stan-dev / stan-dev/rstanarm

Accommodating more than 3 longitudinal biomarkers

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Dominant language
R
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401
Forks
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Description

Description:

In our problem, we have 21 longitudinal biomarkers with one survival outcome. Our goal is to find out which of the biomarkers are significantly associated with the survival outcome. I have used this package with one longitudinal biomarker at a time and found out that not only the mean trajectory but also its slope is significantly affecting the survival outcome for some of the biomarkers. My next plan is to use all the longitudinal biomarkers together to use their association. For variable selection, we can use some standard shrinkage prior for the 'assoc' and the 'assoc_d' parameters.

In this package, I have noticed that the user is not allowed to use more than 3 longitudinal variables. I want to know what can be the issue with using more than 3 longitudinal biomarkers. You have shared the main part of the stan code in a conference paper. My plan is to use that to implement my idea. Do you have any suggestions regarding this?

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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 the package's current restriction to three longitudinal variables and the Stan code referenced in the issue. Trace how the assoc and assoc_d parameters represent biomarker associations, then determine what would need to change to support more than three biomarkers and how the requested variable-selection approach could be evaluated.

Written by the indexing model from the issue text.

Assessment

Tech stack
r
Domain
machine-learning
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
20/100

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