Files in ms609/TreeSearch

Phylogenetic Analysis with Discrete Character Data

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.covrignore

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

.github/workflows/RcppDeepState.yml

.github/workflows/codemeta.yml

.github/workflows/coverage.yml

.github/workflows/gcc-ASAN.yml

.github/workflows/memcheck.yml

.github/workflows/pkgdown.yml

.github/workflows/revdep.yml

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CODE_OF_CONDUCT.md CONTRIBUTING.md

DESCRIPTION

LICENSE

NAMESPACE

NEWS.md R/AdditionTree.R R/Bootstrap.R R/ClusterStrings.R R/Concordance.R R/Consistency.R R/CustomSearch.R R/IWScore.R

R/ImposeConstraint.R

R/Jackknife.R R/MaximizeParsimony.R R/NNI.R R/PlotCharacter.R R/PolEscapa.R R/QuartetResolution.R R/RandomTreeScore.R R/Ratchet.R R/RcppExports.R R/ReleaseQuestions.R R/SPR.R R/Sectorial.R R/SuccessiveApproximations.R R/TBR.R R/TaxonInfluence.R R/TreeSearch_utilities.R R/WhenFirstHit.R R/data.R R/data_manipulation.R R/length_range.R R/mpl_morphy_objects.R R/mpl_morphyex.R R/mpl_visualise.R R/pp_info_extra_step.r R/tree_length.R R/tree_rearrangement.R R/zzz.R README.md

TreeSearch.Rproj

_config.yml

codemeta.json

cran-comments.md

data-raw/Agnarsson2004.nex

data-raw/Aguado2009.nex

data-raw/Aria2015.nex

data-raw/Asher2005.nex

data-raw/Capa2011.nex

data-raw/Conrad2008.nex

data-raw/DeAssis2011.nex

data-raw/Dikow2009.nex

data-raw/Eklund2004.nex

data-raw/Geisler2001.nex

data-raw/Giles2015.nex

data-raw/Griswold1999.nex

data-raw/Liljeblad2008.nex

data-raw/Loconte1991.nex

data-raw/Longrich2010.nex

data-raw/Longrich2010.xlsx

data-raw/OLeary1999.nex

data-raw/OMeara2014.nex

data-raw/Rougier2012.nex

data-raw/Rousset2004.nex

data-raw/Sano2011.nex

data-raw/Sansom2010.nex

data-raw/Schulze2007.nex

data-raw/Shultz2007.nex

data-raw/Sun2018.nex

data-raw/Vinther2008.nex

data-raw/Wetterer2000.nex

data-raw/Wills2012.nex

data-raw/Wilson2003.nex

data-raw/Wortley2006.nex

data-raw/Zanol2014.nex

data-raw/Zhu2013.nex

data-raw/_data_generator.R data-raw/plot-small-tree.R data-raw/profiles.R data-raw/small-tree.R data-raw/tree9.R

data/congreveLamsdellMatrices.RData

data/inapplicable.citations.R

data/inapplicable.datasets.rda

data/inapplicable.phyData.rda

data/inapplicable.trees.rda

data/profiles.rda

data/referenceTree.RData

debug/shinyapp.R

inst/CITATION

inst/Parsimony/app.R inst/Parsimony/tests/shinytest.R

inst/Parsimony/tests/shinytest/.gitignore

inst/Parsimony/tests/shinytest/Distribution-expected/001.json

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inst/Parsimony/tests/shinytest/Distribution-expected/003.json

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inst/Parsimony/tests/shinytest/Distribution-expected/005.json

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inst/Parsimony/tests/shinytest/Distribution-expected/007.json

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inst/Parsimony/tests/shinytest/Distribution-expected/009.json

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inst/Parsimony/tests/shinytest/Distribution-expected/010.download

inst/Parsimony/tests/shinytest/Distribution-expected/011.json

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inst/Parsimony/tests/shinytest/Distribution-expected/012.download

inst/Parsimony/tests/shinytest/Distribution-expected/013.json

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inst/Parsimony/tests/shinytest/Distribution-expected/015.json

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inst/Parsimony/tests/shinytest/Distribution-expected/021.json

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inst/Parsimony/tests/shinytest/Distribution-expected/022.download

inst/Parsimony/tests/shinytest/Distribution.R

inst/Parsimony/tests/shinytest/SearchLog-expected/001.download

inst/Parsimony/tests/shinytest/SearchLog-expected/002.download

inst/Parsimony/tests/shinytest/SearchLog-expected/003.download

inst/Parsimony/tests/shinytest/SearchLog-expected/004.download

inst/Parsimony/tests/shinytest/SearchLog.R

inst/Parsimony/tests/shinytest/ViewChars-expected/001.json

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inst/Parsimony/tests/shinytest/ViewChars-expected/003.json

