API for Caetanods/ratematrix
Bayesian Estimation of the Evolutionary Rate Matrix
| Global functions | |
|---|---|
| anoles | Man page |
| buildQ | Source code |
| calcNodeToNode | Source code |
| calcNodeToTip | Source code |
| calcNodeToTipNode | Source code |
| centrarchidae | Man page |
| checkConvergence | Man page Source code |
| checkHPD | Source code |
| checkHeidelTest | Source code |
| check_phy_list | Source code |
| computeESS | Man page Source code |
| continueMCMC | Man page Source code |
| estimateTimeMCMC | Man page Source code |
| extractCorrelation | Man page Source code |
| fastSimmap | Man page Source code |
| getEllipseMatrix | Source code |
| getOverlap | Source code |
| getStartPointFromPosterior | Man page Source code |
| hastingsDensity | Source code |
| likelihoodFunction | Man page Source code |
| logAnalyzer | Man page Source code |
| logDensityIWish | Source code |
| logDensityMvNorm | Source code |
| logLikMk_C | Source code |
| logLikNode | Source code |
| logLikPrunningMCMC | Source code |
| logLikPrunningMCMC_C | Source code |
| logLikSingleRegime | Source code |
| makeDataTips | Source code |
| makePrior | Man page 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 |
| makeSimmapMappedEdge | Source code |
| makeSimmapMaps | Source code |
| mergePosterior | Man page Source code |
| mergeSimmap | Man page Source code |
| multRegimeJointMCMC | Source code |
| multRegimeMCMC | Source code |
| multiplierProposal | Source code |
| mvLogLik | Source code |
| plotHeatmat | Source code |
| plotPrior | Man page Source code |
| plotRatematrix | Man page Source code |
| plotRootValue | Man page 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 |
| ratematrix | Man page |
| ratematrixJointMCMC | Man page Source code |
| ratematrixMCMC | Man page Source code |
| readMCMC | Man page Source code |
| readMCMC_Mk | Man page Source code |
| readMultRegimeMCMC | Source code |
| readSingleRegimeMCMC | Source code |
| riwish | Source code |
| runRatematrixMCMC_C | Source code |
| runRatematrixMCMC_jointMk_C | Source code |
| runRatematrixMultiMCMC_C | Source code |
| samplePrior | Man page 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 |
