phylepic

0.3.0

Combined Visualisation of Phylogenetic and Epidemiological Data

0packages depend

6.7Kdownloads / year

10.7%test coverage

13/13checks pass

Overview

About

Maintained by Carl SusterFirst published 2024-05-312 releasesCRAN page ↗GitHub ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)openSUSE (OBS)

install.packages("phylepic", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("cidm-ph/phylepic")

Development version from cidm-ph/phylepic. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-phylepic

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-phylepic

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 3.1 min · r-devel-linux-x86_64-fedora-clang

Check history

OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

Documentation signals are not tracked yet for this package.

Downloads

6.7K

CRAN downloads in the past year

Rank #6,688 · ~18/day · ~561/mo

phylepic Releases R versions

Daily download trend is not available in this view yet.

35030 days

1.5K90 days

6.7K1 year

Compare downloads with other packages →

Also on113 r2u35 autocran

Repository

GitHub ↗ cidm-ph/phylepic

1Stars

1Forks

0Open issues

0Open PRs

2Releases

83Commits

2Contributors

genomicsgenomics-visualizationpublic-healthr

83 commits · Last activity 2025-09-12 · 0% stars, 30d

Repository practices

Upstream repositoryBeta

5 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/cidm-ph/phylepic on 2026-07-19.

Continuous integration (1)

GitHub Actions

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Lint, format, editor (2)

lintrRStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1

Imports (13)

ape cli cowplot dplyr forcats ggnewscale ggplot2 (>= 4.0.0)ggraph igraph lifecycle rlang scales tidygraph

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (2)

Maintainer (1)

Carl Suster

Author, Maintainer

Authors (1)

Carl Suster

Author, Maintainer

Western Sydney Local Health District, NSW Health

Package Timeline

2 releases. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.3.0Latest
2025-09-12 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
0.2.0
2024-05-31
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-05-31
Total releases: 2 / 2 yrs
License: MIT + file LICENSE OSI
Download size: 1.0 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Epidemiology

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