outbreaker2

1.1.4

Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data

2packages depend

5.7Kdownloads / year

60.3%test coverage

13/13checks pass

Overview

About

Maintained by Finlay CampbellFirst published 2017-11-287 releasesCRAN 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.

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.

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).

Health

CRAN checks

13OK

Slowest check: 20.9 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.51

60.3%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-04-22
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 282 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 33% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 50%
References docs: 14%

Downloads

5.7K

CRAN downloads in the past year

Rank #8,779 · ~16/day · ~475/mo

Releases R versions

Daily download trend is not available in this view yet.

45430 days

1.3K90 days

5.7K1 year

Compare downloads with other packages →

Also on426 r2u29 autocran55 c2d4u

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

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

2direct

0indirect

o2geosocial o2ools

Code & Tests

Code Composition

R 6,142 (57%)C++ 2,231 (21%)Vignettes 1,154 (11%)Rd 1,099 (10%)C 169 (2%)Other 5 (0%)

Code characteristics

Object systems

S37

Cyclomatic complexity: 1.0 median / 123 max
Test cases: 47 / 0.51 per code line

Test coverage

Line coverage

60%

Expression

59.4%

Tests / Examples

60.3% / – ex

Functions

145 11 exported

Complexity

4.7 avg / 123 max

Call network

145 nodes / 99 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

145 functions

Function	Cyclo	Coverage
cases_pal exp	1	0%
chains_pal exp	1	0%
get_cpp_api exp	2	0%
can_be_swapped	1	0%
check_i	2	0%
look_for_trouble	20	0%

People & History

People (6)

Maintainer (1)

Finlay Campbell

Author, Maintainer

Authors (3)

Finlay Campbell

Author, Maintainer

Rich Fitzjohn

Author

Thibaut Jombart

Author

Contributors (3)

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

Package Timeline

7 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.1.4Latest
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
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
2021-02-09 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.1.1
2020-02-07 · diff ↗
1.1.0
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
2018-03-06 · diff ↗
1.0-0
2017-11-28

Show 1 earlier events

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
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Anomaly Detection Epidemiology

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