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
CohortConstructor_0.3.2.tar.gz(r-4.5-noble)CohortConstructor_0.3.2.tar.gz(r-4.4-noble)
CohortConstructor_0.3.2.tgz(r-4.4-emscripten)CohortConstructor_0.3.2.tgz(r-4.3-emscripten)
CohortConstructor.pdf |CohortConstructor.html✨
CohortConstructor/json (API)

# Install 'CohortConstructor' in R:

install.packages('CohortConstructor', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

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

Datasets:

benchmarkData - Benchmarking results

6.27 score 1 packages 173 scripts 376 downloads 46 exports 46 dependencies

Last updated 10 days agofrom:9b57a0f253. Checks:OK: 2. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Nov 12 2024
R-4.5-linux	OK	Nov 12 2024

Exports:addCohortTableIndex attrition bind cohortCodelist cohortCount collapseCohorts conceptCohort demographicsCohort endDateColumn entryAtFirstDate entryAtLastDate exitAtDeath exitAtFirstDate exitAtLastDate exitAtObservationEnd intersectCohorts matchCohorts measurementCohort mockCohortConstructor padCohortDate padCohortEnd padCohortStart requireAge requireCohortIntersect requireConceptIntersect requireDeathFlag requireDemographics requireFutureObservation requireInDateRange requireIsEntry requireIsFirstEntry requireIsLastEntry requireMinCohortCount requirePriorObservation requireSex requireTableIntersect sampleCohorts settings startDateColumn stratifyCohorts subsetCohorts tableName trimDemographics trimToDateRange unionCohorts yearCohorts

Dependencies:backports bit bit64 blob CDMConnector checkmate cli clipr clock cpp11 crayon DBI dbplyr diffobj dplyr fansi fs generics glue hms jsonlite lifecycle magrittr omopgenerics PatientProfiles pillar pkgconfig prettyunits progress purrr R6 readr rlang snakecase stringi stringr tibble tidyr tidyselect tzdb utf8 vctrs visOmopResults vroom waldo withr

Introduction

Rendered froma00_introduction.Rmdusingknitr::rmarkdownon Nov 12 2024.

Last update: 2024-11-11
Started: 2024-06-02

Building base cohorts

Rendered froma01_building_base_cohorts.Rmdusingknitr::rmarkdownon Nov 12 2024.

Last update: 2024-11-11
Started: 2024-06-02

Applying cohort table requirements

Rendered froma02_cohort_table_requirements.Rmdusingknitr::rmarkdownon Nov 12 2024.

Last update: 2024-11-11
Started: 2024-09-25

Applying demographic requirements to a cohort

Rendered froma03_require_demographics.Rmdusingknitr::rmarkdownon Nov 12 2024.

Last update: 2024-11-11
Started: 2024-09-25

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

Rendered froma04_require_intersections.Rmdusingknitr::rmarkdownon Nov 12 2024.

Last update: 2024-11-11
Started: 2024-09-25

Updating cohort start and end dates

Rendered froma05_update_cohort_start_end.Rmdusingknitr::rmarkdownon Nov 12 2024.

Last update: 2024-11-11
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Concatenating cohort records

Rendered froma06_concatanate_cohorts.Rmdusingknitr::rmarkdownon Nov 12 2024.

Last update: 2024-11-11
Started: 2024-09-25

Filtering cohorts

Rendered froma07_filter_cohorts.Rmdusingknitr::rmarkdownon Nov 12 2024.

Last update: 2024-11-11
Started: 2024-09-25

Splitting cohorts

Rendered froma08_split_cohorts.Rmdusingknitr::rmarkdownon Nov 12 2024.

Last update: 2024-11-11
Started: 2024-09-25

Combining Cohorts

Rendered froma09_combine_cohorts.Rmdusingknitr::rmarkdownon Nov 12 2024.

Last update: 2024-11-11
Started: 2024-09-25

CohortConstructor benchmarking results

Rendered froma11_benchmark.Rmdusingknitr::rmarkdownon Nov 12 2024.

Last update: 2024-11-11
Started: 2024-09-25

Generating a matched cohort

Rendered froma10_match_cohorts.Rmdusingknitr::rmarkdownon Nov 12 2024.

Last update: 2024-11-11
Started: 2024-09-25

Citation

Readme and manuals

Help Manual

Help page	Topics
Add an index to a cohort table	addCohortTableIndex
Benchmarking results	benchmarkData
Collapse cohort entries using a certain gap to concatenate records.	collapseCohorts
Create cohorts based on a concept set	conceptCohort
Create cohorts based on patient demographics	demographicsCohort
Update cohort start date to be the first date from of a set of column dates	entryAtFirstDate
Set cohort start date to the last of a set of column dates	entryAtLastDate
Set cohort end date to death date	exitAtDeath
Set cohort end date to the first of a set of column dates	exitAtFirstDate
Set cohort end date to the last of a set of column dates	exitAtLastDate
Set cohort end date to end of observation	exitAtObservationEnd
Generate a combination cohort set between the intersection of different cohorts.	intersectCohorts
Generate a new cohort matched cohort	matchCohorts
Create cohorts measurement based cohorts	measurementCohort
Function to create a mock cdm reference for CohortConstructor	mockCohortConstructor
Set cohort start or cohort end	padCohortDate
Add days to cohort end	padCohortEnd
Add days to cohort start	padCohortStart
Restrict cohort on age	requireAge
Require cohort subjects are present (or absence) in another cohort	requireCohortIntersect
Require cohort subjects to have (or not have) events of a concept list	requireConceptIntersect
Require cohort subjects have (or do not have) a death record	requireDeathFlag
Restrict cohort on patient demographics	requireDemographics
Restrict cohort on future observation	requireFutureObservation
Require that an index date is within a date range	requireInDateRange
Restrict cohort to specific entry	requireIsEntry
Restrict cohort to first entry	requireIsFirstEntry
Restrict cohort to last entry per person	requireIsLastEntry
Filter cohorts to keep only records for those with a minimum amount of subjects	requireMinCohortCount
Restrict cohort on prior observation	requirePriorObservation
Restrict cohort on sex	requireSex
Require cohort subjects are present in another clinical table	requireTableIntersect
Sample a cohort table for a given number of individuals.	sampleCohorts
Create a new cohort table from stratifying an existing one	stratifyCohorts
Generate a cohort table keeping a subset of cohorts.	subsetCohorts
Restrict cohort on patient demographics	trimDemographics
Trim cohort dates to be within a date range	trimToDateRange
Generate cohort from the union of different cohorts	unionCohorts
Generate a new cohort table restricting cohort entries to certain years	yearCohorts

Usage by other packages (reverse dependencies)