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: 0.2.0
Imports: ape, cli, cowplot, dplyr, forcats, ggnewscale, ggplot2 (≥ 3.5.0), ggraph, igraph, rlang, scales, tidygraph, vctrs
Suggests: knitr, rmarkdown, testthat (≥ 3.0.0)
Published: 2024-05-31
DOI: 10.32614/CRAN.package.phylepic
Author: Carl Suster ORCID iD [aut, cre], Western Sydney Local Health District, NSW Health [cph]
Maintainer: Carl Suster <Carl.Suster at>
License: MIT + file LICENSE
Copyright: see file COPYRIGHTS
NeedsCompilation: no
Citation: phylepic citation info
Materials: README NEWS
CRAN checks: phylepic results


Reference manual: phylepic.pdf
Vignettes: phylepic charts: combining phylogenetic trees with epidemic curves


Package source: phylepic_0.2.0.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
macOS binaries: r-release (arm64): phylepic_0.2.0.tgz, r-oldrel (arm64): phylepic_0.2.0.tgz, r-release (x86_64): phylepic_0.2.0.tgz, r-oldrel (x86_64): phylepic_0.2.0.tgz


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