API for thej022214/corHMM
Hidden Markov Models of Character Evolution
| Global functions | |
|---|---|
| BruteConditionalProbability | Source code |
| CalculateLewisLikelihood | Source code |
| ComputeCI | Man page Source code |
| ConvertPhangornReconstructions | Man page Source code |
| FindGenerations | Source code |
| FloydWalshAlg | Source code |
| GenerateValues | Source code |
| GetEdgeMarginal | Source code |
| GetGridPoints | Source code |
| GetLHSPoints | Source code |
| GetMarginalBrute | Source code |
| GetTipStateBruteForce | Source code |
| HessianConfidence | Source code |
| MatrixToPars | Source code |
| ParsToMatrix | Source code |
| ancRECON | Man page Source code |
| ancRECON_slice | Man page Source code |
| compute_neglnlikelihood | Source code |
| convert2I | Source code |
| convertSubHistoryToEdge | Source code |
| corDISC | Man page Source code |
| corHMM | Man page Source code |
| corHMMDredge | Source code |
| corProcessData | Source code |
| correctMapName | Source code |
| dent_likelihood | Source code |
| dent_propose | Source code |
| dent_walk | Source code |
| dev.cordisc | Source code |
| dev.corhmm | Source code |
| dev.corhmm.ORIGINAL | Source code |
| dev.corhmm.dredge | Source code |
| dev.raydisc | Man page Source code |
| dev.raydisc.rates.and.states | Source code |
| dropStateMatPars | Man page Source code |
| equateStateMatPars | Man page Source code |
| factorData | Source code |
| findAmps | Source code |
| fitCorrelationTest | Man page Source code |
| fixed_corhmm | Source code |
| generate_log_points | Source code |
| getConditionalNodeLik | Source code |
| getFullMat | Man page Source code |
| getInfoPerNode | Source code |
| getLewisLikelihood | Source code |
| getModelTable | Source code |
| getNodePlacementsForSlice | Source code |
| getPIR | Source code |
| getParamVector | Source code |
| getRateCatMat | Man page Source code |
| getRateMatCoord | Source code |
| getRateMats | Source code |
| getSimmapBranchProb | Source code |
| getSimmapLik | Source code |
| getStateMat | Source code |
| getStateMat4Dat | Man page Source code |
| get_batch_profile_lik | Source code |
| get_penalty_score | Source code |
| get_profile_lik | Source code |
| keepStateMatPars | Source code |
| makeSimmap | Man page Source code |
| match.tree.data | Source code |
| multi.which | Source code |
| optimize_fixed_corhmm | Source code |
| plot.dentist | Source code |
| plotMKmodel | Man page Source code |
| plotRECON | Man page Source code |
| plot_batch_profile_lik | Man page Source code |
| plot_slice_recon | Source code |
| primates | Man page |
| primates.paint | Man page |
| print.cordisc | Source code |
| print.corhmm | Source code |
| print.corhmm_confidence | Source code |
| print.corhmm_list | Source code |
| print.dentist | Source code |
| print.raydisc | Source code |
| rate.cat.set.corHMM.JDB | Source code |
| rate.cat.set.rayDISC | Source code |
| rate.mat.maker.JDB | Source code |
| rate.mat.set | Source code |
| rate.par.drop | Source code |
| rate.par.eq | Source code |
| rayDISC | Man page Source code |
| rayDISC.example | Man page |
| silence | Source code |
| simBranchSubstHistory | Source code |
| simCharHistory | Source code |
| simMarkov | Man page Source code |
| simSingleSubstHistory | Source code |
| simSubstHistory | Source code |
| summary.dentist | Source code |
| updateStateMats | Source code |
