coalescentMCMC: MCMC Algorithms for the Coalescent

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

View on CRAN

Functions

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

Files

coalescentMCMC
coalescentMCMC/COPYING
coalescentMCMC/inst
coalescentMCMC/inst/doc
coalescentMCMC/inst/doc/CoalescentModels.pdf
coalescentMCMC/inst/doc/CoalescentModels.R
coalescentMCMC/inst/doc/Running_coalescentMCMC.pdf
coalescentMCMC/inst/doc/Running_coalescentMCMC.R
coalescentMCMC/inst/doc/CoalescentModels.Rnw
coalescentMCMC/inst/doc/Running_coalescentMCMC.Rnw
coalescentMCMC/src
coalescentMCMC/src/Makevars
coalescentMCMC/src/coalescentMCMC.c
coalescentMCMC/NAMESPACE
coalescentMCMC/NEWS
coalescentMCMC/R
coalescentMCMC/R/dcoal.R coalescentMCMC/R/sim.coalescent.R coalescentMCMC/R/treeOperators.R coalescentMCMC/R/coalescentMCMC.R coalescentMCMC/R/zzz.R
coalescentMCMC/vignettes
coalescentMCMC/vignettes/coalescentMCMC.bib
coalescentMCMC/vignettes/CoalescentModels.Rnw
coalescentMCMC/vignettes/Running_coalescentMCMC.Rnw
coalescentMCMC/MD5
coalescentMCMC/build
coalescentMCMC/build/vignette.rds
coalescentMCMC/DESCRIPTION
coalescentMCMC/man
coalescentMCMC/man/treeOperators.Rd coalescentMCMC/man/coalescentMCMC-internal.Rd coalescentMCMC/man/coalesceMCMC.Rd coalescentMCMC/man/sim.coalescent.Rd coalescentMCMC/man/dcoal.Rd

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

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