API for nclark-lab/RERconverge
Analysis of Convergence Between Organismal Traits and DNA/Protein Sequences
| Global functions | |
|---|---|
| CanonicalForm | Source code |
| RERconverge | Man page |
| Root | Man page Source code |
| adaptivePermulation | Man page Source code |
| allPathMasterRelative | Source code |
| allPathMasterRelativeTrackBranches | Source code |
| allPaths | Source code Source code |
| allPathsTrackBranches | Source code |
| areNested | Source code |
| asymmRerootingMethod | Man page Source code |
| between | Source code |
| boxPlotTest | Man page Source code |
| calculateCorPermuted | Man page Source code |
| calculatePermulatedPaths | Source code |
| calculatePermulatedPaths_apply | Man page Source code |
| categoricalPermulations | Source code |
| char2Paths | Man page |
| char2PathsCategorical | Man page Source code |
| char2TreeCategorical | Man page |
| checkOrder | Source code |
| cleanUp | Source code |
| click_plot_base | Source code |
| click_select_foreground_branches | Man page Source code |
| combinePermData | Man page Source code |
| compareClades | Source code |
| compareRateModels | Man page Source code |
| correlateTrees | Source code |
| correlateTreesAll | Source code |
| correlateTreesAll1 | Source code |
| correlateTreesBinary | Source code |
| correlateTreesProj | Source code |
| correlateWithBinaryPhenotype | Man page Source code |
| correlateWithCategoricalPhenotype | Man page Source code |
| correlateWithContinuousPhenotype | Man page Source code |
| distToVec | Source code |
| edgeIndexRelativeMaster | Source code |
| edgeReOrder | Source code |
| edgeVars | Man page Source code |
| estimatePhangornTree | Man page Source code |
| estimatePhangornTreeAll | Man page Source code |
| extractCorResults | Source code |
| extractPermulationResults | Source code |
| fastLm | Source code |
| fastLmPredicted | Source code |
| fastLmPredictedMat | Source code |
| fastLmResid | Source code |
| fastLmResidMat | Source code |
| fastLmResidMatWeighted | Source code |
| fastLmResidMatWeightedNoNACheck | Source code |
| fastLmResidWeighted | Source code |
| fastwilcoxGMT | Source code |
| fastwilcoxGMTall | Man page Source code |
| filterByCriteria | Man page Source code |
| findAllPaths | Source code |
| findGroupedTrees | Source code |
| findJoining | Source code |
| findMappedClade2Node | Source code |
| findPairs | Source code |
| fixPseudoroot | Man page Source code |
| foreground2Paths | Man page Source code |
| foreground2Tree | Man page Source code |
| foreground2TreeClades | Man page Source code |
| generatePermulatedBinPhen | Man page Source code |
| generatePermulatedBinPhenSSMBatched | Man page Source code |
| getAllCladeEdges | Source code |
| getAllCor | Man page Source code |
| getAllCorExtantOnly | Man page |
| getAllCorSSM | Source code |
| getAllResiduals | Man page Source code |
| getAncLiks | Man page Source code |
| getAncestor | Source code |
| getAncestors | Source code Source code |
| getBinaryPermulationInputsFromTree | Man page Source code |
| getBoxPlot | Source code |
| getBranch | Source code |
| getChildren | Source code |
| getClosestVals | Source code |
| getDegreesFreedom | Source code |
| getDepthOrder | Source code |
| getEnrichAllCategories | Source code |
| getEnrichFromPairwiseTest | Source code |
| getEnrichPermPvals | Source code |
| getEnrichPerms | Man page Source code |
| getEnrichPermsCategorical | Source code |
| getForegroundInfoClades | Man page Source code |
| getForegroundsFromBinaryTree | Source code |
| getLRnullDistribution | Man page Source code |
| getLikelihoodRatio | Man page Source code |
| getMatrixFromAbbr | Man page Source code |
| getNV | Source code |
| getNullCor | Source code |
| getNullCorExtantOnly | Source code |
