OHDSI / OHDSI/FeatureExtraction
Create cohort-based standard table 1
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- Dominant language
- R
- Stars
- 74
- Forks
- 63
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Description
The current createTable1() function relies on concept-based covariates. We should create an alternative table 1 based on cohorts. For example, instead of 'Diabetes type 2' being based on the occurrence of a single condition concept, it should be based on a more complex definition, possibly involving antidiabetes treatments, lab values, etc.
I propose to use the same set of items as the current table 1 (see specs here), since those were selected before to be 'good enough'. For each item (except possible demographics) we should find a corresponding cohort definition. We could then
- load those cohort definitions into FeatureExtraction.
- add a function in FeatureExtraction to retrieve all these cohort definitions (in a format suitable for CohortGenerator),
- add a function for creating cohort-based covariates specifically for this set of cohorts.
- adapt the
createTable1()function for working with this new table 1.
@gowthamrao: I'd imagine the cohort definitions would come from the OHDSI Phenotype Library.
Also looping in @pbr6cornell .
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reviewing createTable1() and inst/csv/Table1Specs.csv to understand the existing table 1 items. Then investigate how cohort definitions from the OHDSI Phenotype Library can be loaded and returned in a CohortGenerator-compatible format. Done means cohort-based covariates can be created for the specified items and createTable1() supports the new cohort-based table.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- r
- Domain
- data
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 25/100