coalescentMCMC: MCMC Algorithms for the Coalescent
Version 0.4-1

Flexible framework for coalescent analyses in R. It includes a main function running the MCMC algorithm, auxiliary functions for tree rearrangement, and some functions to compute population genetic parameters.

AuthorEmmanuel Paradis [aut, cre, cph]
Date of publication2015-03-03 22:37:48
MaintainerEmmanuel Paradis <Emmanuel.Paradis@ird.fr>
LicenseGPL (>= 2)
Version0.4-1
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("coalescentMCMC")

Popular man pages

coalesceMCMC: Run MCMC for Coalescent Trees
coalescentMCMC-internal: Internal coalescentMCMC Functions
dcoal: Density Functions of Various Time-Dependent Coalescent Models
sim.coalescent: Coalescent Simulation and Visualisation
treeOperators: Trees Operators for Running MCMC
See all...

All man pages Function index File listing

Man pages

coalesceMCMC: Run MCMC for Coalescent Trees
coalescentMCMC-internal: Internal coalescentMCMC Functions
dcoal: Density Functions of Various Time-Dependent Coalescent Models
sim.coalescent: Coalescent Simulation and Visualisation
treeOperators: Trees Operators for Running MCMC

Functions

EdgeLengthJittering Man page Source code
NeighborhoodRearrangement Man page Source code
TipInterchange Man page Source code
cleanMCMCtrees Man page Source code
coalescentMCMC Man page Source code
dcoal Man page Source code
dcoal.linear Man page Source code
dcoal.step Man page Source code
dcoal.time Man page Source code
dcoal.time2 Man page Source code
get.list.trees Source code
getIndexEdge Man page Source code
getIndexEdge2 Man page Source code
getLastTree Man page Source code
getMCMCstats Man page Source code
getMCMCtrees Man page Source code
saveMCMCtrees Man page Source code
sim.coalescent Man page Source code
treeOperators Man page

Files

COPYING
inst
inst/doc
inst/doc/CoalescentModels.pdf
inst/doc/CoalescentModels.R
inst/doc/Running_coalescentMCMC.pdf
inst/doc/Running_coalescentMCMC.R
inst/doc/CoalescentModels.Rnw
inst/doc/Running_coalescentMCMC.Rnw
src
src/Makevars
src/coalescentMCMC.c
NAMESPACE
NEWS
R
R/dcoal.R
R/sim.coalescent.R
R/treeOperators.R
R/coalescentMCMC.R
R/zzz.R
vignettes
vignettes/coalescentMCMC.bib
vignettes/CoalescentModels.Rnw
vignettes/Running_coalescentMCMC.Rnw
MD5
build
build/vignette.rds
DESCRIPTION
man
man/treeOperators.Rd
man/coalescentMCMC-internal.Rd
man/coalesceMCMC.Rd
man/sim.coalescent.Rd
man/dcoal.Rd
coalescentMCMC documentation built on May 19, 2017, 8:49 a.m.

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