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

1.9Kdownloads / year

70.3%test coverage

13/13flavors OK

Overview

About

Maintained by Cyril GeismarCRAN page ↗GitHub ↗Website ↗Issues ↗

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. 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-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). 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: 1.4 min · r-oldrel-macos-x86_64

Status changes

OK13 OK2026-08-21
ERROR12 OK, 1 ERROR2026-08-17
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09

Show 2 earlier changesHide 2 earlier changes

ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.0

READMEYes · 176 wordsVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsiteYes · pkgdown

Help pages: 13 (6 internal)
Examples that run: 100%6 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

linktree HTML

How these are measured

Downloads

1.9K

CRAN downloads in the past year

Rank #20,827 · ~5/day · ~160/mo

Releases R versions

Daily download trend is not available in this view yet.

26230 days

61790 days

1.9K1 year

Compare downloads with other packages →

Also on67 r2u3 autocran

How downloads are counted

Repository

cygei/linktree ↗Account: CyGei

2Stars

0Forks

0Open issues

0Open PRs

0Releases

34Commits

1Commit identities

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

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 162
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-12-02 · 22026-07-07 · 2

How these are measured

PracticesBeta

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

Checks run against github.com/cygei/linktree on 2026-10-11.

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 2026-06-25 · The repository has a site deploy workflow

pkgdown site last built 2026-06-25

Coverage (1)

Coverage reporting

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Installing linktree adds no packages beyond those that come with R.

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.

How these are counted

Code & Tests

Datasets

People & History

People (1)

Cyril Geismar

Releases (1)

R
R 4.6.0 released · 2026-04-24
0.1.0Latest
record
2025-12-15 · 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

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 package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 v2026-10-17. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-17, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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