R Observatory: Metrics for IncidencePrevalence version 1.2.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

IncidencePrevalence

1.2.1Package record

Estimate Incidence and Prevalence using the OMOP Common Data Model

1packages dependsuggested by 3

10.6Kdownloads / year

95.1%test coverage

13/13flavors OK

Overview

About

Maintained by Edward BurnCRAN page ↗GitHub ↗Website ↗Issues ↗

Calculate incidence and prevalence using data mapped to the Observational Medical Outcomes Partnership (OMOP) common data model. Incidence and prevalence can be estimated for the total population in a database or for a stratification cohort.

Install

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

install.packages("IncidencePrevalence", 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("darwin-eu/IncidencePrevalence")

Development version from darwin-eu/IncidencePrevalence. 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-incidenceprevalence

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-IncidencePrevalence

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-IncidencePrevalence

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: 14.1 min · r-release-macos-x86_64

Status changes

OK13 OK2026-09-30
ERROR12 OK, 1 ERROR2026-09-04
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-23

Show 10 earlier changesHide 10 earlier changes

ERROR12 OK, 1 ERROR2026-06-20
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-24
ERROR12 OK, 1 ERROR2026-05-17
OK13 OK2026-05-15
ERROR12 OK, 1 ERROR2026-05-13
OK13 OK2026-05-02
ERROR11 OK, 1 ERROR2026-04-25
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.2.1

READMEYes · 481 wordsVignettesYes · 7 · evaluation depends on the environmentNEWSYes · 100% structured · does not mention 1.2.1Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 25 (3 internal)includes a package overview page
Examples that run: 10%2 run in a plain check · 19 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 91%
Documented parameters: 97%
Return-value docs: 86%
Help pages citing references: 0%

Vignettes (7)

a01_Introduction_to_IncidencePrevalence HTML
a02_Creating_denominator_cohorts HTML
a03_Creating_target_denominator_populations HTML
a04_Calculating_prevalence HTML
a05_Calculating_incidence HTML
a06_Working_with_IncidencePrevalence_Results HTML
a07_benchmark HTML

How these are measured

Downloads

10.6K

CRAN downloads in the past year

Rank #3,679 · ~29/day · ~880/mo

Releases R versions

Daily download trend is not available in this view yet.

1K30 days

2.7K90 days

10.6K1 year

Compare downloads with other packages →

Also on184 r2u8 autocran

How downloads are counted

Repository

darwin-eu/incidenceprevalence ↗Organization: darwin-eu

15Stars

8Forks

17Open issues

2Open PRs

20Releases

34Commits

2Commit identities

34 commits · Last activity 2025-07-23 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 37
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-09-11 · 102026-09-08 · 15

How these are measured

PracticesBeta

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

Checks run against github.com/darwin-eu/incidenceprevalence on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux

Governance and community (2)

Contributing guideIssue templates

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2025-07-23 · The repository has a site deploy workflow

pkgdown site last built 2025-07-23

Coverage (1)

Coverage reporting

Show all practicesHide 3 practices

Reproducibility and dev environment (1)

data-raw/

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

32 external dependencies (excludes base and recommended)

Installing IncidencePrevalence adds 46 packages (25 with compiled code, 31 MB of source tarballs). Heaviest: stringi 11 MB, CDMConnector 4.0 MB, openssl 1.1 MB.

Depends (1)

R >= 4.1

Imports (12)

CDMConnector cli clock dplyr (>= 1.1.0)glue omopgenerics magrittr (>= 2.0.0)PatientProfiles purrr rlang (>= 1.0.0)stringr tidyr

LinkingTo (0)

none

Suggests (20)

knitr dbplyr rmarkdown RPostgres duckdb DBI odbc here Hmisc epitools tictoc testthat (>= 0.3.1)spelling gt flextable ggplot2 scales (>= 1.1.0)visOmopResults patchwork binom

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Suggested by 3

Depends, Imports or LinkingTo, most downloaded first

PhenotypeR

Suggests, most downloaded first

visOmopResults CohortConstructor EpiStandard

How these are counted

Code & Tests

Datasets

People & History

People (8)

Edward Burn

Author, Maintainer since 0.2.0 (2023)

Martí Català

Author · added in 1.2.1

Author

Contributor

Contributor

Contributor

Contributor

Contributor

Listed in earlier versions (1)

Marti Catala

no longer listed · 0.2.0 to 1.2.0

Releases (24)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.2.1Latest
record
2025-07-22 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
1.2.0
record
2025-03-08 · diff ↗
1.1.0
record
2025-02-20 · diff ↗
1.0.0
record
2025-01-16 · diff ↗ ·
removed 2 exports
mockIncidencePrevalenceRef, optionsPlot

added 6 exports
asIncidenceResult, asPrevalenceResult, availableIncidenceGrouping, availablePrevalenceGrouping, plotIncidencePopulation, plotPrevalencePopulation
0.9.0
record
2024-11-27 · diff ↗ ·
added 2 exports
mockIncidencePrevalence, optionsPlot
0.8.1
record
2024-11-01 · diff ↗
0.8.0
record
2024-10-13 · diff ↗ ·
removed 1 export
participants

added 5 exports
importSummarisedResult, tableIncidence, tableIncidenceAttrition, tablePrevalence, tablePrevalenceAttrition
0.7.4
record
2024-07-01 · diff ↗ ·
removed 7 exports
bindIncidenceEstimates, bindPrevalenceEstimates, exportIncidencePrevalenceResults, incidenceAttrition, incidenceSet, prevalenceAttrition, prevalenceSet

added 6 exports
bind, cohortCodelist, exportSummarisedResult, optionsTableIncidence, optionsTablePrevalence, suppress
0.7.3
record
2024-06-15 · diff ↗
R
R 4.4.0 released · 2024-04-24
0.7.2
record
2024-03-21 · diff ↗
0.7.1
record
2024-02-23 · diff ↗ ·
added 3 exports
attrition, cohortCount, settings
0.7.0
record
2024-02-15 · diff ↗
0.6.1
record
2024-02-09 · diff ↗

Show 13 earlier eventsHide 13 earlier events

0.6.0
record
2023-12-11 · diff ↗ ·
added 1 export
generateTargetDenominatorCohortSet
0.5.3
record
2023-11-23 · diff ↗
0.5.2
record
2023-11-14 · diff ↗
0.5.1
record
2023-10-18 · diff ↗
0.5.0
record
2023-10-18 · diff ↗
0.4.1
record
2023-07-11 · diff ↗
0.4.0
record
2023-06-18 · diff ↗
0.3.1
record
2023-06-12 · diff ↗
0.3.0
record
2023-05-07 · diff ↗ ·
removed 1 export
gatherIncidencePrevalenceResults

added 4 exports
bindIncidenceEstimates, bindPrevalenceEstimates, plotIncidence, plotPrevalence
R
R 4.3.0 released · 2023-04-21
0.2.1
record
2023-04-12 · diff ↗
0.2.0
record
2023-03-27
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2023-03-27
Total releases: 24 / 3 yrs
License: Apache License (>= 2)
Minimum R: ≥ 4.1
Bundled data: 1.1 KB / 1 file
Download size: 1.6 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("IncidencePrevalence")

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

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 IncidencePrevalence version 1.2.1 [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 →