insertCohortDefinitionInPackage: Load a cohort definition and insert it into this package

In OHDSI/ROhdsiWebApi: Interacting With an OHDSI WebApi Instance

Load a cohort definition and insert it into this package

Description

Load a cohort definition and insert it into this package

Usage

insertCohortDefinitionInPackage(
  cohortId,
  name = NULL,
  jsonFolder = "inst/cohorts",
  sqlFolder = "inst/sql/sql_server",
  baseUrl,
  generateStats = FALSE
)

Arguments

cohortId	An integer id representing the id that uniquely identifies a cohort definition in a WebApi instance.
name	The name that will be used for the JSON and SQL files. If not provided, the name in cohort will be used, but this may not lead to valid file names.
jsonFolder	Path to the folder where the JSON representation will be saved.
sqlFolder	Path to the folder where the SQL representation will be saved.
baseUrl	The base URL for the WebApi instance, for example: "http://server.org:80/WebAPI".
generateStats	Should the SQL include the code for generating inclusion rule statistics? Note that if TRUE, several additional tables are expected to exists as described in the details.

Details

Load a cohort definition from a WebApi instance and insert it into this package. This will fetch the JSON object and store it in a folder (defaults to 'the inst/cohorts' folder), and fetch the template SQL and store it in another folder (defaults to the 'inst/sql/sql_server' folder). Both folders will be created if they don't exist. When using generateStats = TRUE, the following tables are required to exist when executing the SQL: cohort_inclusion, cohort_inclusion_result, cohort_inclusion_stats, and cohort_summary_stats. Also note that the cohort_inclusion table should be populated with the names of the rules prior to executing the cohort definition SQL. Note: generate inclusion statistics are created for all by default.

Examples

## Not run: 
# This will create 'inst/cohorts/Angioedema.json' and 'inst/sql/sql_server/Angioedema.sql':

insertCohortDefinitionInPackage(cohortId = 282,
                                name = "Angioedema",
                                baseUrl = "http://server.org:80/WebAPI")

## End(Not run)

OHDSI/ROhdsiWebApi documentation built on March 15, 2023, 1:23 p.m.