Package: IncidencePrevalence 1.0.0

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], Marti Catala [aut], Mike Du [ctb], Yuchen Guo [ctb], Adam Black [ctb], Ger Inberg [ctb], Kim Lopez [ctb]

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IncidencePrevalence.pdf |IncidencePrevalence.html✨
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 site:https://darwin-eu.github.io

Datasets:

On CRAN:

7.96 score 9 stars 1 packages 102 scripts 1.2k downloads 30 exports 42 dependencies

Last updated 1 months agofrom:30e180782d. Checks:5 OK, 3 NOTE. Indexed: yes.

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R-4.4-winOKFeb 15 2025
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R-4.3-winOKFeb 15 2025
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Exports:%>%asIncidenceResultasPrevalenceResultattritionavailableIncidenceGroupingavailablePrevalenceGroupingbenchmarkIncidencePrevalencebindcohortCodelistcohortCountestimateIncidenceestimatePeriodPrevalenceestimatePointPrevalenceexportSummarisedResultgenerateDenominatorCohortSetgenerateTargetDenominatorCohortSetimportSummarisedResultmockIncidencePrevalenceoptionsTableIncidenceoptionsTablePrevalenceplotIncidenceplotIncidencePopulationplotPrevalenceplotPrevalencePopulationsettingssuppresstableIncidencetableIncidenceAttritiontablePrevalencetablePrevalenceAttrition

Dependencies:backportsbitbit64blobCDMConnectorcheckmateclicliprclockcpp11crayonDBIdbplyrdplyrfansigenericsgluehmsjsonlitelifecyclemagrittromopgenericsPatientProfilespillarpkgconfigprettyunitsprogresspurrrR6readrrlangsnakecasestringistringrtibbletidyrtidyselecttzdbutf8vctrsvroomwithr

Introduction to IncidencePrevalence

Rendered froma01_Introduction_to_IncidencePrevalence.Rmdusingknitr::rmarkdownon Feb 15 2025.

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

Creating denominator cohorts

Rendered froma02_Creating_denominator_populations.Rmdusingknitr::rmarkdownon Feb 15 2025.

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

Creating target denominator populations

Rendered froma03_Creating_target_denominator_populations.Rmdusingknitr::rmarkdownon Feb 15 2025.

Last update: 2025-01-16
Started: 2023-12-11

Calculating prevalence

Rendered froma04_Calculating_prevalence.Rmdusingknitr::rmarkdownon Feb 15 2025.

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

Calculating incidence

Rendered froma05_Calculating_incidence.Rmdusingknitr::rmarkdownon Feb 15 2025.

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

Benchmarking the IncidencePrevalence R package

Rendered froma06_benchmark.Rmdusingknitr::rmarkdownon Feb 15 2025.

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

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