coalescentMCMC: MCMC Algorithms for the Coalescent

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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.

Author
Emmanuel Paradis [aut, cre, cph]
Date of publication
2015-03-03 22:37:48
Maintainer
Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
License
GPL (>= 2)
Version
0.4-1

View on CRAN

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

Files in this package

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