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inst/Parsimony/tests/shinytest/ViewChars-expected/008.json

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inst/Parsimony/tests/shinytest/ViewChars-expected/010.json

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inst/Parsimony/tests/shinytest/ViewChars-expected/012.json

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inst/Parsimony/tests/shinytest/ViewChars-expected/014.json

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inst/Parsimony/tests/shinytest/ViewChars.R

inst/Parsimony/www/app.css

inst/Parsimony/www/images/Glade.jpg

inst/REFERENCES.bib

inst/WORDLIST

inst/_pkgdown.yml

inst/apa-old-doi-prefix.csl

inst/datasets/Agnarsson2004.nex

inst/datasets/Aguado2009.nex

inst/datasets/Aria2015.nex

inst/datasets/Asher2005.nex

inst/datasets/Capa2011.nex

inst/datasets/Conrad2008.nex

inst/datasets/DeAssis2011.nex

inst/datasets/Dikow2009.nex

inst/datasets/Eklund2004.nex

inst/datasets/Geisler2001.nex

inst/datasets/Giles2015.nex

inst/datasets/Griswold1999.nex

inst/datasets/Liljeblad2008.nex

inst/datasets/Loconte1991.nex

inst/datasets/Longrich2010.nex

inst/datasets/OLeary1999.nex

inst/datasets/OMeara2014.nex

inst/datasets/Rougier2012.nex

inst/datasets/Rousset2004.nex

inst/datasets/Sano2011.nex

inst/datasets/Sansom2010.nex

inst/datasets/Schulze2007.nex

inst/datasets/Shultz2007.nex

inst/datasets/Sun2018.nex

inst/datasets/Vinther2008.nex

inst/datasets/Wetterer2000.nex

inst/datasets/Wills2012.nex

inst/datasets/Wilson2003.nex

inst/datasets/Wortley2006.nex

inst/datasets/Zanol2014.nex

inst/datasets/Zhu2013.nex

inst/preamble.tex

inst/tests/benchmark_timing.R man-roxygen/CleanUpDataParam.R man-roxygen/EdgeSwapperParam.R man-roxygen/InitializeDataParam.R man-roxygen/MRS.R man-roxygen/compressParam.R man-roxygen/concavityParam.R man-roxygen/dataForFunction.R man-roxygen/datasetParam.r man-roxygen/edgeListParam.R man-roxygen/edgeToBreakParam.R man-roxygen/gapParam.R man-roxygen/labelledTreeParam.R man-roxygen/leftChildParam.R man-roxygen/mergeEdgesParam.R man-roxygen/morphyObjParam.R man-roxygen/nCoresParam.R man-roxygen/parentOfParam.R man-roxygen/pointlessDots.R man-roxygen/returnEdgeList.R man-roxygen/rightChildParam.R man-roxygen/split12Params.R man-roxygen/split1Param.R man-roxygen/split2Param.R man-roxygen/splits12params.R man-roxygen/splitsParam.R man-roxygen/stopAtPeakParam.R man-roxygen/stopAtPlateauParam.R man-roxygen/stopAtScoreParam.R man-roxygen/swappersParam.R man-roxygen/treeChild.R man-roxygen/treeNEdge.R man-roxygen/treeNEdgeOptional.R man-roxygen/treeParam.r man-roxygen/treeParent.r man-roxygen/treeScorerDots.r man-roxygen/treeScorerParam.r man-roxygen/verbosityParam.r man/AdditionTree.Rd man/AllSPR.Rd man/Carter1.Rd man/CharacterLength.Rd man/ClusterStrings.Rd man/ConcordantInformation.Rd man/Consistency.Rd man/DoubleNNI.Rd man/GapHandler.Rd man/JackLabels.Rd man/Jackknife.Rd man/LengthAdded.Rd man/MaximizeParsimony.Rd man/MinimumLength.Rd man/MorphyErrorCheck.Rd man/MorphyTreeLength.Rd man/MorphyWeights.Rd man/NNI.Rd man/PhyDat2Morphy.Rd man/PlotCharacter.Rd man/PrepareDataProfile.Rd man/QuartetResolution.Rd man/RandomMorphyTree.Rd man/RandomTreeScore.Rd man/Ratchet.Rd man/RearrangeEdges.Rd man/SPR.Rd man/SingleCharMorphy.Rd man/SiteConcordance.Rd man/StepInformation.Rd man/StopUnlessBifurcating.Rd man/Suboptimality.Rd man/SuccessiveApproximations.Rd man/TBR.Rd man/TBRWarning.Rd man/TaxonInfluence.Rd man/TreeLength.Rd man/TreeSearch.Rd man/UnloadMorphy.Rd man/WhenFirstHit.Rd man/WithOneExtraStep.Rd man/cSPR.Rd man/congreveLamsdellMatrices.Rd man/dot-CombineResults.Rd man/dot-GapHandler.Rd man/dot-NonDuplicateRoot.Rd man/dot-UniqueExceptHits.Rd

