R Observatory: Metrics for o2geosocial version 1.1.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

o2geosocial

1.1.3

Reconstruction of Transmission Chains from Surveillance Data

0packages depend

3.4Kdownloads / year

86.9%test coverage

13/13flavors OK

Overview

About

Maintained by Alexis RobertCRAN page ↗GitHub ↗Issues ↗

Bayesian reconstruction of who infected whom during past outbreaks using routinely-collected surveillance data. Inference of transmission trees using genotype, age specific social contacts, distance between cases and onset dates of the reported cases. (Robert A, Kucharski AJ, Gastanaduy PA, Paul P, Funk S. (2020) doi:10.1098/rsif.2020.0084).

Changes in 1.1.3

Fix: add extra checks to avoid segfaults in move_alpha and move_swap_alpha

From NEWS.md in the release

Install

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

install.packages("o2geosocial", 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("alxsrobert/o2geosocial")

Development version from alxsrobert/o2geosocial. 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-o2geosocial

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-o2geosocial

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-o2geosocial

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: 11.4 min · r-oldrel-macos-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-04-22
ERROR13 OK, 1 ERROR2026-04-18
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.3

READMEYes · 210 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 1.1.3Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 11
Examples that run: 100%8 run in a plain check
Exported functions with examples: 75%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

o2geosocial

How these are measured

Downloads

3.4K

CRAN downloads in the past year

Rank #12,597 · ~9/day · ~282/mo

Releases R versions

Daily download trend is not available in this view yet.

32530 days

86890 days

3.4K1 year

Compare downloads with other packages →

Also on367 r2u11 autocran81 c2d4u

How downloads are counted

Repository

alxsrobert/o2geosocial ↗Account: alxsrobert

8Stars

2Forks

0Open issues

0Open PRs

3Releases

243Commits

1Commit identities

transmission-chain-reconstructionbaysian-inferencemarkov-chain-monte-carlo

243 commits · Last activity 2024-06-21

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 11
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2024-04-21 · 82026-07-07 · 8

How these are measured

PracticesBeta

3 development-tooling and community-health practices detected across 1 family in the upstream repository

Checks run against github.com/alxsrobert/o2geosocial on 2026-10-11.

Continuous integration (3)

GitHub ActionsTravis CI (config file)AppVeyor

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

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Installing o2geosocial adds 46 packages (25 with compiled code, 46 MB of source tarballs). Heaviest: ggplot2 6.0 MB, data.table 5.7 MB, bslib 5.6 MB.

Depends (1)

R >= 3.5.0

Imports (9)

RcppmethodsstatsgrDevicesgeosphere ggplot2 visNetwork data.table outbreaker2

LinkingTo (1)

Rcpp

Suggests (6)

testthat tigris sf knitr socialmixr rmarkdown

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 (4)

Author

Author

Contributor

Releases (6)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
1.1.3Latest
record
2024-06-21 · current release · diff ↗
R
R 4.4.0 released · 2024-04-24
unarchivedReturned to CRAN
2024-03-26
1.1.2
record
2024-03-26 · diff ↗
archivedRemoved from CRAN
2024-01-11
issues were not corrected in time
1.1.1
record
2023-12-12 · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
1.1.0
record
2021-09-11 · diff ↗
R
R 4.1.0 released · 2021-05-18
unarchivedReturned to CRAN
2020-09-25
1.0.1
record
2020-09-25 · diff ↗
archivedRemoved from CRAN
2020-09-10
check problems were not corrected in time
1.0.0
record
2020-08-26

Show 1 earlier eventHide 1 earlier event

R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-08-26
Total releases: 6 / 6 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.5.0
Bundled data: 97 KB / 2 files
Download size: 462 KB

Appears in task views

Epidemiology

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("o2geosocial")

Format

Robert, A., Funk, S., Jombart, T., & Kucharski, A. J. (2024). o2geosocial: Reconstruction of Transmission Chains from Surveillance Data (Version 1.1.3) [Computer software]. https://doi.org/10.32614/CRAN.package.o2geosocial

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 o2geosocial version 1.1.3 [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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