API for Caetanods/ratematrix
Bayesian estimation of the evolutionary rate matrix

Global functions
calcNodeToNode Source code
calcNodeToTip Source code
calcNodeToTipNode Source code
checkConvergence Man page Source code
checkHPD Source code
checkHeidelTest Source code
continueMCMC Man page Source code
dicMCMC Source code
estimateTimeMCMC Man page Source code
getEllipseAllMatrix Source code
getEllipseMatrix Source code
hastingsDensity Source code
likelihoodFunction Man page Source code
logAnalyzer Man page Source code
logDensityIWish Source code
logDensityMvNorm Source code
logLikMultRegime Source code
logLikNode Source code
logLikPrunningMCMC Source code
logLikSingleRegime Source code
makePrior Man page Source code
makePriorBarnard Source code
makePriorIWish Source code
makePropIWish Source code
makePropMean Source code
makePropMeanForMult Source code
makePropMeanForMultList Source code
makePropMeanList Source code
makePropMultSigma Source code
makePropMultSigmaList Source code
makePropSingleSigma Source code
makePropSingleSigmaList Source code
makeStart Man page Source code
mergePosterior Man page Source code
mergeSimmap Man page Source code
multRegimeMCMC Source code
mvLogLik Man page Source code
parseResults Source code
parseResultsMCMC Source code
plotPrior Man page Source code
plotRatematrix Man page Source code
plotRootValue Man page Source code
postPredicSims Source code
print.ratematrix_multi_chain Man page Source code
print.ratematrix_multi_mcmc Man page Source code
print.ratematrix_prior_function Man page Source code
print.ratematrix_prior_sample Man page Source code
print.ratematrix_single_chain Man page Source code
print.ratematrix_single_mcmc Man page Source code
priorDensityVcvBarnard Source code
ratematrixMCMC Man page Source code
readMCMC Man page Source code
readMultRegimeMCMC Source code
readSingleRegimeMCMC Source code
riwish Source code
samplePrior Man page Source code
samplePriorBarnard Source code
samplePriorSeparationLimits Source code
sampleTreeClade Source code
simRatematrix Man page Source code
singleRegimeMCMC Source code
slideWindow Source code
slideWindowPositive Source code
testRatematrix Man page Source code
writeToFile Source code
writeToMultFile Source code
Caetanods/ratematrix documentation built on Dec. 21, 2017, 9:46 p.m.