├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── R ├── ancRECON.R ├── confidence.R ├── contour_plots.R ├── convertPhangorn.R ├── corDISC.R ├── corHMM.R ├── corHMMDredge.R ├── dentist.R ├── fitCorrelationTest.R ├── jntRECON.R ├── makeSimmap.R ├── plotMKmodel.R ├── plotRECON.R ├── rate.mat.maker.R ├── rayDISC.R ├── testCode.R └── tipHomology.R ├── data ├── primates.paint.rda ├── primates.rda └── rayDISC.example.rda ├── docs ├── 404.html ├── articles │ ├── corHMMv2.1-vignette.html │ ├── corHMMv2.1-vignette_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-10-1.png │ │ │ ├── unnamed-chunk-2-1.png │ │ │ ├── unnamed-chunk-20-1.png │ │ │ ├── unnamed-chunk-29-1.png │ │ │ ├── unnamed-chunk-44-1.png │ │ │ ├── unnamed-chunk-48-1.png │ │ │ ├── unnamed-chunk-53-1.png │ │ │ ├── unnamed-chunk-57-1.png │ │ │ ├── unnamed-chunk-6-1.png │ │ │ ├── unnamed-chunk-7-1.png │ │ │ └── unnamed-chunk-9-1.png │ └── index.html ├── authors.html ├── bootstrap-toc.css ├── bootstrap-toc.js ├── docsearch.css ├── docsearch.js ├── index.html ├── link.svg ├── pkgdown.css ├── pkgdown.js ├── pkgdown.yml ├── reference │ ├── ComputeCI.html │ ├── ConvertPhangornReconstructions.html │ ├── Rplot001.png │ ├── Rplot002.png │ ├── ancRECON.html │ ├── ancRECON_slice.html │ ├── corDISC.html │ ├── corHMM.html │ ├── fitCorrelationTest.html │ ├── getFullMat.html │ ├── getRateMat4Dat.html │ ├── index.html │ ├── makeSimmap.html │ ├── plotMKmodel-1.png │ ├── plotMKmodel-2.png │ ├── plotMKmodel.html │ ├── plotRECON-1.png │ ├── plotRECON.html │ ├── plot_batch_profile_lik.html │ ├── primates.html │ ├── rayDISC-1.png │ ├── rayDISC.html │ └── simMarkov.html └── sitemap.xml ├── man ├── ComputeCI.Rd ├── ConvertPhangornReconstructions.Rd ├── ancRECON.Rd ├── ancRECON_slice.Rd ├── corDISC.Rd ├── corHMM.Rd ├── corHMMDredge.Rd ├── corHMMDredgeBase.Rd ├── fitCorrelationTest.Rd ├── getCVTable.Rd ├── getFullMat.Rd ├── getModelTable.Rd ├── getRateMat4Dat.Rd ├── get_batch_profile_lik.Rd ├── kFoldCrossValidation.Rd ├── makeSimmap.Rd ├── plotDredgeTrace.Rd ├── plotMKmodel.Rd ├── plotRECON.Rd ├── plot_batch_profile_lik.Rd ├── plot_transition_summary.Rd ├── primates.Rd ├── rayDISC.Rd ├── simMarkov.Rd ├── summarize_simmaps.Rd └── tipHomology.Rd ├── tests ├── testthat.R └── testthat │ ├── balanced.tree │ ├── res_old.corhmm.Rsave │ └── testlikelihood.R └── vignettes ├── balanced.tree ├── corHMMResults.Rsave ├── corHMMv2.1-vignette.Rmd ├── corHMMv2.1-vignette.pdf ├── randomBD.tree └── simulatedData.Rsave /.gitignore: -------------------------------------------------------------------------------- 1 | inst/doc 2 | *.Rhistory 3 | .DS_Store 4 | -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/thej022214/corHMM/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /NAMESPACE: 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