap Man page Source code
example_g_pars Man page
example_h_2_pars Man page
example_h_pars Man page
formatArgs Man page Source code
launch.sampletrees Man page Source code
merge.treeoutput Man page Source code
newArgs Man page Source code
plot.treeoutput Man page Source code
print.pars Man page Source code
print.treeoutput Man page Source code
readArgs Man page Source code
readOutput Man page Source code
readTrees Man page Source code
restartRun Man page Source code
setWeights Man page Source code
summary.treeoutput Man page Source code
treeapply Man page Source code
writeArgs Man page Source code
writeTreeoutput Man page Source code

Files

inst
inst/extdata
inst/extdata/example_h_2_pars
inst/extdata/Example-h-2_firsttree.out
inst/extdata/EM-known.out
inst/extdata/Example-g_haplolist.out
inst/extdata/Example-h_samples.out
inst/extdata/Example-g_firsttree.out
inst/extdata/Example-h_trees.out
inst/extdata/example_g_pars
inst/extdata/Example-h_lasttree.out
inst/extdata/Example-h-2_trees.out
inst/extdata/Example-g_trees.out
inst/extdata/Example-g_samples.out
inst/extdata/weights-h.txt
inst/extdata/Example-h_accept.out
inst/extdata/geno_Theta8_Rho8.txt
inst/extdata/Example-h-2_samples.out
inst/extdata/Example-h_firsttree.out
inst/extdata/Example-g_postprob.out
inst/extdata/Example-g_accept.out
inst/extdata/EM-initial.out
inst/extdata/EM-hapfreqs.out
inst/extdata/Example-g_sequences.out
inst/extdata/Example-g_lasttree.out
inst/extdata/Example-h-2_lasttree.out
inst/extdata/Example-h-2_accept.out
inst/extdata/example_h_pars
inst/extdata/sequences_Theta8_Rho8.txt
inst/extdata/weights-g.txt
inst/extdata/locations_Theta8_Rho8.txt
src
src/Makevars
src/treesummaries.h
src/misc.cpp
src/p5.h
src/readFiles.cpp
src/p3.cpp
src/sampletrees.cpp
src/p6.cpp
src/p5.cpp
src/misc.h
src/p6.h
src/p3.h
src/registerDynamicSymbol.c
src/sampletrees.h
src/p7.cpp
src/rcpp_sampletrees.cpp
src/models.h
src/treeBuild.h
src/nodefunctions.cpp
src/proposal.cpp
src/treeBuild.cpp
src/p1p2.cpp
src/models.cpp
src/rcpp_sampletrees.h
src/UPGMA.h
src/treesummaries.cpp
src/proposal.h
src/nodefunctions.h
src/Makevars.win
src/p4.h
src/p1p2.h
src/rng.h
src/p4.cpp
src/p7.h
src/rng.cpp
src/readFiles.h
src/UPGMA.cpp
NAMESPACE
R
R/haplo_initialization.R
R/post_sampletrees.R
R/pre_sampletrees.R
MD5
DESCRIPTION
man
man/plot.treeoutput.Rd
man/addTrees.Rd
man/readArgs.Rd
man/estimateHap.Rd
man/checkArgs.Rd
man/print.treeoutput.Rd
man/addTreeStats.Rd
man/restartRun.Rd
man/example_g_pars.Rd
man/newArgs.Rd
man/changeArgs.treeoutput.Rd
man/readTrees.Rd
man/readOutput.Rd
man/pkg-internal.Rd
man/launch.sampletrees.Rd
man/print.pars.Rd
man/merge.treeoutput.Rd
man/Rsampletrees-package.Rd
Rsampletrees documentation built on May 19, 2017, 12:55 p.m.