OHDSI / OHDSI/FeatureExtraction

Create cohort-based standard table 1

Open
#169 7 comments 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

enhancement
Dominant language
R
Stars
74
Forks
63
PR merge metrics
No merged PRs in 30d

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

  1. load those cohort definitions into FeatureExtraction.
  2. add a function in FeatureExtraction to retrieve all these cohort definitions (in a format suitable for CohortGenerator),
  3. add a function for creating cohort-based covariates specifically for this set of cohorts.
  4. 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 .

Contributor guide

No contributing guide indexed for this repository

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. 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

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.