R Observatory: Metrics for outbreaker2 version 1.1.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

outbreaker2

1.1.4Package record

Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data

1packages dependsuggested by 1

5Kdownloads / year

60.3%test coverage

13/13flavors OK

Overview

About

Maintained by Finlay CampbellCRAN page ↗

Bayesian reconstruction of disease outbreaks using epidemiological and genetic information. Jombart T, Cori A, Didelot X, Cauchemez S, Fraser C and Ferguson N. 2014. doi:10.1371/journal.pcbi.1003457. Campbell, F, Cori A, Ferguson N, Jombart T. 2019. doi:10.1371/journal.pcbi.1006930.

Changes in 1.1.4

Bug fixes

Added negative_si option to create_config to allow ancestries with negative serial intervals to be immediately discarded.
Removed C++11 SystemRequirements specification (R 4.0+ defaults to C++11)

<br>

From NEWS.md in the release

Install

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

install.packages("outbreaker2", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

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-outbreaker2

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-outbreaker2

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-outbreaker2

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: 15.5 min · r-oldrel-windows-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 1.1.4

READMEYes · 282 wordsVignettesYes · 4 · dynamicNEWSYes · 33% structured · mentions 1.1.4Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 14
Examples that run: 100%10 run in a plain check
Exported functions with examples: 80%
Documented parameters: 100%
Return-value docs: 50%
Help pages citing references: 14%

Vignettes (4)

How these are measured

Downloads

5K

CRAN downloads in the past year

Rank #8,111 · ~14/day · ~413/mo

Releases R versions

Daily download trend is not available in this view yet.

44530 days

1.1K90 days

5K1 year

Compare downloads with other packages →

Also on407 r2u7 autocran85 c2d4u

How downloads are counted

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Installing outbreaker2 adds 43 packages (22 with compiled code, 38 MB of source tarballs). Heaviest: ggplot2 6.0 MB, bslib 5.6 MB, visNetwork 4.1 MB.

Depends (1)

R >= 3.5.0

Imports (9)

utilsmethodsstatsgrDevicesRcpp ape ggplot2 magrittr visNetwork

LinkingTo (1)

Rcpp

Suggests (8)

coda microbenchmark testthat knitr rmarkdown igraph epicontacts adegenet

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Suggested by 1

Depends, Imports or LinkingTo, most downloaded first

o2geosocial

Suggests, most downloaded first

o2ools

How these are counted

Code & Tests

Datasets

People & History

People (6)

Finlay Campbell

Author, Maintainer since 1.0-0 (2017)

Rich Fitzjohn

Author

Thibaut Jombart

Author

Kristjan Eldjarn

Contributor · added in 1.1.2

Alexis Robert

Contributor · added in 1.1.0

Gerry Tonkin-Hill

Contributor · added in 1.0.1

Releases (7)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.1.4Latest
record
2025-12-17 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
1.1.3
record
2022-05-23 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.1.2
record
2021-02-09 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.1.1
record
2020-02-07 · diff ↗
1.1.0
record
2019-06-13 · diff ↗
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
1.0.1
record
2018-03-06 · diff ↗
1.0-0
record
2017-11-28

Show 1 earlier eventHide 1 earlier event

R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2017-11-28
Total releases: 7 / 9 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.5.0
Bundled data: 9.9 KB / 1 file
Download size: 1.3 MB

Appears in task views

Anomaly Detection Epidemiology

Cite

Cite this package

Run in R for the authors' entry:

citation("outbreaker2")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1371/journal.pcbi.1003457.

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 outbreaker2 version 1.1.4 [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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