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TreeTools-1.3.0.zip

ms609-TreeTools-09685b0
- .Rbuildignore 330 Bytes
- .covrignore 47 Bytes
- .gitattributes 378 Bytes
- .gitignore 235 Bytes
- .travis.yml 1.7 kB
- CODE_OF_CONDUCT.md 1.4 kB
- CONTRIBUTING.md 2.3 kB
- DESCRIPTION 1.7 kB
- NAMESPACE 8.5 kB
- NEWS.md 3.6 kB
- R
  - ArtificialExtinction.R 4.3 kB
  - BigInteger.R 0 Bytes
  - Combinatorics.R 9.4 kB
  - Information.R 8.8 kB
  - RcppExports-manual.R 391 Bytes
  - RcppExports.R 911 Bytes
  - SplitFunctions.R 11.5 kB
  - Splits.R 13.9 kB
  - Stemwardness.R 3.1 kB
  - Support.R 6.3 kB
  - TotalCopheneticIndex.R 4.4 kB
  - TreeNumber.R 8.3 kB
  - TreeTools-package.R 862 Bytes
  - data.R 2.3 kB
  - helper_functions.R 3.1 kB
  - mst.R 1.7 kB
  - parse_files.R 28.1 kB
  - phylo.R 13.6 kB
  - split_analysis.R 2.1 kB
  - sysdata.rda 553.7 kB
  - tree_display.R 4.6 kB
  - tree_generation.R 7.7 kB
  - tree_information.R 3.3 kB
  - tree_numbering.R 14.5 kB
  - tree_properties.R 20.8 kB
  - tree_rearrangement.R 18.1 kB
  - tree_shape.R 9.2 kB
  - tree_write.R 3.2 kB
  - zzz.R 1.1 kB
- README.md 2.4 kB
- codemeta.json 8.1 kB
- cran-comments.md 730 Bytes
- data
  - Lobo.RData 3.2 kB
  - brewer.R 960 Bytes
  - nRootedShapes.R 802 Bytes
  - nUnrootedShapes.R 960 Bytes
  - unrootedKeys.rda 49.5 kB
- data-raw
  - _double_factorials.R 1.7 kB
  - unrootedKeys.R 926 Bytes
- inst
  - CITATION 437 Bytes
  - REFERENCES.bib 5.2 kB
  - WORDLIST 727 Bytes
  - _pkgdown.yml 2.7 kB
  - apa-old-doi-prefix.csl 25.1 kB
  - extdata
    - input
      - dataset.nex 174 Bytes
    - otherfolder
      - empty.file 0 Bytes
    - output
      - named.tre 136 Bytes
      - numbered.tre 116 Bytes
    - tests
      - ape-tree.nex 67 Bytes
      - continuous.nex 332 Bytes
      - parse-nexus.nexus 19.7 kB
      - tnt-matrix.tnt 14.1 kB
      - tnt-namedtree.tre 2.7 kB
      - tnt-tree.tre 390 Bytes
  - include
    - TreeTools
      - renumber_tree.h 8.7 kB
      - root_tree.h 5.5 kB
      - types.h 349 Bytes
    - TreeTools.h 183 Bytes
- man
  - AddTip.Rd 2.8 kB
  - AncestorEdge.Rd 1.3 kB
  - ApeTime.Rd 820 Bytes
  - ArtificialExtinction.Rd 2.9 kB
  - CharacterInformation.Rd 1.2 kB
  - CladeSizes.Rd 1.3 kB
  - CladisticInfo.Rd 2.1 kB
  - CollapseNode.Rd 2.0 kB
  - CompatibleSplits.Rd 1.3 kB
  - ConsensusWithout.Rd 2.7 kB
  - DescendantEdges.Rd 2.1 kB
  - DoubleFactorial.Rd 1.6 kB
  - DropTip.Rd 1.8 kB
  - EdgeAncestry.Rd 1.8 kB
  - EdgeDistances.Rd 1.3 kB
  - EnforceOutgroup.Rd 1.9 kB
  - ExtractTaxa.Rd 1.7 kB
  - GenerateTree.Rd 2.1 kB
  - LabelSplits.Rd 2.0 kB
  - LeafLabelInterchange.Rd 1.7 kB
  - ListAncestors.Rd 3.2 kB
  - Lobo.data.Rd 522 Bytes
  - MRCA.Rd 1.8 kB
  - MSTEdges.Rd 1.5 kB
  - MakeTreeBinary.Rd 1.5 kB
  - MatrixToPhyDat.Rd 1.2 kB
  - N1Spr.Rd 1.1 kB
  - NDescendants.Rd 1.2 kB
  - NJTree.Rd 924 Bytes
  - NPartitionPairs.Rd 1.4 kB
  - NRooted.Rd 2.9 kB
  - NSplits.Rd 1.7 kB
  - NTip.Rd 1.2 kB
  - NewickTree.Rd 689 Bytes
  - Neworder.Rd 1.9 kB
  - NodeDepth.Rd 1.9 kB
  - NodeOrder.Rd 1.5 kB
  - NonDuplicateRoot.Rd 1.9 kB
  - PhyToString.Rd 2.9 kB
  - ReadCharacters.Rd 3.2 kB
  - ReadTntTree.Rd 4.6 kB
  - Renumber.Rd 1.6 kB
