Files in xavierdidelot/TransPhylo

Inference of Transmission Tree from a Dated Phylogeny

.Rbuildignore

.gitignore

.travis.yml

DESCRIPTION

LICENSE

NAMESPACE

R/RcppExports.R R/TransPhylo-package.R R/computeHost.R R/computeMats.R R/consTTree.R R/convergence.R R/extractPTree.R R/extractTTree.R R/extras/getIncidentCases.R R/extras/transphylo_extras.R R/glueTrees.R R/inferTTree.R R/infer_multittree_share_param.R R/interpret.R R/makeCTreeFromPTree.R R/makeTTree.R R/medTTree.R R/methods.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

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inst/CITATION

man/TransPhylo-package.Rd man/as.mcmc.resTransPhylo.Rd man/computeMatTDist.Rd man/computeMatWIW.Rd man/consTTree.Rd man/convertToCoda.Rd man/dateLastSample.Rd man/extractCTree.Rd man/extractPTree.Rd man/extractTTree.Rd man/getGenerationTimeDist.Rd man/getIncidentCases.Rd man/getInfectionTimeDist.Rd man/getOffspringDist.Rd man/getSamplingTimeDist.Rd man/inferTTree.Rd man/infer_multittree_share_param.Rd man/makeCtreeFromPTree.Rd man/makeTTree.Rd man/medTTree.Rd man/phyloFromPTree.Rd man/plot.ctree.Rd man/plot.ptree.Rd man/plot.resTransPhylo.Rd man/plot.ttree.Rd man/plotCTree.Rd man/plotTTree.Rd man/plotTTree2.Rd man/plotTraces.Rd man/print.ctree.Rd man/print.ptree.Rd man/print.resTransPhylo.Rd man/print.ttree.Rd man/probPTreeGivenTTree.Rd man/probPTreeGivenTTreeR.Rd man/probTTree.Rd man/probTTreeR.Rd man/ptreeFromPhylo.Rd man/selectTTree.Rd man/simulateOutbreak.Rd man/summary.resTransPhylo.Rd

src/RcppExports.cpp

src/probPTreeGivenTTree.cpp

src/probTTree.cpp

tests/testthat.R tests/testthat/test_coal.R tests/testthat/test_session.R tests/testthat/test_trans.R vignettes/TransPhylo.Rmd vignettes/infer.Rmd vignettes/multitree.Rmd vignettes/simulate.rmd

xavierdidelot/TransPhylo documentation built on Sept. 28, 2023, 7:20 p.m.