Package: CohortGenerator 0.11.2

Anthony Sena

CohortGenerator: Cohort Generation for the OMOP Common Data Model

Generate cohorts and subsets using an Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) Database. Cohorts are defined using 'CIRCE' (<https://github.com/ohdsi/circe-be>) or SQL compatible with 'SqlRender' (<https://github.com/OHDSI/SqlRender>).

Authors:Anthony Sena [aut, cre], Jamie Gilbert [aut], Gowtham Rao [aut], Martijn Schuemie [aut], Observational Health Data Science and Informatics [cph]

CohortGenerator_0.11.2.tar.gz
CohortGenerator_0.11.2.tar.gz(r-4.5-noble)CohortGenerator_0.11.2.tar.gz(r-4.4-noble)
CohortGenerator_0.11.2.tgz(r-4.4-emscripten)CohortGenerator_0.11.2.tgz(r-4.3-emscripten)
CohortGenerator.pdf |CohortGenerator.html✨
CohortGenerator/json (API)
NEWS

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

Peer review:

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

Uses libs:
  • openjdk– OpenJDK Java runtime, using Hotspot JIT

4.70 score 167 scripts 758 downloads 47 exports 55 dependencies

Last updated 2 months agofrom:89f9d8ecc5. Checks:OK: 1 WARNING: 1. Indexed: no.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-linuxWARNINGOct 31 2024

Exports:addCohortSubsetDefinitioncheckAndFixCohortDefinitionSetDataTypesCohortSubsetDefinitionCohortSubsetOperatorcomputeChecksumcreateCohortSubsetcreateCohortSubsetDefinitioncreateCohortTablescreateDemographicSubsetcreateEmptyCohortDefinitionSetcreateEmptyNegativeControlOutcomeCohortSetcreateLimitSubsetcreateResultsDataModelcreateSubsetCohortWindowDemographicSubsetOperatordropCohortStatsTablesexportCohortStatsTablesgenerateCohortSetgenerateNegativeControlOutcomeCohortsgetCohortCountsgetCohortDefinitionSetgetCohortInclusionRulesgetCohortStatsgetCohortTableNamesgetDataMigratorgetRequiredTasksgetResultsDataModelSpecificationsgetSubsetDefinitionsinsertInclusionRuleNamesisCamelCaseisCohortDefinitionSetisFormattedForDatabaseUploadisSnakeCaseisTaskRequiredLimitSubsetOperatormigrateDataModelreadCsvrecordTasksDonerunCohortGenerationsampleCohortDefinitionSetsaveCohortDefinitionSetsaveCohortSubsetDefinitionsaveIncrementalSubsetCohortWindowSubsetOperatoruploadResultswriteCsv

Dependencies:backportsbitbit64blobcheckmateclicliprcpp11crayonDatabaseConnectorDBIdbplyrdigestdplyrfansifastmapgenericsgluehmsjsonlitelaterlifecyclelubridatemagrittrParallelLoggerpillarpkgconfigpoolprettyunitsprogresspurrrR6RcppreadrResultModelManagerrJavaRJSONIOrlangsnowSqlRenderstringistringrtibbletidyrtidyselecttimechangetriebeardtzdburltoolsutf8vctrsvroomwithrxml2zip

Creating Cohort Subset Definitions

James P. Gilbert and Anthony G. Sena

Rendered fromCreatingCohortSubsetDefinitions.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-10-01
Started: 2024-09-16

Generating Cohorts

Anthony G. Sena and Martijn J. Schuemie

Rendered fromGeneratingCohorts.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-10-01
Started: 2024-09-16

Sampling Cohorts

James P. Gilbert

Rendered fromSamplingCohorts.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-10-01
Started: 2024-09-16

Readme and manuals

Help Manual

Help pageTopics
Add cohort subset definition to a cohort definition setaddCohortSubsetDefinition
Check if a cohort definition set is using the proper data typescheckAndFixCohortDefinitionSetDataTypes
Cohort Subset DefinitionCohortSubsetDefinition
Cohort Subset OperatorCohortSubsetOperator
Computes the checksum for a valuecomputeChecksum
A definition of subset functions to be applied to a set of cohortscreateCohortSubset
Create Subset DefinitioncreateCohortSubsetDefinition
Create cohort tablescreateCohortTables
Create createDemographicSubset SubsetcreateDemographicSubset
Create an empty cohort definition setcreateEmptyCohortDefinitionSet
Create an empty negative control outcome cohort setcreateEmptyNegativeControlOutcomeCohortSet
Create Limit SubsetcreateLimitSubset
Create the results data model tables on a database server.createResultsDataModel
A definition of subset functions to be applied to a set of cohortscreateSubsetCohortWindow
Demographic Subset OperatorDemographicSubsetOperator
Drop cohort statistics tablesdropCohortStatsTables
Export the cohort statistics tables to the file systemexportCohortStatsTables
Generate a set of cohortsgenerateCohortSet
Generate a set of negative control outcome cohortsgenerateNegativeControlOutcomeCohorts
Count the cohort(s)getCohortCounts
Get a cohort definition setgetCohortDefinitionSet
Get Cohort Inclusion Rules from a cohort definition setgetCohortInclusionRules
Get Cohort Inclusion Stats Table DatagetCohortStats
Used to get a list of cohort table names to use when creating the cohort tablesgetCohortTableNames
Get database migrations instancegetDataMigrator
Get a list of tasks required when running in incremental modegetRequiredTasks
Get specifications for CohortGenerator results data modelgetResultsDataModelSpecifications
Get cohort subset definitions from a cohort definition setgetSubsetDefinitions
Used to insert the inclusion rule names from a cohort definition set when generating cohorts that include cohort statisticsinsertInclusionRuleNames
Used to check if a string is in lower camel caseisCamelCase
Is the data.frame a cohort definition set?isCohortDefinitionSet
Is the data.frame formatted for uploading to a database?isFormattedForDatabaseUpload
Used to check if a string is in snake caseisSnakeCase
Is a task required when running in incremental modeisTaskRequired
Limit Subset OperatorLimitSubsetOperator
Migrate Data modelmigrateDataModel
Used to read a .csv filereadCsv
Record a task as completerecordTasksDone
Run a cohort generation and export resultsrunCohortGeneration
Sample Cohort Definition SetsampleCohortDefinitionSet
Save the cohort definition set to the file systemsaveCohortDefinitionSet
Save cohort subset definitions to jsonsaveCohortSubsetDefinition
Used in incremental mode to save values to a filesaveIncremental
Time Window For Cohort Subset OperatorSubsetCohortWindow
Abstract base class for subsets.SubsetOperator
Upload results to the database server.uploadResults
Used to write a .csv filewriteCsv