  - RenumberTips.Rd 1.7 kB
  - Reorder.Rd 7.6 kB
  - RightmostCharacter.Rd 734 Bytes
  - RootNode.Rd 1.3 kB
  - RootTree.Rd 2.3 kB
  - SampleOne.Rd 679 Bytes
  - SingleTaxonTree.Rd 1.2 kB
  - SortTree.Rd 1.8 kB
  - SplitFrequency.Rd 2.6 kB
  - SplitInformation.Rd 5.2 kB
  - SplitMatchProbability.Rd 1.6 kB
  - SplitsInBinaryTree.Rd 1.8 kB
  - Stemwardness.Rd 2.9 kB
  - Subsplit.Rd 1.2 kB
  - Subtree.Rd 1.5 kB
  - SupportColour.Rd 1.7 kB
  - TipLabels.Rd 2.2 kB
  - TipsInSplits.Rd 2.0 kB
  - TotalCopheneticIndex.Rd 2.8 kB
  - TreeIsRooted.Rd 829 Bytes
  - TreeNumber.Rd 4.6 kB
  - TreeShape.Rd 5.4 kB
  - TreeTools-package.Rd 1.3 kB
  - TreesMatchingSplit.Rd 1.3 kB
  - TreesMatchingTree.Rd 1.4 kB
  - TrivialSplits.Rd 1.3 kB
  - UnrootedTreesMatchingSplit.Rd 1.5 kB
  - UnshiftTree.Rd 1.2 kB
  - WriteTntCharacters.Rd 1.7 kB
  - as.Newick.Rd 1.3 kB
  - as.Splits.Rd 2.7 kB
  - brewer.Rd 838 Bytes
  - dot-RandomParent.Rd 709 Bytes
  - doubleFactorials.Rd 651 Bytes
  - figures
    - Stemwardness.png 3.7 kB
  - logDoubleFactorials.Rd 571 Bytes
  - match.Rd 1.8 kB
  - nRootedShapes.Rd 747 Bytes
  - print.TreeNumber.Rd 426 Bytes
  - sapply64.Rd 2.6 kB
- man-roxygen
  - LoboMods.R 1.7 kB
  - MRS.R 57 Bytes
  - characterNumParam.R 126 Bytes
  - datasetParam.R 153 Bytes
  - edgeParam.R 177 Bytes
  - exampleNodeSupport.R 431 Bytes
  - nTipParam.R 59 Bytes
  - outgroupTipsParam.R 0 Bytes
  - preorderTreeParam.r 180 Bytes
  - returnPhydat.R 89 Bytes
  - sessionParam.R 125 Bytes
  - split12Params.R 213 Bytes
  - splitsObjectParam.R 59 Bytes
  - tipLabelsParam.R 131 Bytes
  - tipsForTreeGeneration.R 174 Bytes
  - tree(s)Param.R 113 Bytes
  - treeChild.R 151 Bytes
  - treeNEdgeOptional.R 139 Bytes
  - treeParam.r 58 Bytes
  - treeParent.r 150 Bytes
  - xPhylo.R 78 Bytes
- src
  - RcppExports-manual.cpp 1.8 kB
  - RcppExports.cpp 4.2 kB
  - TreeTools-init.c 2.2 kB
  - ape_reorder.h 6.5 kB
  - as_newick.cpp 1.6 kB
  - int_to_tree.cpp 4.2 kB
  - splits.cpp 2.6 kB
  - tips_in_splits.cpp 1.3 kB
  - tree_shape.cpp 7.1 kB
- tests
  - figs
    - deps.txt 69 Bytes
    - mst-r
      - mst-plotting.svg 7.1 kB
  - testthat
    - test-ArtificialExtinction.R 1.2 kB
    - test-BigInteger.R 0 Bytes
    - test-SplitFunctions.R 8.0 kB
    - test-Splits.R 11.3 kB
    - test-Stemwardness.R 410 Bytes
    - test-Support.R 1.2 kB
    - test-TotalCopheneticIndex.R 1.4 kB
    - test-TreeNumber.R 1.6 kB
    - test-combinatorics.R 3.3 kB
    - test-helper_functions.R 332 Bytes
    - test-information.R 1.4 kB
    - test-int_to_tree.cpp.R 1.6 kB
    - test-mst.R 567 Bytes
    - test-parsers.R 5.0 kB
    - test-phylo.R 2.3 kB
    - test-root_tree.h.R 1.3 kB
    - test-split_analysis.R 369 Bytes
    - test-splits.cpp.R 314 Bytes
    - test-tree_display.R 1.3 kB
    - test-tree_generation-random.R 1.4 kB
    - test-tree_generation.R 2.8 kB
    - test-tree_information.R 585 Bytes
    - test-tree_numbering.R 6.7 kB
    - test-tree_properties.R 7.4 kB
    - test-tree_rearrange.R 12.0 kB
    - test-tree_shape.R 6.0 kB
    - test-tree_write.R 1.4 kB
  - testthat.R 138 Bytes
- vignettes
  - filesystem-navigation.Rmd 1.5 kB
  - load-data.Rmd 6.5 kB
  - load-trees.Rmd 4.4 kB