TransPhylo: Inference of Transmission Tree from a Dated Phylogeny
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>.
| Version: | 1.4.5 |
| Depends: | R (≥ 3.0.0) |
| Imports: | Rcpp (≥ 0.12.8), stats, graphics,ape |
| LinkingTo: | Rcpp |
| Suggests: | knitr,testthat,purrr,coda, grDevices,lattice,rmarkdown |
| Published: | 2021-04-20 |
| DOI: | 10.32614/CRAN.package.TransPhylo |
| Author: | Xavier Didelot [aut, cre], Yuanwei Xu [ctb] |
| Maintainer: | Xavier Didelot <xavier.didelot at gmail.com> |
| License: | GPL-2 |GPL-3 [expanded from: GPL (≥ 2)] |
| NeedsCompilation: | yes |
| SystemRequirements: | C++11 |
| Citation: | TransPhylo citation info |
| Materials: | README |
| In views: | Epidemiology |
| CRAN checks: | TransPhylo results[issues need fixing before 2025-12-18] |
Documentation:
Downloads:
| Package source: | TransPhylo_1.4.5.tar.gz |
| Windows binaries: | r-devel:TransPhylo_1.4.5.zip, r-release:TransPhylo_1.4.5.zip, r-oldrel:TransPhylo_1.4.5.zip |
| macOS binaries: | r-release (arm64):TransPhylo_1.4.5.tgz, r-oldrel (arm64):TransPhylo_1.4.5.tgz, r-release (x86_64):TransPhylo_1.4.5.tgz, r-oldrel (x86_64):TransPhylo_1.4.5.tgz |
| Old sources: | TransPhylo archive |
Linking:
Please use the canonical formhttps://CRAN.R-project.org/package=TransPhyloto link to this page.