Files in xavierdidelot/TransPhylo
Inference of Transmission Tree under a Within-Host Evolution Model

.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
R/RcppExports.R R/TransPhylo.R R/computeHost.R R/computeMats.R R/consTTree.R R/extractPTree.R R/extractTTree.R R/extras/getIncidentCases.R R/extras/transphylo_extras.R R/glueTrees.R R/inferTTree.R R/makeCTreeFromPTree.R R/makeTTree.R R/phyloFromPtree.R R/plotCTree.R R/plotTTree.R R/plotTTree2.R R/probPTreeGivenTTree.R R/probTTree.R R/proposal.R R/ptreeFromPhylo.R R/selectTTree.R R/simulateOutbreak.R R/withinhost.R README.Rmd README.md
TransPhylo.Rproj
docs/articles/TransPhylo.html
docs/articles/TransPhylo_files/figure-html/unnamed-chunk-15-1.png
docs/articles/TransPhylo_files/figure-html/unnamed-chunk-16-1.png
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docs/articles/TransPhylo_files/figure-html/unnamed-chunk-8-1.png
docs/articles/index.html
docs/authors.html
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/jquery.sticky-kit.min.js
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/TransPhylo.html
docs/reference/computeMatTDist.html
docs/reference/computeMatWIW.html
docs/reference/consTTree.html
docs/reference/extractPTree.html
docs/reference/extractTTree.html
docs/reference/index.html
docs/reference/inferTTree.html
docs/reference/makeCtreeFromPTree.html
docs/reference/makeTTree.html
docs/reference/phyloFromPTree.html
docs/reference/plotCTree-1.png
docs/reference/plotCTree.html
docs/reference/plotTTree.html
docs/reference/plotTTree2.html
docs/reference/probPTreeGivenTTree.html
docs/reference/probTTree.html
docs/reference/probTTreeR.html
docs/reference/ptreeFromPhylo.html
docs/reference/selectTTree.html
docs/reference/simulateOutbreak-1.png
docs/reference/simulateOutbreak.html
inst/CITATION
man/TransPhylo.Rd man/computeMatTDist.Rd man/computeMatWIW.Rd man/consTTree.Rd man/extractPTree.Rd man/extractTTree.Rd man/inferTTree.Rd man/makeCtreeFromPTree.Rd man/makeTTree.Rd man/phyloFromPTree.Rd man/plotCTree.Rd man/plotTTree.Rd man/plotTTree2.Rd man/probPTreeGivenTTree.Rd man/probTTree.Rd man/probTTreeR.Rd man/ptreeFromPhylo.Rd man/selectTTree.Rd man/simulateOutbreak.Rd
src/RcppExports.cpp
src/probTTree.cpp
tests/testthat.R tests/testthat/test_coal.R tests/testthat/test_trans.R vignettes/TransPhylo.Rmd
xavierdidelot/TransPhylo documentation built on Sept. 5, 2018, 5:36 p.m.