R Observatory: Metrics for incidence version 1.7.6

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

incidence

1.7.6Package record

Compute, Handle, Plot and Model Incidence of Dated Events

4packages dependsuggested by 2

27.1Kdownloads / year

98.7%test coverage

13/13flavors OK

Overview

About

Maintained by Tim TaylorCRAN page ↗GitHub ↗Website ↗Issues ↗

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.

Changes in 1.7.6

No user facing changes. Fixes some internal oddities flagged by @teunbrand whilst running ggplot2 reverse dependency checks.

From NEWS.md in the release

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)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. 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-incidence

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-incidence

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: 2.8 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.7.6

README· In the repository, left out of the releaseVignettesYes · 5 · dynamicNEWSYes · 33% structured · mentions 1.7.6Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 16
Examples that run: 100%16 run in a plain check
Exported functions with examples: 100%
Documented parameters: 98%
Return-value docs: 73%
Help pages citing references: 0%

Also includes 1 demo script (run with demo())

Vignettes (5)

How these are measured

Downloads

27.1K

CRAN downloads in the past year

Rank #2,215 · ~74/day · ~2.3K/mo

Releases R versions

Daily download trend is not available in this view yet.

1.7K30 days

7.7K90 days

27.1K1 year

Compare downloads with other packages →

Also on211 r2u15 autocran93 c2d4u

How downloads are counted

Repository

reconhub/incidence ↗Organization: reconhub

57Stars

14Forks

17Open issues

4Open PRs

16Releases

687Commits

10Commit identities

rr-packageoutbreak

687 commits · Last activity 2025-06-19 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 92%
Median days to close, 50 most recently updated closed issues: 2
Median days to close, 50 most recently updated closed PRs: 1

Stars over time

2024-04-19 · 572026-07-07 · 57

How these are measured

PracticesBeta

12 development-tooling and community-health practices detected across 7 families in the upstream repository

Checks run against github.com/reconhub/incidence on 2026-10-11.

Continuous integration (4)

GitHub ActionsR CMD check workflowTravis CI (config file)AppVeyor

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Governance and community (1)

Code of conduct

Docs source (3)

README.Rmdpkgdown

GitHub Pages site last deployed 2025-06-19

Coverage (1)

Coverage reporting (Codecov)

Show all practicesHide 3 practices

Reproducibility and dev environment (1)

Makefile

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Installing incidence adds 18 packages (7 with compiled code, 14 MB of source tarballs). Heaviest: ggplot2 6.0 MB, isoband 1.5 MB, farver 1.2 MB.

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

4direct

3indirect

Imports 4

Suggested by 2

Depends, Imports or LinkingTo, most downloaded first

EpiEstim projections epiCo ViroReportR

Suggests, most downloaded first

outbreaks epitrix

How these are counted

Code & Tests

People & History

People (8)

Tim Taylor

Maintainer since 1.7.3 (2020) · added in 1.7.3

Rich FitzJohn

Author

Thibaut Jombart

Author

Zhian N. Kamvar

Author · added in 1.4.1

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

Previously maintained by Zhian N. Kamvar (1.4.1 to 1.7.2) and Thibaut Jombart (1.0.0 to 1.3.1).

Releases (20)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.7.6Latest
record
2025-06-19 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
1.7.5
record
2024-05-31 · diff ↗
1.7.4
record
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
record
2020-11-04 · diff ↗
1.7.2
record
2020-07-24 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.7.1
record
2020-03-25 · diff ↗
R
R 3.6.0 released · 2019-04-26
1.7.0
record
2019-03-14 · diff ↗ ·
added 2 exports
make_breaks, scale_x_incidence
1.5.4
record
2019-01-15 · diff ↗

Show 15 earlier eventsHide 15 earlier events

1.5.2
record
2018-11-30 · diff ↗
1.5.0
record
2018-11-01 · diff ↗ ·
added 4 exports
group_names<-, get_n, get_timespan, group_names
1.4.1
record
2018-08-24 · diff ↗ ·
added 8 exports
bootstrap, estimate_peak, find_peak, get_counts, get_dates, get_fit, get_info, get_interval
1.3.1
record
2018-06-11 · diff ↗
1.3.0
record
2018-06-01 · diff ↗ ·
removed 3 exports
pal1, pal1dark, pal1light

added 5 exports
add_incidence_fit, cumulate, incidence_pal1, incidence_pal1_dark, incidence_pal1_light
R
R 3.5.0 released · 2018-04-23
1.2.1
record
2017-11-12 · diff ↗
1.2.0
record
2017-05-15 · diff ↗ ·
added 1 export
as.incidence
R
R 3.4.0 released · 2017-04-21
1.1.2
record
2017-03-24 · diff ↗
1.1.1
record
2017-02-15 · diff ↗
1.1.0
record
2016-12-13 · diff ↗
1.0.1
record
2016-11-23 · diff ↗
1.0.0
record
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

Appears in task views

Epidemiology

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("incidence")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

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 incidence version 1.7.6 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →