IncidencePrevalence

1.2.1

Estimate Incidence and Prevalence using the OMOP Common Data Model

5packages depend

11Kdownloads / year

95.1%test coverage

13/13checks pass

Overview

About

Maintained by Edward BurnFirst published 2023-03-2724 releasesCRAN page ↗GitHub ↗

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)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.

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-IncidencePrevalence

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

Health

CRAN checks

13OK

Slowest check: 16.0 min · r-devel-linux-x86_64-fedora-clang

Check history

OK2026-06-23
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-20
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-24
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 6 earlier snapshots

ERROR2026-05-17
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-15
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-05-13
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-02
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-25
11 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

Documentation signals are not tracked yet for this package.

Downloads

11K

CRAN downloads in the past year

Rank #3,817 · ~30/day · ~920/mo

IncidencePrevalence Releases R versions

Daily download trend is not available in this view yet.

78930 days

2.7K90 days

11K1 year

Compare downloads with other packages →

Also on214 r2u26 autocran

Repository

GitHub ↗ darwin-eu/incidenceprevalence

13Stars

8Forks

15Open issues

2Open PRs

20Releases

34Commits

2Contributors

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

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/darwin-eu/incidenceprevalence on 2026-07-19.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Docs source (1)

README.Rmd

Show all practices

Lint, format, editor (1)

RStudio project

Governance and community (1)

Issue templates

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

Dependencies

Declared dependencies

32 external dependencies (excludes base and recommended)

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

5direct

0indirect

PhenotypeR CohortConstructor EpiStandard OmopViewer visOmopResults

Code & Tests

Datasets

People & History

People (8)

Maintainer (1)

Edward Burn

Author, Maintainer

Authors (3)

Edward Burn

Author, Maintainer

Martí Català

Author · added in 1.2.1

Berta Raventos

Author

Contributors (5)

Contributor

Contributor

Contributor

Contributor

Contributor

Listed in earlier versions (1)

Marti Catala

no longer listed · 0.2.0 to 1.2.0

Package Timeline

24 releases. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.2.1Latest
2025-07-22 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
1.2.0
2025-03-08 · diff ↗
1.1.0
2025-02-20 · diff ↗
1.0.0
2025-01-16 · diff ↗
0.9.0
2024-11-27 · diff ↗
0.8.1
2024-11-01 · diff ↗
0.8.0
2024-10-13 · diff ↗
0.7.4
2024-07-01 · diff ↗
0.7.3
2024-06-15 · diff ↗
R
R 4.4.0 released · 2024-04-24
0.7.2
2024-03-21 · diff ↗
0.7.1
2024-02-23 · diff ↗
0.7.0
2024-02-15 · diff ↗
0.6.1
2024-02-09 · diff ↗

Show 13 earlier events

0.6.0
2023-12-11 · diff ↗
0.5.3
2023-11-23 · diff ↗
0.5.2
2023-11-14 · diff ↗
0.5.1
2023-10-18 · diff ↗
0.5.0
2023-10-18 · diff ↗
0.4.1
2023-07-11 · diff ↗
0.4.0
2023-06-18 · diff ↗
0.3.1
2023-06-12 · diff ↗
0.3.0
2023-05-07 · diff ↗
R
R 4.3.0 released · 2023-04-21
0.2.1
2023-04-12 · diff ↗
0.2.0
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)
Download size: 1.6 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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