Files in TransPhylo
Inference of Transmission Tree from a Dated Phylogeny
MD5
README.md
NAMESPACE
DESCRIPTION
R/RcppExports.R
R/TransPhylo-package.R
R/probTTree.R
R/simulateOutbreak.R
R/computeHost.R
R/methods.R
R/consTTree.R
R/interpret.R
R/plotTTree.R
R/phyloFromPTree.R
R/glueTrees.R
R/medTTree.R
R/infer_multittree_share_param.R
R/makeCTreeFromPTree.R
R/plotTTree2.R
R/computeMats.R
R/inferTTree.R
R/extractTTree.R
R/withinhost.R
R/convergence.R
R/extractPTree.R
R/ptreeFromPhylo.R
R/plotCTree.R
R/selectTTree.R
R/proposal.R
R/probPTreeGivenTTree.R
R/makeTTree.R
R/extras/transphylo_extras.R
R/extras/getIncidentCases.R
src/RcppExports.cpp
src/probTTree.cpp
src/probPTreeGivenTTree.cpp
inst/CITATION
inst/doc/TransPhylo.Rmd
inst/doc/multitree.R
inst/doc/simulate.R
inst/doc/infer.html
inst/doc/TransPhylo.html
inst/doc/infer.R
inst/doc/multitree.Rmd
inst/doc/simulate.html
inst/doc/TransPhylo.R
inst/doc/multitree.html
inst/doc/simulate.rmd
inst/doc/infer.Rmd
build/vignette.rds
tests/testthat.R
tests/testthat/test_coal.R
tests/testthat/test_trans.R
tests/testthat/test_session.R
tests/testthat/Rplots.pdf
vignettes/TransPhylo.Rmd
vignettes/multitree.Rmd
vignettes/simulate.rmd
vignettes/infer.Rmd
man/getOffspringDist.Rd
man/plotTTree2.Rd
man/probTTreeR.Rd
man/probPTreeGivenTTreeR.Rd
man/plotTraces.Rd
man/computeMatWIW.Rd
man/print.resTransPhylo.Rd
man/getInfectionTimeDist.Rd
man/infer_multittree_share_param.Rd
man/ptreeFromPhylo.Rd
man/inferTTree.Rd
man/print.ttree.Rd
man/plot.resTransPhylo.Rd
man/plotTTree.Rd
man/medTTree.Rd
man/dateLastSample.Rd
man/plot.ctree.Rd
man/plot.ptree.Rd
man/extractPTree.Rd
man/phyloFromPTree.Rd
man/extractCTree.Rd
man/as.mcmc.resTransPhylo.Rd
man/makeTTree.Rd
man/probPTreeGivenTTree.Rd
man/plot.ttree.Rd
man/probTTree.Rd
man/convertToCoda.Rd
man/plotCTree.Rd
man/simulateOutbreak.Rd
man/summary.resTransPhylo.Rd
man/selectTTree.Rd
man/computeMatTDist.Rd
man/consTTree.Rd
man/TransPhylo-package.Rd
man/getGenerationTimeDist.Rd
man/print.ptree.Rd
man/getIncidentCases.Rd
man/print.ctree.Rd
man/extractTTree.Rd
man/makeCTreeFromPTree.Rd
man/getSamplingTimeDist.Rd
