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✨
DESCRIPTION |NEWS
card.svg |card.png
IncidencePrevalence/json (API)

# 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:

On CRAN:

Conda:

7.37 score 12 stars 1 packages 156 scripts 1.2k downloads 30 exports 47 dependencies

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

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source / vignettesOK423
linux-release-x86_64OK223
macos-release-arm64OK126
macos-oldrel-arm64OK152
windows-develOK3060
windows-releaseOK2923
windows-oldrelOK2793
wasm-releaseOK133

Exports:%>%asIncidenceResultasPrevalenceResultattritionavailableIncidenceGroupingavailablePrevalenceGroupingbenchmarkIncidencePrevalencebindcohortCodelistcohortCountestimateIncidenceestimatePeriodPrevalenceestimatePointPrevalenceexportSummarisedResultgenerateDenominatorCohortSetgenerateTargetDenominatorCohortSetimportSummarisedResultmockIncidencePrevalenceoptionsTableIncidenceoptionsTablePrevalenceplotIncidenceplotIncidencePopulationplotPrevalenceplotPrevalencePopulationsettingssuppresstableIncidencetableIncidenceAttritiontablePrevalencetablePrevalenceAttrition

Dependencies:askpassbackportsbitbit64blobCDMConnectorcheckmateclicliprclockcpp11crayoncurlDBIdbplyrdplyrgenericsgluehmshttr2jsonlitelifecyclemagrittromopgenericsopensslPatientProfilespillarpkgconfigprettyunitsprogresspurrrR6rappdirsreadrrlangsnakecasestringistringrsystibbletidyrtidyselecttzdbutf8vctrsvroomwithr

Calculating prevalence
Introduction | Outcome definition | Using estimatePointPrevalence() and estimatePeriodPrevalence() | Using estimatePointPrevalence() | Using estimatePeriodPrevalence() | Stratified analyses | Other parameters | Attrition
Rendered froma04_Calculating_prevalence.Rmdusingknitr::rmarkdown

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

Calculating incidence
Introduction | No washout, no repetitive events | Washout all history, no repetitive events | Some washout, no repetitive events | Some washout, repetitive events | Some washout, repetitive events, censoring event | Outcome definition | Using estimateIncidence() | Stratified analyses | Other parameters | Analysis attrition
Rendered froma05_Calculating_incidence.Rmdusingknitr::rmarkdown

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

Benchmarking the IncidencePrevalence R package
Results from test databases | Results from real databases | Sharing your benchmarking results
Rendered froma07_benchmark.Rmdusingknitr::rmarkdown

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

Working with IncidencePrevalence results
Standardardised results format | Exporting and importing results | Validate minimum cell count suppression | Tidying results for further analysis
Rendered froma06_Working_with_IncidencePrevalence_Results.Rmdusingknitr::rmarkdown

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

Creating denominator cohorts
Introduction | No specific requirements | Specified study period | Specified study period and prior history requirement | Specified study period, prior history requirement, and age and sex criteria | Using generateDenominatorCohortSet() | Multiple options to return multiple denominator populations | Output
Rendered froma02_Creating_denominator_populations.Rmdusingknitr::rmarkdown

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

Creating target denominator populations
Using generateDenominatorCohortSet() with a target cohort | Applying cohort restrictions | Specifying time at risk
Rendered froma03_Creating_target_denominator_populations.Rmdusingknitr::rmarkdown

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

Introduction to IncidencePrevalence
Rendered froma01_Introduction_to_IncidencePrevalence.Rmdusingknitr::rmarkdown

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

Readme and manuals

Help Manual

Help pageTopics
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 plotsavailableIncidenceGrouping
Variables that can be used for faceting and colouring prevalence plotsavailablePrevalenceGrouping
Run benchmark of incidence and prevalence analysesbenchmarkIncidencePrevalence
Collect population incidence estimatesestimateIncidence
Estimate period prevalenceestimatePeriodPrevalence
Estimate point prevalenceestimatePointPrevalence
Identify a set of denominator populationsgenerateDenominatorCohortSet
Identify a set of denominator populations using a target cohortgenerateTargetDenominatorCohortSet
Benchmarking resultsIncidencePrevalenceBenchmarkResults
Generate example subset of the OMOP CDM for estimating incidence and prevalencemockIncidencePrevalence
Additional arguments for the functions tableIncidence.optionsTableIncidence
Additional arguments for the functions tablePrevalence.optionsTablePrevalence
Plot incidence resultsplotIncidence
Bar plot of denominator counts, outcome counts, and person-time from incidence resultsplotIncidencePopulation
Plot prevalence resultsplotPrevalence
Bar plot of denominator and outcome counts from prevalence resultsplotPrevalencePopulation
Table of incidence resultstableIncidence
Table of incidence attrition resultstableIncidenceAttrition
Table of prevalence resultstablePrevalence
Table of prevalence attrition resultstablePrevalenceAttrition