API for villandre/CovidClusterAlgo
Library for Clustering Sequencing Data with the CovidCovariateCluster algorithm.
| Global functions | |
|---|---|
| .addTransTreeEdgeLengths | Source code |
| .clearNodeRegions | Source code |
| .clusterIndicesFromAdjMat | Source code |
| .collapseIntoMulti | Source code |
| .combineClusMembershipIndices | Source code |
| .combineRegionalEstimatesAndScores | Source code |
| .computeClusMembershipDistribution | Source code |
| .computeCoalRateSubtree | Source code |
| .computeCondClusterScore | Source code |
| .computeCondClusterScoreBySubtree | Source code |
| .computeMeanCoalRate | Source code |
| .computeSubtreeRootNums | Source code |
| .convertClusterListToVecOfIndices | Source code |
| .convertToPhylo | Source code |
| .convertToTransTree | Source code |
| .editTaxonNames | Source code |
| .formatParameterFiles | Source code |
| .funForLambdaOptim | Source code |
| .genStartPhyloAndTransTree | Source code |
| .getAdjacencyFromVec | Source code |
| .getCoclusterMat | Source code |
| .getNodeLabel | Source code |
| .getNodeUpdateOrderForMulti | Source code |
| .getSubtreeRootNums | Source code |
| .getTipLabel | Source code |
| .getVertexLabel | Source code |
| .getVertexOrderByDepth | Source code |
| .getVertexTimes | Source code |
| .identifyNodeRegions | Source code |
| .incrementPhylo | Source code |
| .nodeTimesSubtreeLogPriorFun | Source code |
| .numMigrationsLogPriorFunWithMeanPar | Source code |
| .obtainClusMembershipDistrib | Source code |
| .plotTransmissionTree.control | Source code |
| .produceDistTipsAncestorsMatrix | Source code |
| .produceMrBayesScript | Source code |
| .rNNItransTree | Source code |
| .regionNodeTimesLogPrior | Source code |
| .regionalDescendants | Source code |
| .resolveMulti | Source code |
| .rootTimeLogPriorFun | Source code |
| .simulateNodeTimes | Source code |
| .sortNumberListDecreasing | Source code |
| .standardiseClusterIndices | Source code |
| .updateTransTreeEdgeLengths | Source code |
| .writeMrBayesFiles | Source code |
| clusterFromMrBayesOutput | Source code |
| computeLogNormMMpars | Source code |
| computeLogSum | Source code |
| computeParetoMMpars | Source code |
| covidCluster | Source code |
| dist.node.ancestor | Source code |
| dist.tipPairs.mrca | Source code |
| dist.tips.mrca | Source code |
| dist.tips.root.phylo | Source code |
| dpareto | Source code |
| gen.MrBayes.control | Source code |
| gen.covidCluster.control | Source code |
| gen.priors.control | Source code |
| getCopheneticClustersRcpp | Source code |
| getDistanceBasedClusters | Source code |
| getLambdas | Source code |
| getLogClockRates | Source code |
| getMRCA_Rcpp | Source code |
| getMRCAclustersRcpp | Source code |
| getNodeTimes | Source code |
| getPhyloEdgeLengths | Source code |
| getRegionClusters | Source code |
| getTipTimes | Source code |
| getTransTreeEdgeLengths | Source code |
| phylo | Source code |
| plotClusters | Source code |
| plotTransmissionTree | Source code |
| produceClusters | Source code |
| produceDistTipsAncestorsMatrixRcpp | Source code |
| prune.tree | Source code |
| reorder_cormat | Source code |
| simulateNodeTimesRcpp | Source code |
