R Observatory: Metrics for bumblebee version 0.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

bumblebee

0.1.0

Quantify Disease Transmission Within and Between Population Groups

0packages depend

2.7Kdownloads / year

67.3%test coverage

9/13checks pass

Overview

About

Maintained by Lerato E MagosiFirst published 2021-05-111 releasesCRAN page ↗GitHub ↗

A simple tool to quantify the amount of transmission of an infectious disease of interest occurring within and between population groups. 'bumblebee' uses counts of observed directed transmission pairs, identified phylogenetically from deep-sequence data or from epidemiological contacts, to quantify transmission flows within and between population groups accounting for sampling heterogeneity. Population groups might include: geographical areas (e.g. communities, regions), demographic groups (e.g. age, gender) or arms of a randomized clinical trial. See the 'bumblebee' website for statistical theory, documentation and examples https://magosil86.github.io/bumblebee/.

Install

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

install.packages("bumblebee", 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("magosil86/bumblebee")

Development version from magosil86/bumblebee. 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-bumblebee

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-bumblebee

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-bumblebee

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

Health

CRAN checks

4NOTE9OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc
NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc

Slowest check: 1.8 min · r-release-macos-x86_64

Code health

Yes

Tests · ratio 0.04

67.3%

Coverage · measured lines

100%

Documentation · exports

5

Dependencies · direct

Check history

NOTE2026-06-09
9 OK · 4 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
9 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
10 OK · 4 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 33% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 89%
Return-value docs: 100%
References docs: 100%

Downloads

2.7K

CRAN downloads in the past year

Rank #14,168 · ~7/day · ~223/mo

Releases R versions

Daily download trend is not available in this view yet.

24130 days

73390 days

2.7K1 year

Compare downloads with other packages →

Also on120 r2u21 autocran

Repository

GitHub ↗ magosil86/bumblebee

0Stars

0Forks

0Open issues

0Open PRs

0Releases

transmissionepidemiologygeneticsheterogeneityphylogenetics

Last activity 2022-02-27

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/magosil86/bumblebee on 2026-08-09.

Continuous integration (1)

GitHub Actions

CRAN release process (1)

cran-comments.md

Coverage (1)

Codecov

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

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Depends (1)

R >= 2.10

Imports (5)

dplyr gtools Hmisc magrittr rmarkdown

LinkingTo (0)

none

Suggests (4)

covr knitr markdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (3)

Maintainer (1)

Lerato E Magosi

Maintainer

Authors (2)

Marc Lipsitch

Author

Lerato E Magosi

Author

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: 2021-05-11
Total releases: 1 / 5 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 2.10
Bundled data: 1.9 KB / 3 files
Download size: 351 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("bumblebee")

Format

Magosi, L. E., Lipsitch, M., & Magosi, L. E. (2021). bumblebee: Quantify Disease Transmission Within and Between Population Groups (Version 0.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.bumblebee

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 bumblebee version 0.1.0 [Data set]. HJJB, LLC. Data release v2026-08-15. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-15, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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