R Observatory: Metrics for phylepic version 0.3.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

phylepic

0.3.0Package record

Combined Visualisation of Phylogenetic and Epidemiological Data

0packages depend

6.2Kdownloads / year

10.7%test coverage

13/13flavors OK

Overview

About

Maintained by Carl SusterCRAN page ↗GitHub ↗Website ↗Issues ↗

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.

Changes in 0.3.0

Update citation to published manuscript.
Overhaul the way that binning works. Instead of special stats that handled weekly binning, these now take their bin definitions from the scale breaks. This means that whereas before you could only do weekly binning or no binning, now you can use arbitrary bins by configuring the scale breaks.

From NEWS.md in the release

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)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. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-phylepic

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# 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). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 2.5 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.3.0

READMEYes · 104 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 0.3.0Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 19 (1 internal)includes a package overview page
Examples that run: 100%5 run in a plain check
Exported functions with examples: 29%
Documented parameters: 57%
Return-value docs: 94%
Help pages citing references: 0%

Vignettes (1)

phylepic charts: combining phylogenetic trees with epidemic curves HTML

How these are measured

Downloads

6.2K

CRAN downloads in the past year

Rank #9,995 · ~17/day · ~514/mo

Releases R versions

Daily download trend is not available in this view yet.

37630 days

1K90 days

6.2K1 year

Compare downloads with other packages →

Also on96 r2u7 autocran

How downloads are counted

Repository

cidm-ph/phylepic ↗Organization: cidm-ph

1Stars

1Forks

0Open issues

0Open PRs

2Releases

83Commits

2Commit identities

genomicsgenomics-visualizationpublic-healthr

83 commits · Last activity 2025-09-12 · Default branch at 0.3.0.9000, ahead of CRAN 0.3.0 (checked 2026-10-18)

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 40
Median days to close, 50 most recently updated closed PRs: 2

Stars over time

2025-08-26 · 12026-07-07 · 1

How these are measured

PracticesBeta

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

Checks run against github.com/cidm-ph/phylepic on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2025-09-12 · The repository has a site deploy workflow

pkgdown site last built 2025-09-12

CRAN release process (1)

cran-comments.md

Lint, format, editor (3)

lintrLint workflowRStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

Installing phylepic adds 52 packages (32 with compiled code, 52 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, igraph 4.8 MB.

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.

How these are counted

Code & Tests

People & History

People (2)

Carl Suster

Author, Maintainer since 0.2.0 (2024)

Western Sydney Local Health District, NSW Health

Copyright holder

2024-2025

Releases (2)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.3.0Latest
record
2025-09-12 · current release · diff ↗ ·
removed 4 exports
StatWeek, StatWeek2d, stat_week, stat_week_2d

added 8 exports
StatBin2dAuto, StatBinAuto, StatBinLocation, breaks_cached, stat_bin2d_auto, stat_bin_2d_auto, stat_bin_auto, stat_bin_location
R
R 4.5.0 released · 2025-04-11
0.2.0
record
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
Minimum R: ≥ 4.1
Download size: 1.0 MB

Appears in task views

Epidemiology

Cite

Cite this package

Run in R for the authors' entry:

citation("phylepic")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1017/s0950268824001092.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for phylepic version 0.3.0 [Data set]. HJJB, LLC. Data release v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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