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TransPhylo
View on CRAN: Click
here
Download and install TransPhylo package within the R console
Install from CRAN:
install.packages("TransPhylo")
Install from Github:
library("remotes")
install_github("cran/TransPhylo")
Install by package version:
library("remotes")
install_version("TransPhylo", "1.4.5")
Attach the package and use:
library("TransPhylo")
Maintained by
Xavier Didelot
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
10.32614/CRAN.package.TransPhylo . TransPhylo citation info . TransPhylo results . TransPhylo.pdf . Introducing the R package TransPhylo . TransPhylo_1.4.5.tar.gz . TransPhylo_1.4.5.zip . TransPhylo_1.4.5.zip . TransPhylo_1.4.5.zip . TransPhylo_1.4.5.tgz . TransPhylo_1.4.5.tgz . TransPhylo_1.4.5.tgz . TransPhylo_1.4.5.tgz . TransPhylo archive . https://CRAN.R-project.org/package=TransPhylo .
First Published: 2020-05-13
Latest Update: 2021-04-20
Description:
Inference of transmission tree from a dated phylogeny. Includes methods to simulate and analyse outbreaks. The methodology is described in Didelot et al. (2014) <doi:10.1093/molbev/msu121>, Didelot et al. (2017) <doi:10.1093/molbev/msw275>.
How to cite:
Xavier Didelot (2020). TransPhylo: Inference of Transmission Tree from a Dated Phylogeny. R package version 1.4.5, https://cran.r-project.org/web/packages/TransPhylo. Accessed 10 May. 2025.
Other packages that cited TransPhylo R package
View TransPhylo citation profile
Other R packages that TransPhylo depends,
imports, suggests or enhances
Complete documentation for TransPhylo
Functions, R codes and Examples using
the TransPhylo R package
Some associated functions: TransPhylo-package . as.mcmc.resTransPhylo . computeMatTDist . computeMatWIW . consTTree . convertToCoda . dateLastSample . extractCTree . extractPTree . extractTTree . getGenerationTimeDist . getIncidentCases . getInfectionTimeDist . getOffspringDist . getSamplingTimeDist . inferTTree . infer_multittree_share_param . makeCTreeFromPTree . makeTTree . medTTree . phyloFromPTree . plot.ctree . plot.ptree . plot.resTransPhylo . plot.ttree . plotCTree . plotTTree . plotTTree2 . plotTraces . print.ctree . print.ptree . print.resTransPhylo . print.ttree . probPTreeGivenTTree . probPTreeGivenTTreeR . probTTree . probTTreeR . ptreeFromPhylo . selectTTree . simulateOutbreak . summary.resTransPhylo .
Some associated R codes: RcppExports.R . TransPhylo-package.R . computeHost.R . computeMats.R . consTTree.R . convergence.R . extractPTree.R . extractTTree.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 . Full TransPhylo package functions and examples
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