Package: CohortConstructor 0.3.5

Edward Burn

CohortConstructor: Build and Manipulate Study Cohorts Using a Common Data Model

Create and manipulate study cohorts in data mapped to the Observational Medical Outcomes Partnership Common Data Model.

Authors:Edward Burn [aut, cre], Marti Catala [aut], Nuria Mercade-Besora [aut], Marta Alcalde-Herraiz [aut], Mike Du [aut], Yuchen Guo [aut], Xihang Chen [aut], Kim Lopez-Guell [aut], Elin Rowlands [aut]

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CohortConstructor.pdf |CohortConstructor.html✨
CohortConstructor/json (API)

# Install 'CohortConstructor' in R:
install.packages('CohortConstructor', repos = c('https://ohdsi.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ohdsi/cohortconstructor/issues

Pkgdown site:https://ohdsi.github.io

Datasets:

On CRAN:

Conda-Forge:

9.70 score 2 stars 2 packages 207 scripts 602 downloads 49 exports 42 dependencies

Last updated 1 days agofrom:27d4187ff9. Checks:9 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 06 2025
R-4.5-winOKMar 06 2025
R-4.5-macOKMar 06 2025
R-4.5-linuxOKMar 06 2025
R-4.4-winOKMar 06 2025
R-4.4-macOKMar 06 2025
R-4.4-linuxOKMar 06 2025
R-4.3-winOKMar 06 2025
R-4.3-macOKMar 06 2025

Exports:addCohortTableIndexattritionbenchmarkCohortConstructorbindcohortCodelistcohortCountcollapseCohortsconceptCohortcopyCohortsdemographicsCohortendDateColumnentryAtFirstDateentryAtLastDateexitAtDeathexitAtFirstDateexitAtLastDateexitAtObservationEndintersectCohortsmatchCohortsmeasurementCohortmockCohortConstructorpadCohortDatepadCohortEndpadCohortStartrenameCohortrequireAgerequireCohortIntersectrequireConceptIntersectrequireDeathFlagrequireDemographicsrequireFutureObservationrequireInDateRangerequireIsEntryrequireIsFirstEntryrequireIsLastEntryrequireMinCohortCountrequirePriorObservationrequireSexrequireTableIntersectsampleCohortssettingsstartDateColumnstratifyCohortssubsetCohortstableNametrimDemographicstrimToDateRangeunionCohortsyearCohorts

Dependencies:backportsbitbit64blobCDMConnectorcheckmateclicliprclockcpp11crayonDBIdbplyrdplyrfansigenericsgluehmsjsonlitelifecyclemagrittromopgenericsPatientProfilespillarpkgconfigprettyunitsprogresspurrrR6readrrlangsnakecasestringistringrtibbletidyrtidyselecttzdbutf8vctrsvroomwithr

Introduction

Rendered froma00_introduction.Rmdusingknitr::rmarkdownon Mar 06 2025.

Last update: 2024-05-22
Started: 2024-05-11

Building base cohorts

Rendered froma01_building_base_cohorts.Rmdusingknitr::rmarkdownon Mar 06 2025.

Last update: 2025-01-14
Started: 2024-05-10

Applying cohort table requirements

Rendered froma02_cohort_table_requirements.Rmdusingknitr::rmarkdownon Mar 06 2025.

Last update: 2025-01-14
Started: 2024-08-28

Applying demographic requirements to a cohort

Rendered froma03_require_demographics.Rmdusingknitr::rmarkdownon Mar 06 2025.

Last update: 2025-01-14
Started: 2024-08-28

Applying requirements related to other cohorts, concept sets, or tables

Rendered froma04_require_intersections.Rmdusingknitr::rmarkdownon Mar 06 2025.

Last update: 2025-01-14
Started: 2024-08-28

Updating cohort start and end dates

Rendered froma05_update_cohort_start_end.Rmdusingknitr::rmarkdownon Mar 06 2025.

