API for OUwie
Analysis of Evolutionary Rates in an OU Framework
| Global functions | |
|---|---|
| DredgeCombinations | Source code |
| GetLikelihood | Source code |
| GetParameterPainting | Source code |
| GetShiftMap | Source code |
| GetShiftModel | Source code |
| GetShiftModel.bom | Source code |
| GetThetas | Source code |
| MakeAgeTable | Source code |
| OUwie | Man page Source code |
| OUwie.anc | Man page Source code |
| OUwie.anc.older.simultaneous | Source code |
| OUwie.basic | Source code |
| OUwie.basic.dev | Source code |
| OUwie.boot | Man page Source code |
| OUwie.contour | Man page Source code |
| OUwie.dredge | Man page Source code |
| OUwie.dredge.bom | Source code |
| OUwie.fixed | Man page Source code |
| OUwie.format | Man page Source code |
| OUwie.semifixed | Source code |
| OUwie.sim | Man page Source code |
| OptimizeDredgeLikelihood | Source code |
| add.stub.taxa.to.data | Source code |
| add.stub.taxon.to.data | Source code |
| alphaIndexForSigma | Source code |
| anc.likelihood | Source code |
| applyContinuousNodeFactors | Source code |
| attach.stub.taxa | Source code |
| attach.stub.taxon | Source code |
| bindMessages | Source code |
| check | Source code |
| check.identify | Man page Source code |
| check.identify.dredge | Source code |
| checkParameterLength | Source code |
| checkPruningFeasible | Source code |
| checkStartingUBLB | Source code |
| composeIntervalPair | Source code |
| continuousMapMoments | Source code |
| contourSearchOUwie | Source code |
| contourSearchPoints | Source code |
| convertSubHistoryToEdge | Source code |
| corProcessData | Source code |
| correct_edge | Source code |
| correct_map_edges | Source code |
| dent_likelihood | Man page Source code |
| dent_propose | Man page Source code |
| dent_walk | Man page Source code |
| drawFromWeights | Source code |
| emptyMessage | Source code |
| expected.trendy | Source code |
| fix.kappa | Man page Source code |
| fixEdgeLiksLiks | Source code |
| fix_lower | Source code |
| fix_upper | Source code |
| fromStationaryPars | Source code |
| generateMultiStarting | Source code |
| getAllJointProbs | Source code |
| getConditionalInternodeLik | Source code |
| getContinuousNodeFactors | Source code |
| getDiscreteModel | Source code |
| getEdgeLiks | Source code |
| getExpectedValues | Source code |
| getHOUwieTreePlan | Source code |
| getHouwieObj | Source code |
| getIP.sigma | Source code |
| getIP.theta | Source code |
| getInternodeMap | Source code |
| getInternodeStateSample | Source code |
| getMapFromNode | Source code |
| getMapFromStateSample | Source code |
| getMapFromStateSampleBridge | Source code |
| getMapFromSubstHistory | Source code |
| getMapProb | Source code |
| getModelAvgParams | Man page Source code |
| getModelAvgStartingPars | Source code |
| getModelTable | Man page Source code |
| getNumberOfStates | Source code |
| getOUExpectations | Source code |
| getOUIntervalMoments | Source code |
| getOULik | Source code |
| getOUParamStructure | Man page Source code |
| getObjTraitShift | Source code |
| getPathMapProb | Source code |
| getPathStateProb | Source code |
| getPathToRoot | Source code |
| getReferenceVariances | Source code |
| getRootLiks | Source code |
| getStateSampleProb | Source code |
| getTipStateSets | Source code |
| getTraitShift | Source code |
| get_tip_states | Source code |
| get_tip_values | Source code |
| hOUwie | Man page Source code |
| hOUwie.dev | Source code |
| hOUwie.fixed | Man page Source code |
| hOUwie.fixed.dev | Source code |
| hOUwie.recon | Man page Source code |
| hOUwie.sim | Man page Source code |
| hOUwie.thorough | Man page Source code |
| hOUwie.walk | Man page Source code |
| houwieDevFailure | Source code |
| houwiePruningLik | Source code |
| index_paramers_from_tip_states | Source code |
| logMessageAgainstReference | Source code |
| logSumExpSafe | Source code |
| makeCommonRandomObjective | Source code |
| makeMapEdgesNumeric | Source code |
| makeUniformizationTable | Source code |
| mat.gen | Source code Source code Source code |
| matchTipsAndData | Source code |
| multiplyMessages | Source code |
| organizeHOUwieDat | Source code |
| organizeHOUwiePars | Source code |
| ouwie.col.to.row.names | Source code |
| ouwie.row.names.to.col | Source code |
| plot.OUwie.anc | Source code |
| plot.OUwie.contour | Man page Source code |
| plot.OUwie.dredge | Source code |
| plot.dentist | Man page Source code |
| print.OUwie | Source code |
| print.OUwie.dredge | Source code |
| print.OUwie.fixed | Source code |
| print.dentist | Man page Source code |
| print.houwie | Source code |
| pushMessage | Source code |
| quickVCV | Source code |
| reduceMessageMixture | Source code |
| replaceName | Source code |
| runSingleThorough | Source code |
| sampleBranchBridge | Source code |
| scoreInternodeStateSample | Source code |
| selectStartOnCommonSeed | Source code |
| silence | Source code |
| simCharacterHistory | Source code |
| stateSampleId | Source code |
| stationaryParPositions | Source code |
| summary.dentist | Man page Source code |
| toStationaryPars | Source code |
| trait | Man page |
| transformPhy | Source code |
| transformPhy.old | Source code |
| tree | Man page |
| tree.kappa | Source code |
| varcov.ou | Source code |
| varcov.ou.old | Source code |
| weight.mat | Source code |
| weight.mat.old | Source code |
| withHOUwieSeed | Source code |
