Files in Caetanods/ratematrix
Bayesian Estimation of the Evolutionary Rate Matrix
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/RcppExports.R
R/calcNodeToNode.R
R/calcNodeToTip.R
R/calcNodeToTipNode.R
R/checkConvergence.R
R/checkHPD.R
R/checkHeidelTest.R
R/check_phy_list.R
R/computeESS.R
R/continueMCMC.R
R/dataset_anoles.R
R/dataset_centrarchidae.R
R/estimateTimeMCMC.R
R/extractCorrelation.R
R/fastSimmap.R
R/getEllipseMatrix.R
R/getStartPointFromPosterior.R
R/hastingsDensity.R
R/likelihoodFunction.R
R/logAnalyzer.R
R/logDensityIWish.R
R/logDensityMvNorm.R
R/logLikNode.R
R/logLikPrunningMCMC.R
R/logLikSingleRegime.R
R/makeDataTips.R
R/makePrior.R
R/makePriorIWish.R
R/makePropIWish.R
R/makePropMean.R
R/makePropMeanForMult.R
R/makePropMeanForMultList.R
R/makePropMeanList.R
R/makePropMultSigma.R
R/makePropMultSigmaList.R
R/makePropSingleSigma.R
R/makePropSingleSigmaList.R
R/mergePosterior.R
R/mergeSimmap.R
R/multRegimeJointMCMC.R
R/multRegimeMCMC.R
R/multiplierProposal.R
R/mvLogLik.R
R/plotPrior.R
R/plotRatematrix.R
R/plotRootValue.R
R/print.ratematrix_multi_chain.R
R/print.ratematrix_multi_mcmc.R
R/print.ratematrix_prior_function.R
R/print.ratematrix_prior_sample.R
R/print.ratematrix_single_chain.R
R/print.ratematrix_single_mcmc.R
R/priorDensityVcvBarnard.R
R/ratematrix-package.R
R/ratematrixJointMCMC.R
R/ratematrixMCMC.R
R/readMCMC.R
R/readMultRegimeMCMC.R
R/readSingleRegimeMCMC.R
R/riwish.R
R/samplePrior.R
R/samplePriorSeparationLimits.R
R/sampleTreeClade.R
R/simRatematrix.R
R/singleRegimeMCMC.R
R/slideWindow.R
R/slideWindowPositive.R
R/testRatematrix.R
R/writeToFile.R
R/writeToMultFile.R
README.md
data/anoles.RData
data/centrarchidae.RData
inst/extdata/corr.zero.RData
inst/extdata/handle.start.point.tutorial.RData
inst/extdata/intro_vignette.RData
inst/extdata/mcmc.start.point.tutorial.RData
inst/extdata/norm.root.RData
inst/extdata/unif.root.RData
inst/include/distributions_and_helpers.h
inst/include/likelihood_pruning.h
inst/include/log_functions.h
inst/include/priors.h
inst/include/proposals.h
inst/include/stochastic_mapping.h
man/anoles.Rd
man/centrarchidae.Rd
man/checkConvergence.Rd
man/computeESS.Rd
man/continueMCMC.Rd
man/estimateTimeMCMC.Rd
man/extractCorrelation.Rd
man/fastSimmap.Rd
man/getStartPointFromPosterior.Rd
man/likelihoodFunction.Rd
man/logAnalyzer.Rd
man/makePrior.Rd
man/mergePosterior.Rd
man/mergeSimmap.Rd
man/plotPrior.Rd
man/plotRatematrix.Rd
man/plotRootValue.Rd
man/print.ratematrix_multi_chain.Rd
man/print.ratematrix_multi_mcmc.Rd
man/print.ratematrix_prior_function.Rd
man/print.ratematrix_prior_sample.Rd
man/print.ratematrix_single_chain.Rd
man/print.ratematrix_single_mcmc.Rd
man/ratematrix.Rd
man/ratematrixJointMCMC.Rd
man/ratematrixMCMC.Rd
man/readMCMC.Rd
man/readMCMC_Mk.Rd
man/samplePrior.Rd
man/simRatematrix.Rd
man/testRatematrix.Rd
src/.gitignore
src/Makevars
src/Makevars.win
src/MultRegimeMCMC.cpp
src/RcppExports.cpp
vignettes/Intro_on_the_package.Rmd
vignettes/Making_prior_on_ratematrix.Rmd
vignettes/Set_custom_starting_point.Rmd
