Files in ms609/Tetrad

Comparison of Phylogenetic Trees Using Quartet and Split Measures

.Rbuildignore

.covrignore

.gitattributes

.github/workflows/R-CMD-check.yml

.github/workflows/RcppDeepState.yml

.github/workflows/codemeta.yml

.github/workflows/memcheck.yml

.github/workflows/pkgdown.yml

.github/workflows/revdepcheck.yml

.github/workflows/rhub.yaml

.gitignore

CODE_OF_CONDUCT.md CONTRIBUTING.md

DESCRIPTION

NAMESPACE

NEWS.md

Quartet.Rproj

R/CompareQuartets.R R/Metrics.R R/PartitionDistance.R R/Quartet-package.R R/QuartetDistance.R R/RcppExports.R R/ResolvedQuartets.R R/TernaryPoints.R R/VisualizeQuartets.R R/data.R R/tqDist.r R/zzz.R README.md

_config.yml

codemeta.json

cran-comments.md data-raw/sq_trees.R

data/sq_trees.rda

inst/CITATION

inst/Get_stuck_in.md

inst/REFERENCES.bib

inst/WORDLIST

inst/_pkgdown.yml

inst/preamble.tex

inst/trees/all_quartets.new

inst/trees/five_trees.new

inst/trees/none.new

inst/trees/one_quartet_twice.new

inst/trees/quartet1.new

inst/trees/quartet2.new

inst/trees/quartet_unresolved.new

inst/trees/test_tree1.new

inst/trees/test_tree2.new

inst/trees/test_tree3.new

inst/trees/test_tree4.new

inst/trees/tree_ab-c.new

inst/trees/tree_ac-b.new

inst/trees/two_quartets.new

inst/trees/two_trees.new

inst/trees/unresolved1.new

inst/trees/unresolved2.new

inst/trees/unresolved_list.new

man-roxygen/MRS.R man-roxygen/elementStatusParam.R man-roxygen/refTqDist.R man-roxygen/returnEstabrook.R man-roxygen/splitsParam.R man-roxygen/treeParam.R man-roxygen/treesCfParam.R man-roxygen/treesParam.R man/AllQuartets.Rd man/CompareQuartets.Rd man/CompareQuartetsMulti.Rd man/CompareSplits.Rd man/Distances.Rd man/PairSharedQuartetStatus.Rd man/PairSharedSplitStatus.Rd man/PlotQuartet.Rd man/Quartet-package.Rd man/QuartetPoints.Rd man/QuartetState.Rd man/QuartetStatus.Rd man/ResolvedQuartets.Rd man/SimilarityMetrics.Rd man/SplitStatus.Rd man/SymmetricDifferenceLineEnds.Rd man/TQDist.Rd man/TQFile.Rd man/ValidateQuartetFile.Rd man/VisualizeQuartets.Rd man/dot-AddSlice.Rd man/dot-CheckSize.Rd man/dot-NormalizeStatus.Rd man/dot-StatusToMatrix.Rd man/sq_trees.Rd man/tqdist_QuartetDistance.Rd memcheck/examples.R memcheck/tests.R memcheck/vignettes.R

src/AbstractDistanceCalculator.cpp

src/AbstractDistanceCalculator.h

src/AllQuartets.cpp

src/EdgeParser.cpp

src/HDT.cpp

src/HDTCountingCCToC.cpp

src/HDTCountingCTransform.cpp

src/HDTCountingG.cpp

src/HDTCountingIGToC.cpp

src/HDTCountingLeaf.cpp

src/HDTFactory.cpp

src/HDTListUtils.cpp

src/NewickParser.cpp

src/QuartetDistanceCalculator.cpp

src/QuartetDistanceCalculator.h

src/RcppExports.cpp

src/RootedTree.cpp

src/RootedTreeFactory.cpp

src/TripletDistanceCalculator.cpp

src/TripletDistanceCalculator.h

src/counting_linked_list.h

src/counting_linked_list_num_only.h

src/edge_parser.h

src/hdt.h

src/hdt_factory.h

src/int_stuff.cpp

src/int_stuff.h

src/memory_allocator.h

src/newick_parser.h

src/quartet_calc.h

src/rQuartetDist.cpp

src/rTripletDist.cpp

src/rooted_tree.h

src/rooted_tree_factory.h

src/templated_linked_list.h

src/triplet_calc.h

src/unrooted_tree.h

src/util.h

tests/figs/deps.txt

tests/figs/quartetdistance-r/plotquartet-gain.svg

tests/figs/quartetdistance-r/plotquartet-one-star.svg

tests/figs/quartetdistance-r/plotquartet.svg

tests/figs/vq-label.svg

tests/figs/vq-size.svg

tests/figs/vq-tworow.svg

tests/testthat.R

tests/testthat/_snaps/QuartetDistance/plotquartet-gain.svg

tests/testthat/_snaps/QuartetDistance/plotquartet-one-star.svg

tests/testthat/_snaps/QuartetDistance/plotquartet.svg

tests/testthat/_snaps/VisualizeQuartet/vq-label.svg

tests/testthat/_snaps/VisualizeQuartet/vq-size.svg

tests/testthat/_snaps/VisualizeQuartet/vq-tworow.svg

tests/testthat/test-1-tqdist.R tests/testthat/test-AllQuartets.cpp.R tests/testthat/test-CompareQuartets.R tests/testthat/test-NewickParser.cpp.R tests/testthat/test-PartitionDistance.R tests/testthat/test-QuartetDistance.R tests/testthat/test-QuartetStates.R tests/testthat/test-ResolvedQuartets.R tests/testthat/test-TernaryPoints.R tests/testthat/test-VisualizeQuartet.R tests/testthat/test-ZZZ-Metrics.R tests/testthat/test-rQuartetDist.cpp.R vignettes/Quartet-Distance.Rmd vignettes/Using-Quartet.Rmd

ms609/Tetrad documentation built on April 19, 2024, 4:24 p.m.