Last update: 2024-10-23
Started: 2024-08-28

Concatenating cohort records

Rendered froma06_concatanate_cohorts.Rmdusingknitr::rmarkdownon Mar 06 2025.

Last update: 2025-02-16
Started: 2024-08-28

Filtering cohorts

Rendered froma07_filter_cohorts.Rmdusingknitr::rmarkdownon Mar 06 2025.

Last update: 2025-01-17
Started: 2024-08-28

Splitting cohorts

Rendered froma08_split_cohorts.Rmdusingknitr::rmarkdownon Mar 06 2025.

Last update: 2025-02-16
Started: 2024-08-28

Combining Cohorts

Rendered froma09_combine_cohorts.Rmdusingknitr::rmarkdownon Mar 06 2025.

Last update: 2025-02-16
Started: 2024-08-28

CohortConstructor benchmarking results

Rendered froma11_benchmark.Rmdusingknitr::rmarkdownon Mar 06 2025.

Last update: 2025-02-04
Started: 2024-09-10

Behind the scenes

Rendered froma12_behind_the_scenes.Rmdusingknitr::rmarkdownon Mar 06 2025.

Last update: 2025-02-22
Started: 2025-02-22

Generating a matched cohort

Rendered froma10_match_cohorts.Rmdusingknitr::rmarkdownon Mar 06 2025.

Last update: 2025-01-14
Started: 2024-08-28

Readme and manuals

Help Manual

Help pageTopics
Add an index to a cohort tableaddCohortTableIndex
Run benchmark of CohortConstructor packagebenchmarkCohortConstructor
Benchmarking resultsbenchmarkData
Collapse cohort entries using a certain gap to concatenate records.collapseCohorts
Create cohorts based on a concept setconceptCohort
Copy a cohort tablecopyCohorts
Create cohorts based on patient demographicsdemographicsCohort
Update cohort start date to be the first date from of a set of column datesentryAtFirstDate
Set cohort start date to the last of a set of column datesentryAtLastDate
Set cohort end date to death dateexitAtDeath
Set cohort end date to the first of a set of column datesexitAtFirstDate
Set cohort end date to the last of a set of column datesexitAtLastDate
Set cohort end date to end of observationexitAtObservationEnd
Generate a combination cohort set between the intersection of different cohorts.intersectCohorts
Generate a new cohort matched cohortmatchCohorts
Create cohorts measurement based cohortsmeasurementCohort
Function to create a mock cdm reference for CohortConstructormockCohortConstructor
Set cohort start or cohort endpadCohortDate
Add days to cohort endpadCohortEnd
Add days to cohort startpadCohortStart
Utility function to change the name of a cohort.renameCohort
Restrict cohort on agerequireAge
Require cohort subjects are present (or absence) in another cohortrequireCohortIntersect
Require cohort subjects to have (or not have) events of a concept listrequireConceptIntersect
Require cohort subjects have (or do not have) a death recordrequireDeathFlag
Restrict cohort on patient demographicsrequireDemographics
Restrict cohort on future observationrequireFutureObservation
Require that an index date is within a date rangerequireInDateRange
Restrict cohort to specific entryrequireIsEntry
Restrict cohort to first entryrequireIsFirstEntry
Restrict cohort to last entry per personrequireIsLastEntry
Filter cohorts to keep only records for those with a minimum amount of subjectsrequireMinCohortCount
Restrict cohort on prior observationrequirePriorObservation
Restrict cohort on sexrequireSex
Require cohort subjects are present in another clinical tablerequireTableIntersect
Sample a cohort table for a given number of individuals.sampleCohorts
Create a new cohort table from stratifying an existing onestratifyCohorts
Generate a cohort table keeping a subset of cohorts.subsetCohorts
Restrict cohort on patient demographicstrimDemographics
Trim cohort dates to be within a date rangetrimToDateRange
Generate cohort from the union of different cohortsunionCohorts
Generate a new cohort table restricting cohort entries to certain yearsyearCohorts