man/figures/Flow.svg

man/inapplicable.datasets.Rd man/is.morphyPtr.Rd man/mpl_apply_tipdata.Rd man/mpl_attach_rawdata.Rd man/mpl_attach_symbols.Rd man/mpl_delete_Morphy.Rd man/mpl_delete_rawdata.Rd man/mpl_first_down_recon.Rd man/mpl_first_up_recon.Rd man/mpl_get_charac_weight.Rd man/mpl_get_gaphandl.Rd man/mpl_get_num_charac.Rd man/mpl_get_num_internal_nodes.Rd man/mpl_get_numtaxa.Rd man/mpl_get_symbols.Rd man/mpl_init_Morphy.Rd man/mpl_new_Morphy.Rd man/mpl_second_down_recon.Rd man/mpl_second_up_recon.Rd man/mpl_set_charac_weight.Rd man/mpl_set_num_internal_nodes.Rd man/mpl_set_parsim_t.Rd man/mpl_translate_error.Rd man/mpl_update_lower_root.Rd man/mpl_update_tip.Rd man/profiles.Rd man/referenceTree.Rd man/summary.morphyPtr.Rd memcheck/all.R memcheck/examples.R memcheck/tests.R memcheck/vignettes.R

src/RMorphy.c

src/RMorphy.h

src/RMorphyUtils.c

src/RMorphyUtils.h

src/RcppExports.cpp

src/TreeSearch-init.c

src/build_postorder.h

src/fitch.c

src/fitch.h

src/morphy.c

src/morphy.h

src/morphy_score.cpp

src/morphydefs.h

src/mpl.c

src/mpl.h

src/mplerror.h

src/rearrange.cpp

src/statedata.c

src/statedata.h

src/wagner.c

src/wagner.h

tests/spelling.R tests/testthat.R

tests/testthat/_snaps/Jackknife/plot-jackknife.svg

tests/testthat/_snaps/PlotCharacter/plotchar-000011110000.svg

tests/testthat/_snaps/PlotCharacter/plotchar-000011qqqq00.svg

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tests/testthat/_snaps/PlotCharacter/plotchar-out-of-sequence.svg

tests/testthat/_snaps/PlotCharacter/plotchar-qqqqiiii1qqq.svg

tests/testthat/_snaps/PlotCharacter/plotchar-qqqqqqqqqqqq.svg

tests/testthat/test-AdditionTree.R tests/testthat/test-ClusterStrings.R tests/testthat/test-Concordance.R tests/testthat/test-Consistency.R tests/testthat/test-CustomSearch.R tests/testthat/test-Jackknife.R tests/testthat/test-MaximizeParsimony.R tests/testthat/test-NNI.R tests/testthat/test-PlotCharacter.R tests/testthat/test-PolEscapa.R tests/testthat/test-QuartetResolution.R tests/testthat/test-RMorphy.R tests/testthat/test-RandomTreeScore.R tests/testthat/test-TaxonInfluence.R tests/testthat/test-TreeSearch_utilities.R tests/testthat/test-WhenFirstHit.R tests/testthat/test-data_manipulation.R tests/testthat/test-iw-scoring.R tests/testthat/test-length_range.R tests/testthat/test-mpl_morphy_objects.R tests/testthat/test-pp-fitch.R tests/testthat/test-pp-info_extra_step.R tests/testthat/test-pp-random-tree.R tests/testthat/test-rearrange.cpp.R tests/testthat/test-tree_length.R tests/testthat/test-zzz-tree-rearrange.R vignettes/custom.Rmd vignettes/getting-started.Rmd

vignettes/gui_char.png

vignettes/gui_cluster_cons.png

vignettes/gui_consensus.png

vignettes/gui_rogue.png

vignettes/gui_space.png

vignettes/gui_start.png

vignettes/gui_sun_space.png

vignettes/gui_trees_loaded.png

vignettes/profile-scores.Rmd vignettes/profile.Rmd vignettes/tree-search.Rmd vignettes/tree-space.Rmd

ms609/TreeSearch documentation built on Sept. 8, 2024, 3:26 a.m.