Package: CohortConstructor 0.2.2

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 [aut]

CohortConstructor_0.2.2.tar.gz
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CohortConstructor_0.2.2.tgz(r-4.4-any)CohortConstructor_0.2.2.tgz(r-4.3-any)
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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'))

Peer review:

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

On CRAN:

43 exports 1 stars 2.74 score 46 dependencies 145 scripts 369 downloads

Last updated 7 days agofrom:5c2144acd9. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 11 2024
R-4.5-winOKSep 11 2024
R-4.5-linuxOKSep 11 2024
R-4.4-winOKSep 11 2024
R-4.4-macOKSep 11 2024
R-4.3-winOKSep 11 2024
R-4.3-macOKSep 11 2024

Exports:attritionbindcohortCodelistcohortCountcollapseCohortsconceptCohortdemographicsCohortendDateColumnentryAtFirstDateentryAtLastDateexitAtDeathexitAtFirstDateexitAtLastDateexitAtObservationEndintersectCohortsmatchCohortsmeasurementCohortmockCohortConstructorpadCohortStartrequireAgerequireCohortIntersectrequireConceptIntersectrequireDeathFlagrequireDemographicsrequireFutureObservationrequireInDateRangerequireIsEntryrequireIsFirstEntryrequireIsLastEntryrequireMinCohortCountrequirePriorObservationrequireSexrequireTableIntersectsampleCohortssettingsstartDateColumnstratifyCohortssubsetCohortstableNametrimDemographicstrimToDateRangeunionCohortsyearCohorts

Dependencies:backportsbitbit64blobCDMConnectorcheckmateclicliprcpp11crayonDBIdbplyrdiffobjdplyrfansifsgenericsgluehmsjsonlitelifecyclemagrittromopgenericsPatientProfilespillarpkgconfigprettyunitsprogresspurrrR6readrrematch2rlangsnakecasestringistringrtibbletidyrtidyselecttzdbutf8vctrsvisOmopResultsvroomwaldowithr

Introduction

Rendered froma00_introduction.Rmdusingknitr::rmarkdownon Sep 11 2024.

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

Building base cohorts

Rendered froma01_building_base_cohorts.Rmdusingknitr::rmarkdownon Sep 11 2024.

Last update: 2024-09-06
Started: 2024-05-10

Cohort Requirements

Rendered froma02_cohort_table_requirements.Rmdusingknitr::rmarkdownon Sep 11 2024.

Last update: 2024-09-04
Started: 2024-08-28

Demographic Requirements

Rendered froma03_require_demographics.Rmdusingknitr::rmarkdownon Sep 11 2024.

Last update: 2024-09-03
Started: 2024-08-28

Requirements on Presence and Absence

Rendered froma04_require_intersections.Rmdusingknitr::rmarkdownon Sep 11 2024.

Last update: 2024-09-10
Started: 2024-08-28

Update cohort start and end dates

Rendered froma05_update_cohort_start_end.Rmdusingknitr::rmarkdownon Sep 11 2024.

Last update: 2024-09-11
Started: 2024-08-28

Concatenate Cohorts

Rendered froma06_concatanate_cohorts.Rmdusingknitr::rmarkdownon Sep 11 2024.

Last update: 2024-09-11
Started: 2024-08-28

a06_filter_cohorts

Rendered froma07_filter_cohorts.Rmdusingknitr::rmarkdownon Sep 11 2024.

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

a07_split_cohorts

Rendered froma08_split_cohorts.Rmdusingknitr::rmarkdownon Sep 11 2024.

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

a08_combine_cohorts

Rendered froma09_combine_cohorts.Rmdusingknitr::rmarkdownon Sep 11 2024.

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

CohortConstructor benchmark

Rendered froma11_benchmark.Rmdusingknitr::rmarkdownon Sep 11 2024.

Last update: 2024-09-10
Started: 2024-09-10

Generate a matched age and sex cohort

Rendered froma10_match_cohorts.Rmdusingknitr::rmarkdownon Sep 11 2024.

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

Readme and manuals

Help Manual

Help pageTopics
Collapse cohort entries using a certain gap to concatenate records.collapseCohorts
Create cohorts based on a concept setconceptCohort
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
Add days to cohort startpadCohortStart
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