A collection of utilities and 'ggplot2' extensions to assist with visualisations in genomic epidemiology. This includes the 'phylepic' chart, a visual combination of a phylogenetic tree and a matched epidemic curve. The included 'ggplot2' extensions such as date axes binned by week are relevant for other applications in epidemiology and beyond. The approach is described in Suster et al. (2024) <doi:10.1101/2024.04.02.24305229>.
| Version: | 0.3.0 |
| Depends: | R (≥ 4.1) |
| Imports: | ape,cli,cowplot,dplyr,forcats,ggnewscale,ggplot2 (≥4.0.0),ggraph,igraph,lifecycle,rlang,scales,tidygraph |
| Suggests: | knitr,rmarkdown,testthat (≥ 3.0.0) |
| Published: | 2025-09-12 |
| DOI: | 10.32614/CRAN.package.phylepic |
| Author: | Carl Suster [aut, cre], Western Sydney Local Health District, NSW Health [cph] (2024-2025) |
| Maintainer: | Carl Suster <carl.suster at sydney.edu.au> |
| BugReports: | https://github.com/cidm-ph/phylepic/issues |
| License: | MIT + fileLICENSE |
| Copyright: | see fileCOPYRIGHTS |
| URL: | https://github.com/cidm-ph/phylepic,https://cidm-ph.github.io/phylepic/ |
| NeedsCompilation: | no |
| Citation: | phylepic citation info |
| Materials: | README,NEWS |
| In views: | Epidemiology |
| CRAN checks: | phylepic results |