Package: CohortConstructor 0.3.2

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-Guell [aut], Elin Rowlands [aut]

CohortConstructor_0.3.2.tar.gz
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CohortConstructor_0.3.2.tgz(r-4.4-any)CohortConstructor_0.3.2.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

Datasets:

On CRAN:

8.96 score 1 stars 1 packages 173 scripts 389 downloads 46 exports 46 dependencies

Last updated 9 days agofrom:ea309623e4. Checks:OK: 1 ERROR: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 12 2024
R-4.5-winERRORNov 12 2024
R-4.5-linuxERRORNov 12 2024
R-4.4-winERRORNov 12 2024
R-4.4-macERRORNov 12 2024
R-4.3-winERRORNov 12 2024
R-4.3-macERRORNov 12 2024

Exports:addCohortTableIndexattritionbindcohortCodelistcohortCountcollapseCohortsconceptCohortdemographicsCohortendDateColumnentryAtFirstDateentryAtLastDateexitAtDeathexitAtFirstDateexitAtLastDateexitAtObservationEndintersectCohortsmatchCohortsmeasurementCohortmockCohortConstructorpadCohortDatepadCohortEndpadCohortStartrequireAgerequireCohortIntersectrequireConceptIntersectrequireDeathFlagrequireDemographicsrequireFutureObservationrequireInDateRangerequireIsEntryrequireIsFirstEntryrequireIsLastEntryrequireMinCohortCountrequirePriorObservationrequireSexrequireTableIntersectsampleCohortssettingsstartDateColumnstratifyCohortssubsetCohortstableNametrimDemographicstrimToDateRangeunionCohortsyearCohorts

Dependencies:backportsbitbit64blobCDMConnectorcheckmateclicliprclockcpp11crayonDBIdbplyrdiffobjdplyrfansifsgenericsgluehmsjsonlitelifecyclemagrittromopgenericsPatientProfilespillarpkgconfigprettyunitsprogresspurrrR6readrrlangsnakecasestringistringrtibbletidyrtidyselecttzdbutf8vctrsvisOmopResultsvroomwaldowithr

Introduction

Rendered froma00_introduction.Rmdusingknitr::rmarkdownon Nov 12 2024.

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

Building base cohorts

Rendered froma01_building_base_cohorts.Rmdusingknitr::rmarkdownon Nov 12 2024.

Last update: 2024-10-23
Started: 2024-05-10

Applying cohort table requirements

Rendered froma02_cohort_table_requirements.Rmdusingknitr::rmarkdownon Nov 12 2024.

Last update: 2024-10-25
Started: 2024-08-28

Applying demographic requirements to a cohort

Rendered froma03_require_demographics.Rmdusingknitr::rmarkdownon Nov 12 2024.

Last update: 2024-10-25
Started: 2024-08-28

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

Rendered froma04_require_intersections.Rmdusingknitr::rmarkdownon Nov 12 2024.

Last update: 2024-10-25
Started: 2024-08-28

Updating cohort start and end dates

Rendered froma05_update_cohort_start_end.Rmdusingknitr::rmarkdownon Nov 12 2024.

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

Concatenating cohort records

Rendered froma06_concatanate_cohorts.Rmdusingknitr::rmarkdownon Nov 12 2024.

Last update: 2024-10-25
Started: 2024-08-28

Filtering cohorts

Rendered froma07_filter_cohorts.Rmdusingknitr::rmarkdownon Nov 12 2024.

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

Splitting cohorts

Rendered froma08_split_cohorts.Rmdusingknitr::rmarkdownon Nov 12 2024.

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

Combining Cohorts

Rendered froma09_combine_cohorts.Rmdusingknitr::rmarkdownon Nov 12 2024.

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

CohortConstructor benchmarking results

Rendered froma11_benchmark.Rmdusingknitr::rmarkdownon Nov 12 2024.

Last update: 2024-10-23
Started: 2024-09-10

Generating a matched cohort

Rendered froma10_match_cohorts.Rmdusingknitr::rmarkdownon Nov 12 2024.

Last update: 2024-10-25
Started: 2024-08-28

Readme and manuals

Help Manual

Help pageTopics
Add an index to a cohort tableaddCohortTableIndex
Benchmarking resultsbenchmarkData
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
Set cohort start or cohort endpadCohortDate
Add days to cohort endpadCohortEnd
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