API for ndukler/epiAllele
Tests for signals of variable rates of evolution between gene classes and lineages for probabalistic alleles
| Global functions | |
|---|---|
| alleleData | Man page Source code |
| alleleData-class | Man page |
| alleleDataValidityCheck | Source code |
| bic | Man page |
| branchRateMatrix | Man page Source code |
| branchTransitions | Man page |
| clone | Man page |
| disCharToProb | Man page Source code |
| epiAllele | Man page Man page |
| epiAllele-package | Man page Man page |
| exportScaledTree | Man page |
| fit | Man page |
| getAlleleData | Man page |
| getEdgeGroupTable | Man page |
| getEdgeTable | Man page |
| getIndexLabels | Man page |
| getLabelIndices | Man page |
| getParamIndex | Man page |
| getParamValue | Man page |
| getParams | Man page |
| getPiIndex | Man page |
| getRateIndex | Man page |
| getSiblings | Man page Source code |
| getSiteInfo | Man page |
| getTree | Man page |
| logLikelihood | Man page |
| logSumExp | Man page Source code |
| lrt | Man page |
| marginalTransitionsCpp | Source code |
| multiProbToStick | Man page Source code |
| multiStickToProb | Man page Source code |
| nSites | Man page |
| plotTree | Man page |
| postorderMessagePassing | Source code |
| preorderMessagePassing | Source code |
| probToStick | Man page Source code |
| rateModel | Man page Source code |
| rateModel-class | Man page |
| rateModelValidityCheck | Source code |
| rateSE | Man page |
| rcpp_hello_world | Man page |
| readPAF | Man page Source code |
| scaledLL | Man page |
| setParamValue | Man page |
| setValues | Source code |
| simData | Man page Source code |
| siteGainLossCpp | Source code |
| siteTransitions | Man page |
| stickToProb | Man page Source code |
| tieRates | Man page |
| treeLL | Source code |
