incidence

1.7.6

Compute, Handle, Plot and Model Incidence of Dated Events

7packages depend

33.4Kdownloads / year

98.7%test coverage

13/13checks pass

Overview

About

Maintained by Tim TaylorFirst published 2016-11-0320 releasesCRAN page ↗GitHub ↗

Provides functions and classes to compute, handle and visualise incidence from dated events for a defined time interval. Dates can be provided in various standard formats. The class 'incidence' is used to store computed incidence and can be easily manipulated, subsetted, and plotted. In addition, log-linear models can be fitted to 'incidence' objects using 'fit'. This package is part of the RECON (https://www.repidemicsconsortium.org/) toolkit for outbreak analysis.

Install

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

install.packages("incidence", 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("reconhub/incidence")

Development version from reconhub/incidence. 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-incidence

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

# 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-incidence

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

Health

CRAN checks

13OK

Slowest check: 3.2 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.40

98.7%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 33% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 98%
Return-value docs: 73%
References docs: 0%

Downloads

33.4K

CRAN downloads in the past year

Rank #3,151 · ~91/day · ~2.8K/mo

Releases R versions

Daily download trend is not available in this view yet.

1.5K30 days

4.2K90 days

33.4K1 year

Compare downloads with other packages →

Also on185 r2u37 autocran39 c2d4u

Repository

GitHub ↗ reconhub/incidence

57Stars

14Forks

17Open issues

4Open PRs

16Releases

687Commits

10Contributors

rr-packageoutbreak

687 commits · Last activity 2025-06-19

Stars over time

2024-04-19 · 572026-07-07 · 57

Repository practices

Upstream repositoryBeta

8 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/reconhub/incidence on 2026-07-19.

Continuous integration (3)

GitHub ActionsTravis CIAppVeyor

Reproducibility and dev environment (1)

Makefile

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Show all practices

Lint, format, editor (1)

RStudio project

Coverage (1)

Codecov

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

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (2)

ggplot2 aweek

LinkingTo (0)

none

Suggests (8)

magrittr outbreaks testthat vdiffr knitr rmarkdown scales cowplot

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

7direct

4indirect

EpiEstim ViroReportR epiCo projections earlyR epitrix outbreaks

Code & Tests

People & History

People (8)

Maintainer (1)

Tim Taylor

Maintainer · added in 1.7.3

Authors (3)

Rich FitzJohn

Author

Thibaut Jombart

Author

Zhian N. Kamvar

Author · added in 1.4.1

Contributors (4)

Sangeeta Bhatia

Contributor · added in 1.3.0

Jun Cai

Contributor · added in 1.1.0

Juliet R.C. Pulliam

Contributor · added in 1.5.4

Jakob Schumacher

Contributor · added in 1.5.0

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.7.6Latest
2025-06-19 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
1.7.5
2024-05-31 · diff ↗
1.7.4
2024-05-15 · diff ↗
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.7.3
2020-11-04 · diff ↗
1.7.2
2020-07-24 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.7.1
2020-03-25 · diff ↗
R
R 3.6.0 released · 2019-04-26
1.7.0
2019-03-14 · diff ↗
1.5.4
2019-01-15 · diff ↗

Show 15 earlier events

1.5.2
2018-11-30 · diff ↗
1.5.0
2018-11-01 · diff ↗
1.4.1
2018-08-24 · diff ↗
1.3.1
2018-06-11 · diff ↗
1.3.0
2018-06-01 · diff ↗
R
R 3.5.0 released · 2018-04-23
1.2.1
2017-11-12 · diff ↗
1.2.0
2017-05-15 · diff ↗
R
R 3.4.0 released · 2017-04-21
1.1.2
2017-03-24 · diff ↗
1.1.1
2017-02-15 · diff ↗
1.1.0
2016-12-13 · diff ↗
1.0.1
2016-11-23 · diff ↗
1.0.0
2016-11-03
R
R 3.3.0 released · 2016-05-03

Package metadata

First published: 2016-11-03
Total releases: 20 / 10 yrs
License: MIT + file LICENSE OSI
Download size: 1.5 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Epidemiology

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