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I have a use case where I need to programmatically modify a set of existing cohort definitions that are already defined in ATLAS (e.g., OHDSI Phenotype Library). Specifically, I would like to modify around 100+ cohort definitions by doing things like:
Editing an existing inclusion rule
Adding new inclusion rules with new concept sets
Changing the exit criteria
Other similar modifications
Capr seems like a fantastic tool for achieving this, but to proceed, I first need to convert an existing cohort expression from ATLAS into a Capr object. Currently, it appears there is no straightforward way to achieve this conversion.
Reproducible Code Example:
Here’s an example of what I’m trying to do. I want to convert the cohort definition to a Capr object, programmatically modify it, and post it back into Atlas:
Target cohort definition: Cohort 1790466 - added new inclusion rules.
Steps:
baseUrl<-"https://atlas-demo.ohdsi.org/WebAPI"# Retrieve the cohort definition from ATLAS, which includes metadata like the cohort namecohortDefinition<-ROhdsiWebApi::getCohortDefinition(cohortId=1790465, baseUrl=baseUrl)
# Extract only the cohort expression component as a list from cohortDefinitioncohortExpressionList<-cohortDefinition$expression# Convert the expression to JSONcohortExpressionJson<-cohortExpressionList|>RJSONIO::toJSON(digits=23)
# stuck - should cohortExpressionJson be converted to Capr object?
Feature Request: asCapr
Could a function be added to Capr that allows for the conversion of a cohort expression JSON (retrieved from ATLAS via WebAPI) into a Capr object, such as 'asCapr'? This would enable users to leverage Capr’s powerful programmatic interface to modify existing cohort definitions easily.
# This is the step where I would like to convert the JSON to a Capr object, but there is no function like 'asCapr'cohortExpressionCapr<-Capr::asCapr(cohortExpressionJson)
Thank you for considering this feature request!
Gowtham
The text was updated successfully, but these errors were encountered:
I have a use case where I need to programmatically modify a set of existing cohort definitions that are already defined in ATLAS (e.g., OHDSI Phenotype Library). Specifically, I would like to modify around 100+ cohort definitions by doing things like:
Capr seems like a fantastic tool for achieving this, but to proceed, I first need to convert an existing cohort expression from ATLAS into a Capr object. Currently, it appears there is no straightforward way to achieve this conversion.
Reproducible Code Example:
Here’s an example of what I’m trying to do. I want to convert the cohort definition to a Capr object, programmatically modify it, and post it back into Atlas:
Steps:
Feature Request: asCapr
Could a function be added to Capr that allows for the conversion of a cohort expression JSON (retrieved from ATLAS via WebAPI) into a Capr object, such as 'asCapr'? This would enable users to leverage Capr’s powerful programmatic interface to modify existing cohort definitions easily.
Thank you for considering this feature request!
Gowtham
The text was updated successfully, but these errors were encountered: