phylepic: Combined Visualisation of Phylogenetic and Epidemiological Data
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 + file LICENSE |
| Copyright: | see file COPYRIGHTS |
| 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 |
Documentation:
| Reference manual: | phylepic.html , phylepic.pdf |
| Vignettes: |
phylepic charts: combining phylogenetic trees with epidemic curves (source, R code) |
Downloads:
| Package source: | phylepic_0.3.0.tar.gz |
| Windows binaries: | r-devel: phylepic_0.3.0.zip, r-release: phylepic_0.3.0.zip, r-oldrel: phylepic_0.3.0.zip |
| macOS binaries: | r-release (arm64): phylepic_0.3.0.tgz, r-oldrel (arm64): phylepic_0.3.0.tgz, r-release (x86_64): phylepic_0.3.0.tgz, r-oldrel (x86_64): phylepic_0.3.0.tgz |
| Old sources: | phylepic archive |
Linking:
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