R Observatory: Metrics for branchingprocess version 0.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

branchingprocess

0.1.0Package record

Calculate Outbreak Probabilities for a Branching Process Model

0packages depend

5.7Kdownloads / year

88.0%test coverage

13/13flavors OK

Overview

About

Maintained by Damon TothCRAN page ↗GitHub ↗Website ↗Issues ↗Declared funder: Centers for Disease Control and Prevention's Center for Forecasting and Outbreak Analytics

Quantify outbreak risk posed by individual importers of a transmissible pathogen. Input parameters of negative binomial offspring distributions for the number of transmissions from each infected individual and initial number of infected. Calculate probabilities of final outbreak size and generations of transmission, as described in Toth et al. (2015) doi:10.3201/eid2108.150170 and Toth et al. (2016) doi:10.1016/j.epidem.2016.04.002.

Changes in 0.1.0

Initial CRAN submission.

From NEWS.md in the release

Install

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

install.packages("branchingprocess", 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("EpiForeSITE/branchingprocess")

Development version from EpiForeSITE/branchingprocess. 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-branchingprocess

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-branchingprocess

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-branchingprocess

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: 1.8 min · r-oldrel-macos-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.0

READMEYes · 201 wordsVignettesYes · 1 · dynamicNEWSYes · 67% structured · mentions 0.1.0Citation fileYes · computed when R runs itWebsiteYes · pkgdown

Help pages: 10
Examples that run: 100%10 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

H5N1 Example HTML

How these are measured

Downloads

5.7K

CRAN downloads in the past year

Rank #13,089 · ~16/day · ~474/mo

Releases R versions

Daily download trend is not available in this view yet.

35030 days

85990 days

5.7K1 year

Compare downloads with other packages →

Also on82 r2u20 autocran

How downloads are counted

Repository

epiforesite/branchingprocess ↗Organization: EpiForeSITE

0Stars

1Forks

1Open issues

0Open PRs

1Releases

141Commits

4Commit identities

141 commits · Last activity 2026-10-02 · Default branch at 0.2.0, ahead of CRAN 0.1.0 (checked 2026-10-11)

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 14
Median days to close, 50 most recently updated closed PRs: 0

Forks over time

2024-11-14 · 12026-07-07 · 1

How these are measured

PracticesBeta

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

Checks run against github.com/epiforesite/branchingprocess 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 2026-10-02 · The repository has a site deploy workflow

Reproducibility and dev environment (1)

Makefile

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

Dependencies

Declared dependencies

3 external dependencies (excludes base and recommended)

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

Depends (0)

none

Imports (1)

stats

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 (3)

Damon Toth

Author, Maintainer since 0.1.0 (2025)

Erin Clancey

Contributor

Centers for Disease Control and Prevention's Center for Forecasting and Outbreak Analytics

Funder

Cooperative agreement CDC-RFA-FT-23-0069

Releases (1)

R
R 4.6.0 released · 2026-04-24
0.1.0Latest
record
2025-04-25 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-04-25
Total releases: 1 / 1 yrs
License: MIT + file LICENSE OSI
Download size: 31 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("branchingprocess")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

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 branchingprocess version 0.1.0 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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