R Observatory: Metrics for linktree version 0.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

linktree

0.1.0

Estimate Transmission Assortativity Coefficients

0packages depend

1.4Kdownloads / year

70.3%test coverage

12/13checks pass

Overview

About

Maintained by Cyril GeismarFirst published 2025-12-151 releasesCRAN page ↗GitHub ↗

Estimates group transmission assortativity coefficients from transmission trees. Group transmission assortativity coefficients measure the tendency for individuals to transmit within their own group (e.g. age group, vaccination status, or location) compared to other groups. The package requires information on who infected whom, group membership for all individuals, and the relative sizes of each group in the population. For more details see Geismar et al. (2024) doi:10.1371/journal.pone.0313037.

Install

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

install.packages("linktree", 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("CyGei/linktree")

Development version from CyGei/linktree. 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-linktree

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

# 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-linktree

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-linktree

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

Health

CRAN checks

1ERROR12OK

Failing flavors

ERROR r-release-windows-x86_64

Slowest check: 1.4 min · r-oldrel-macos-x86_64

Code health

Yes

Tests · ratio 0.41

70.3%

Coverage · measured lines

100%

Documentation · exports

0

Dependencies · direct

Check history

ERROR2026-08-17
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
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

Show 1 earlier snapshots

OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 176 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

1.4K

CRAN downloads in the past year

Rank #21,880 · ~4/day · ~119/mo

Releases R versions

Daily download trend is not available in this view yet.

13730 days

50090 days

1.4K1 year

Compare downloads with other packages →

Also on61 r2u23 autocran

Repository

GitHub ↗ cygei/linktree

2Stars

0Forks

0Open issues

0Open PRs

0Releases

34Commits

1Contributors

License CC-BY-4.0 · 34 commits · Last activity 2026-06-25 · 0% stars, 30d

Stars over time

2025-12-02 · 22026-07-07 · 2

Repository practices

Upstream repositoryBeta

3 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/cygei/linktree on 2026-08-16.

Continuous integration (1)

GitHub Actions

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5

Imports (0)

none

LinkingTo (0)

none

Suggests (6)

knitr rmarkdown testthat pak epicontacts visNetwork

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (1)

Maintainer (1)

Cyril Geismar

Author, Maintainer, Copyright holder

Authors (1)

Cyril Geismar

Author, Maintainer, Copyright holder

Copyright holders (1)

Cyril Geismar

Author, Maintainer, Copyright holder

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.1.0Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-12-15
Total releases: 1 / 1 yrs
License: CC BY 4.0
Minimum R: ≥ 3.5
Bundled data: 3.8 KB / 1 file
Download size: 2.9 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("linktree")

Format

Geismar, C. (2025). linktree: Estimate Transmission Assortativity Coefficients (Version 0.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.linktree

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 linktree version 0.1.0 [Data set]. HJJB, LLC. Data release v2026-08-17. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-17, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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