Files in ms609/TreeTools

Create, Modify and Analyse Phylogenetic Trees

CODE_OF_CONDUCT.md CONTRIBUTING.md NEWS.md R/AddTip.R R/ArtificialExtinction.R R/ClusterTable.R R/Combinatorics.R R/Consensus.R R/Decompose.R R/DropTip.R R/ImposeConstraint.R R/Information.R R/KeptPaths.R R/KeptVerts.R R/MatchNodes.R R/PathLengths.R R/RUtreebalance.R R/RcppExports-manual.R R/RcppExports.R R/ReadMrBayes.R R/ReadTntTree.R R/RoguePlot.R R/SplitFunctions.R R/Splits.R R/Stemwardness.R R/Support.R R/TipTimedTree.R R/TopologyOnly.R R/TotalCopheneticIndex.R R/TreeNumber.R R/TreeTools-package.R R/as.matrix.R R/as.multiPhylo.R R/data.R R/helper_functions.R R/match.R R/mst.R R/parse_files.R R/phylo.R R/sort.R R/split_analysis.R R/tree_ancestors.R R/tree_comparison.R R/tree_descendants.R R/tree_display.R R/tree_generation.R R/tree_information.R R/tree_numbering.R R/tree_properties.R R/tree_rearrangement.R R/tree_shape.R R/tree_write.R R/zzz.R README.md benchmark/DropTip.R benchmark/SplitList.R cran-comments.md data-raw/_double_factorials.R data-raw/unrootedKeys.R data/brewer.R data/nRootedShapes.R data/nUnrootedShapes.R man-roxygen/LoboMods.R man-roxygen/MRS.R man-roxygen/characterNumParam.R man-roxygen/constraintParam.R man-roxygen/datasetParam.R man-roxygen/edgeLengthParam.R man-roxygen/edgeParam.R man-roxygen/exampleNodeSupport.R man-roxygen/nTipParam.R man-roxygen/preorderTreeParam.r man-roxygen/returnPhydat.R man-roxygen/split12Params.R man-roxygen/splitsObjectParam.R man-roxygen/tipLabelsParam.R man-roxygen/tipsForTreeGeneration.R man-roxygen/tree(s)Param.R man-roxygen/treeChild.R man-roxygen/treeNEdgeOptional.R man-roxygen/treeParam.r man-roxygen/treeParent.r man-roxygen/xPhylo.R man/AddTip.Rd man/AncestorEdge.Rd man/ApeTime.Rd man/ArtificialExtinction.Rd man/CharacterInformation.Rd man/CladeSizes.Rd man/CladisticInfo.Rd man/ClusterTable-methods.Rd man/ClusterTable.Rd man/CollapseNode.Rd man/CompatibleSplits.Rd man/Consensus.Rd man/ConsensusWithout.Rd man/ConstrainedNJ.Rd man/Decompose.Rd man/DescendantEdges.Rd man/DoubleFactorial.Rd man/DropTip.Rd man/EdgeAncestry.Rd man/EdgeDistances.Rd man/EndSentence.Rd man/EnforceOutgroup.Rd man/ExtractTaxa.Rd man/GenerateTree.Rd man/Hamming.Rd man/ImposeConstraint.Rd man/J1Index.Rd man/KeptPaths.Rd man/KeptVerts.Rd man/LabelSplits.Rd man/LeafLabelInterchange.Rd man/ListAncestors.Rd man/Lobo.data.Rd man/MRCA.Rd man/MSTEdges.Rd man/MakeTreeBinary.Rd man/MatchEdges.Rd man/MatrixToPhyDat.Rd man/MorphoBankDecode.Rd man/N1Spr.Rd man/NDescendants.Rd man/NJTree.Rd man/NPartitionPairs.Rd man/NRooted.Rd man/NSplits.Rd man/NTip.Rd man/NewickTree.Rd man/Neworder.Rd man/NodeDepth.Rd man/NodeNumbers.Rd man/NodeOrder.Rd man/PairwiseDistances.Rd man/PathLengths.Rd man/PhyToString.Rd man/PolarizeSplits.Rd man/ReadCharacters.Rd man/ReadMrBayesTrees.Rd man/ReadTntTree.Rd man/Renumber.Rd man/RenumberTips.Rd man/Reorder.Rd man/RightmostCharacter.Rd man/RoguePlot.Rd man/RootNode.Rd man/RootTree.Rd