| getNullTips | Source code |
| getNullTrees | Source code |
| getPercentMatch | Source code |
| getPermPvalsCategorical | Source code |
| getPermsBinary | Man page Source code |
| getPermsBinaryExtantOnly | Man page Source code |
| getPermsBinaryFudged | Source code |
| getPermsContinuous | Man page Source code |
| getPermsContinuousExtantOnly | Man page Source code |
| getProjection | Source code |
| getProjectionPaths | Source code |
| getRealEnrichments | Source code |
| getRelativeEntropies | Source code |
| getRoot | Source code |
| getSimplerRateModel | Source code |
| getSpeciesMembershipStats | Source code |
| getStat | Man page Source code |
| getStatesAtNodes | Man page Source code |
| getStatesFromPhenTree | Man page Source code |
| getancedgexlims | Source code |
| getancedgeylims | Source code |
| getcolorpal | Source code |
| groupTrees | Source code |
| improveTree | Source code |
| inferBidirectionalForegroundClades | Source code |
| inferUnidirectionalForegroundClades | Source code |
| isNA | Source code |
| isNotNArowvec | Source code |
| kwdunn.test | Man page Source code |
| linearizeCorResults | Source code |
| makeBinaryPaths | Man page Source code |
| mapEdge | Source code |
| matchAllNodes | Source code |
| matchAllNodesClades | Man page Source code |
| matrixToVector | Source code |
| missingSampler | Source code |
| myAUC | Source code |
| nameEdges | Source code |
| nameEdgesPerms | Source code |
| namePaths | Source code |
| namePathsWSpecies | Man page Source code |
| naresid | Source code |
| naresidCPP | Source code |
| nvmaster | Source code |
| permpvalcor | Man page Source code |
| permpvalenrich | Man page Source code |
| permutevec | Man page Source code |
| plotContinuousCharXY | Source code |
| plotPositivesFromPermulations | Man page Source code |
| plotRers | Man page Source code |
| plotResidsVsChar | Source code |
| plotTreeCategorical | Man page Source code |
| plotTreeHighlightBranches | Man page Source code |
| plotTreesBinary | Source code |
| plotWtext | Source code |
| printClade | Source code |
| printLeaveEdges | Source code |
| printTipDist | Source code |
| projectRLM | Source code |
| projection | Source code |
| projectionSQ | Source code |
| pruneAlnFromTree | Source code |
| pruneTree | Man page Source code |
| read.gmt | Man page |
| readTrees | Man page Source code |
| rep_tree | Source code |
| rescaleTree | Source code |
| resid | Source code |
| residLN | Source code |
| residLN0 | Source code |
| residLO | Source code |
| residSQ | Source code |
| returnRersAsNewickStrings | Man page Source code |
| returnRersAsTree | Man page Source code |
| returnRersAsTreesAll | Man page Source code |
| scaleDist | Source code |
| scaleDistNa | Source code |
| scaleMat | Source code |
| searchRateModels | Man page Source code |
| shuffleInternalNodes | Source code |
| simBinPheno | Man page Source code |
| simBinPhenoCC | Man page Source code |
| simBinPhenoCCmidpoint | Man page Source code |
| simBinPhenoRank | Man page Source code |
| simBinPhenoSSM | Man page Source code |
| simBinPhenoVec | Man page Source code |
| simpermvec | Man page Source code |
| simpleAUCgenesRanks | Source code |
| simpleAUCmat | Source code |
| simulatevec | Man page Source code |
| standardize | Source code |
| timesTwo | Source code |
| transformMat | Source code |
| tree2Paths | Man page Source code |
| tree2PathsClades | Man page Source code |
| tree2Paths_map | Source code |
| treePlot | Source code |
| treePlotGG | Source code |
| treePlotNew | Man page Source code |
| treePlotRers | Man page Source code |
| treeSum | Source code |
| treeTraverse | Source code |
| vectToMatrix | Source code |
| visCompareTwoRateModels | Man page Source code |
| wilcoxGMT | Source code |
| wilcoxGMTall | Source code |
