├── .Rbuildignore ├── .gitignore ├── .travis.yml ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── R ├── RcppExports.R ├── TransPhylo-package.R ├── computeHost.R ├── computeMats.R ├── consTTree.R ├── convergence.R ├── extractPTree.R ├── extractTTree.R ├── extras │ ├── getIncidentCases.R │ └── transphylo_extras.R ├── glueTrees.R ├── inferTTree.R ├── infer_multittree_share_param.R ├── interpret.R ├── makeCTreeFromPTree.R ├── makeTTree.R ├── medTTree.R ├── methods.R ├── phyloFromPtree.R ├── plotCTree.R ├── plotTTree.R ├── plotTTree2.R ├── probPTreeGivenTTree.R ├── probTTree.R ├── proposal.R ├── ptreeFromPhylo.R ├── selectTTree.R ├── simulateOutbreak.R └── withinhost.R ├── README.Rmd ├── README.md ├── TransPhylo.Rproj ├── _pkgdown.yaml ├── docs ├── 404.html ├── LICENSE-text.html ├── articles │ ├── TransPhylo.html │ ├── TransPhylo_files │ │ ├── accessible-code-block-0.0.1 │ │ │ └── empty-anchor.js │ │ └── figure-html │ │ │ ├── unnamed-chunk-15-1.png │ │ │ ├── unnamed-chunk-16-1.png │ │ │ ├── unnamed-chunk-17-1.png │ │ │ ├── unnamed-chunk-18-1.png │ │ │ ├── unnamed-chunk-19-1.png │ │ │ ├── unnamed-chunk-20-1.png │ │ │ ├── unnamed-chunk-21-1.png │ │ │ ├── unnamed-chunk-22-1.png │ │ │ ├── unnamed-chunk-23-1.png │ │ │ ├── unnamed-chunk-24-1.png │ │ │ ├── unnamed-chunk-25-1.png │ │ │ ├── unnamed-chunk-5-1.png │ │ │ ├── unnamed-chunk-6-1.png │ │ │ ├── unnamed-chunk-7-1.png │ │ │ └── unnamed-chunk-8-1.png │ ├── index.html │ ├── infer.html │ ├── infer_files │ │ ├── accessible-code-block-0.0.1 │ │ │ └── empty-anchor.js │ │ └── figure-html │ │ │ ├── unnamed-chunk-10-1.png │ │ │ ├── unnamed-chunk-11-1.png │ │ │ ├── unnamed-chunk-12-1.png │ │ │ ├── unnamed-chunk-13-1.png │ │ │ ├── unnamed-chunk-14-1.png │ │ │ ├── unnamed-chunk-15-1.png │ │ │ ├── unnamed-chunk-16-1.png │ │ │ ├── unnamed-chunk-17-1.png │ │ │ ├── unnamed-chunk-18-1.png │ │ │ ├── unnamed-chunk-2-1.png │ │ │ ├── unnamed-chunk-3-1.png │ │ │ ├── unnamed-chunk-4-1.png │ │ │ ├── unnamed-chunk-7-1.png │ │ │ ├── unnamed-chunk-8-1.png │ │ │ └── unnamed-chunk-9-1.png │ ├── multitree.html │ ├── multitree_files │ │ ├── accessible-code-block-0.0.1 │ │ │ └── empty-anchor.js │ │ └── figure-html │ │ │ ├── unnamed-chunk-1-1.png │ │ │ ├── unnamed-chunk-1-2.png │ │ │ ├── unnamed-chunk-2-1.png │ │ │ ├── unnamed-chunk-2-2.png │ │ │ ├── unnamed-chunk-5-1.png │ │ │ ├── unnamed-chunk-6-1.png │ │ │ ├── unnamed-chunk-7-1.png │ │ │ └── unnamed-chunk-8-1.png │ ├── simulate.html │ └── simulate_files │ │ ├── accessible-code-block-0.0.1 │ │ └── empty-anchor.js │ │ └── figure-html │ │ ├── unnamed-chunk-16-1.png │ │ ├── unnamed-chunk-17-1.png │ │ ├── unnamed-chunk-19-1.png │ │ ├── unnamed-chunk-20-1.png │ │ ├── unnamed-chunk-21-1.png │ │ ├── unnamed-chunk-22-1.png │ │ ├── unnamed-chunk-23-1.png │ │ ├── unnamed-chunk-24-1.png │ │ ├── unnamed-chunk-25-1.png │ │ ├── unnamed-chunk-4-1.png │ │ ├── unnamed-chunk-5-1.png │ │ ├── unnamed-chunk-6-1.png │ │ ├── unnamed-chunk-7-1.png │ │ ├── unnamed-chunk-8-1.png │ │ └── unnamed-chunk-9-1.png ├── authors.html ├── bootstrap-toc.css ├── bootstrap-toc.js ├── docsearch.css ├── docsearch.js ├── index.html ├── jquery.sticky-kit.min.js ├── link.svg ├── pkgdown.css ├── pkgdown.js ├── pkgdown.yml ├── reference │ ├── Rplot001.png │ ├── TransPhylo-package.html │ ├── TransPhylo.html │ ├── as.mcmc.resTransPhylo.html │ ├── computeMatTDist.html │ ├── computeMatWIW.html │ ├── consTTree.html │ ├── convertToCoda.html │ ├── dateLastSample.html │ ├── extractCTree.html │ ├── extractPTree.html │ ├── extractTTree.html │ ├── getGenerationTimeDist.html │ ├── getIncidentCases.html │ ├── getInfectionTimeDist.html │ ├── getOffspringDist.html │ ├── getSamplingTimeDist.html │ ├── index.html │ ├── inferTTree.html │ ├── infer_multittree_share_param.html │ ├── makeCtreeFromPTree.html │ ├── makeTTree.html │ ├── medTTree.html │ ├── phyloFromPTree.html │ ├── plot.ctree-1.png │ ├── plot.ctree.html │ ├── plot.ptree-1.png │ ├── plot.ptree.html │ ├── plot.resTransPhylo.html │ ├── plot.ttree-1.png │ ├── plot.ttree.html │ ├── plotCTree-1.png │ ├── plotCTree.html │ ├── plotTTree-1.png │ ├── plotTTree.html │ ├── plotTTree2-1.png │ ├── plotTTree2.html │ ├── plotTraces.html │ ├── print.ctree.html │ ├── print.ptree.html │ ├── print.resTransPhylo.html │ ├── print.ttree.html │ ├── probPTreeGivenTTree.html │ ├── probPTreeGivenTTreeR.html │ ├── probTTree.html │ ├── probTTreeR.html │ ├── ptreeFromPhylo.html │ ├── selectTTree.html │ ├── simulateOutbreak-1.png │ ├── simulateOutbreak.html │ └── summary.resTransPhylo.html └── sitemap.xml ├── inst └── CITATION ├── man ├── TransPhylo-package.Rd ├── as.mcmc.resTransPhylo.Rd ├── computeMatTDist.Rd ├── computeMatWIW.Rd ├── consTTree.Rd ├── convertToCoda.Rd ├── dateLastSample.Rd ├── extractCTree.Rd ├── extractPTree.Rd ├── extractTTree.Rd ├── getGenerationTimeDist.Rd ├── getIncidentCases.Rd ├── getInfectionTimeDist.Rd ├── getOffspringDist.Rd ├── getSamplingTimeDist.Rd ├── inferTTree.Rd ├── infer_multittree_share_param.Rd ├── 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