man/SampleOne.Rd man/SortTree.Rd man/SpectrumLegend.Rd man/SplitFrequency.Rd man/SplitInformation.Rd man/SplitMatchProbability.Rd man/Splits.Rd man/SplitsInBinaryTree.Rd man/Stemwardness.Rd man/Subsplit.Rd man/Subtree.Rd man/SupportColour.Rd man/TipLabels.Rd man/TipTimedTree.Rd man/TipsInSplits.Rd man/TopologyOnly.Rd man/TotalCopheneticIndex.Rd man/TreeIsRooted.Rd man/TreeNumber.Rd man/TreeShape.Rd man/TreeTools-package.Rd man/TreesMatchingSplit.Rd man/TreesMatchingTree.Rd man/TrivialSplits.Rd man/TrivialTree.Rd man/Unquote.Rd man/UnrootedTreesMatchingSplit.Rd man/UnshiftTree.Rd man/WriteTntCharacters.Rd man/as.Newick.Rd man/as.multiPhylo.Rd man/brewer.Rd man/dot-RandomParent.Rd man/doubleFactorials.Rd man/edge_to_splits.Rd man/is.TreeNumber.Rd man/logDoubleFactorials.Rd man/match.Splits.Rd man/match.multiPhylo.Rd man/nRootedShapes.Rd man/print.TreeNumber.Rd man/root_on_node.Rd man/sapply64.Rd man/sort.multiPhylo.Rd man/xor.Rd memcheck/examples.R memcheck/tests.R memcheck/vignettes.R tests/benchmark/benchmark-as.splits.R tests/benchmark/benchmark-consensus.R tests/benchmark/benchmark-preorder.R tests/spelling.R tests/testthat.R tests/testthat/Rplots.pdf tests/testthat/test-AddTip.R tests/testthat/test-ArtificialExtinction.R tests/testthat/test-ClusterTable.R tests/testthat/test-Decompose.R tests/testthat/test-DropTip.R tests/testthat/test-ImposeConstraint.R tests/testthat/test-KeptPaths.R tests/testthat/test-KeptVerts.R tests/testthat/test-MatchNodes.R tests/testthat/test-PathLengths.R tests/testthat/test-RUtreebalance.R tests/testthat/test-ReadMrBayes.R tests/testthat/test-ReadTntTree.R tests/testthat/test-RoguePlot.R tests/testthat/test-SplitFunctions.R tests/testthat/test-Splits.R tests/testthat/test-Stemwardness.R tests/testthat/test-Support.R tests/testthat/test-TipTimedTree.R tests/testthat/test-TopologyOnly.R tests/testthat/test-TotalCopheneticIndex.R tests/testthat/test-TreeNumber.R tests/testthat/test-as.matrix.R tests/testthat/test-as.multiPhylo.R tests/testthat/test-combinatorics.R tests/testthat/test-consensus.R tests/testthat/test-helper_functions.R tests/testthat/test-information.R tests/testthat/test-int_to_tree.cpp.R tests/testthat/test-match.R tests/testthat/test-mst.R tests/testthat/test-parsers.R tests/testthat/test-phylo.R tests/testthat/test-root_tree.h.R tests/testthat/test-sort.R tests/testthat/test-split_analysis.R tests/testthat/test-splits.cpp.R tests/testthat/test-tree_ancestors.R tests/testthat/test-tree_comparison.R tests/testthat/test-tree_descendants.R tests/testthat/test-tree_display.R tests/testthat/test-tree_generation-random.R tests/testthat/test-tree_generation.R tests/testthat/test-tree_information.R tests/testthat/test-tree_numbering.R tests/testthat/test-tree_properties.R tests/testthat/test-tree_rearrange.R tests/testthat/test-tree_shape.R tests/testthat/test-tree_write.R vignettes/filesystem-navigation.Rmd vignettes/load-data.Rmd vignettes/load-trees.Rmd