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 [aut, cre], Western Sydney Local Health District, NSW Health [cph]
Maintainer:	Carl Suster <Carl.Suster at health.nsw.gov.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
CRAN checks:	phylepic results

Documentation:

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

Downloads:

Package source:	phylepic_0.2.0.tar.gz
Windows binaries:	r-devel: phylepic_0.2.0.zip, r-release: phylepic_0.2.0.zip, r-oldrel: phylepic_0.2.0.zip
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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