getdPatientCohort: This function builds a patient cohort (and controls) based on...

In OHDSI/Aphrodite: Automated PHenotype Routine for Observational Definition Identification Training and Evaluation (APHRODITE) - Phenotype building tool using Fuzzy labels

Description

This function will build a patient cohort with its respective controls using an inclusion concept_id list as well as an exclussion concept_id list. The user specifies the number of both cases and controls for his cohort.

Usage

getdPatientCohort(connection, dbms, includeConceptlist, excludeConceptlist,
  schema, cohortSize, controlSize, searchDomain)

Arguments

connection	The connection to the database server.
dbms	The target DBMS for SQL to be rendered in.
includeConceptlist	The list of concept_id's used to build the cohort.
excludeConceptlist	The list of concept_id's used as exclusion criteria for the cohort.
schema	The database schema being used.
cohortSize	The number of desired patients to appear in the cohort.
controlSize	The number of desired patients to be in the control group.

Details

This function takes the lists of include and exclude concept_ids and finds all patients that satisfy this characteristics from the Observation and Condition_occurrence tables in CDM V5.

Value

A list of dataframes containing both cases and control patient_id's.

Examples

## Not run: 

casesANDcontrolspatient_ids_df<- getdPatientCohort(conn, dbms,
         as.character(keywordList_FF$V3), as.character(ignoreList_FF$V3),
         cdmSchema,nCases,nControls)
if (nCases > nrow(casesANDcontrolspatient_ids_df[[1]])) {
     message("Not enough patients to get the number of cases specified")
     stop
} else {
   if (nCases > nrow(casesANDcontrolspatient_ids_df[[2]])) {
       message("Not enough patients to get the number of controls specified")
       stop
   }
}


## End(Not run)

OHDSI/Aphrodite documentation built on Sept. 18, 2020, 10:26 p.m.