Package: IncidencePrevalence 1.2.1

Edward Burn

IncidencePrevalence: Estimate Incidence and Prevalence using the OMOP Common Data Model

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.

Authors:Edward Burn [aut, cre], Berta Raventos [aut], Martí Català [aut], Mike Du [ctb], Yuchen Guo [ctb], Adam Black [ctb], Ger Inberg [ctb], Kim Lopez [ctb]

IncidencePrevalence_1.2.1.tar.gz
IncidencePrevalence_1.2.1.zip(r-4.7)IncidencePrevalence_1.2.1.zip(r-4.6)IncidencePrevalence_1.2.1.zip(r-4.5)
IncidencePrevalence_1.2.1.tgz(r-4.6-any)IncidencePrevalence_1.2.1.tgz(r-4.5-any)
IncidencePrevalence_1.2.1.tar.gz(r-4.7-any)IncidencePrevalence_1.2.1.tar.gz(r-4.6-any)
IncidencePrevalence_1.2.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
IncidencePrevalence/json (API)
NEWS

# Install 'IncidencePrevalence' in R:

install.packages('IncidencePrevalence', repos = c('https://darwin-eu.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/darwin-eu/incidenceprevalence/issues

Pkgdown/docs site:https://darwin-eu.github.io

Datasets:

IncidencePrevalenceBenchmarkResults - Benchmarking results

On CRAN:

7.32 score 12 stars 1 packages 164 scripts 976 downloads 30 exports 47 dependencies

Last updated from:1bbb79f5f1. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	230
source / vignettes	OK	444
linux-release-x86_64	OK	238
macos-release-arm64	OK	187
macos-oldrel-arm64	OK	193
windows-devel	OK	233
windows-release	OK	173
windows-oldrel	OK	190
wasm-release	OK	142

Exports:%>%asIncidenceResult asPrevalenceResult attrition availableIncidenceGrouping availablePrevalenceGrouping benchmarkIncidencePrevalence bind cohortCodelist cohortCount estimateIncidence estimatePeriodPrevalence estimatePointPrevalence exportSummarisedResult generateDenominatorCohortSet generateTargetDenominatorCohortSet importSummarisedResult mockIncidencePrevalence optionsTableIncidence optionsTablePrevalence plotIncidence plotIncidencePopulation plotPrevalence plotPrevalencePopulation settings suppress tableIncidence tableIncidenceAttrition tablePrevalence tablePrevalenceAttrition

Dependencies:askpass backports bit bit64 blob CDMConnector checkmate cli clipr clock cpp11 crayon curl DBI dbplyr dplyr generics glue hms httr jsonlite lifecycle magrittr mime omopgenerics openssl PatientProfiles pillar pkgconfig prettyunits progress purrr R6 readr rlang snakecase stringi stringr sys tibble tidyr tidyselect tzdb utf8 vctrs vroom withr

Introduction to IncidencePrevalence

Rendered froma01_Introduction_to_IncidencePrevalence.Rmdusingknitr::rmarkdownon May 08 2026.

Last update: 2025-01-16
Started: 2023-01-27

Creating denominator cohorts

Rendered froma02_Creating_denominator_populations.Rmdusingknitr::rmarkdownon May 08 2026.

Last update: 2025-02-20
Started: 2023-01-27

Creating target denominator populations

Rendered froma03_Creating_target_denominator_populations.Rmdusingknitr::rmarkdownon May 08 2026.

Last update: 2025-02-20
Started: 2023-12-11

Calculating prevalence

Rendered froma04_Calculating_prevalence.Rmdusingknitr::rmarkdownon May 08 2026.

Last update: 2025-07-23
Started: 2023-01-27

Calculating incidence

Rendered froma05_Calculating_incidence.Rmdusingknitr::rmarkdownon May 08 2026.

Last update: 2025-07-23
Started: 2023-01-27

Working with IncidencePrevalence results

Rendered froma06_Working_with_IncidencePrevalence_Results.Rmdusingknitr::rmarkdownon May 08 2026.

Last update: 2025-03-10
Started: 2025-03-10

Benchmarking the IncidencePrevalence R package

Rendered froma07_benchmark.Rmdusingknitr::rmarkdownon May 08 2026.

Last update: 2025-07-23
Started: 2025-03-10

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
A tidy implementation of the summarised_result object for incidence results.	asIncidenceResult
A tidy implementation of the summarised_result object for prevalence results.	asPrevalenceResult
Variables that can be used for faceting and colouring incidence plots	availableIncidenceGrouping
Variables that can be used for faceting and colouring prevalence plots	availablePrevalenceGrouping
Run benchmark of incidence and prevalence analyses	benchmarkIncidencePrevalence
Collect population incidence estimates	estimateIncidence
Estimate period prevalence	estimatePeriodPrevalence
Estimate point prevalence	estimatePointPrevalence
Identify a set of denominator populations	generateDenominatorCohortSet
Identify a set of denominator populations using a target cohort	generateTargetDenominatorCohortSet
Benchmarking results	IncidencePrevalenceBenchmarkResults
Generate example subset of the OMOP CDM for estimating incidence and prevalence	mockIncidencePrevalence
Additional arguments for the functions tableIncidence.	optionsTableIncidence
Additional arguments for the functions tablePrevalence.	optionsTablePrevalence
Plot incidence results	plotIncidence
Bar plot of denominator counts, outcome counts, and person-time from incidence results	plotIncidencePopulation
Plot prevalence results	plotPrevalence
Bar plot of denominator and outcome counts from prevalence results	plotPrevalencePopulation
Table of incidence results	tableIncidence
Table of incidence attrition results	tableIncidenceAttrition
Table of prevalence results	tablePrevalence
Table of prevalence attrition results	tablePrevalenceAttrition