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Most recent note/work update

  • September 26: Some reorganization to use cmdstanr, compile models only once, and save just samples instead of the full stan model in the hopes that this will resolve the issues I had with tar_make_future slowing to near 0 after some hours of running
  • TO DO: Summary plots currently only dependent on a single coefficient that will vary among runs, but this won’t be how parameter exploration will actually work. Need to work on summary and plotting across a variety of parameters

Simulations to compare alternative methods of analyzing serology data

Project Vision/Objectives

  • Show under coverage of two-step cluster + regression
  • Illustrate potential of Bayesian clustering models that simultaneously consider covariates that affect grouping and values within those groups

Repository Structure and Reproducibility

  • data/ contains data (empirical and/or saved simulated)
  • R/ contains functions used in this analysis.
  • stan_models/ contains stan model definitions
  • reports/ contains literate code for R Markdown reports generated in the analysis
  • outputs/ contains compiled reports and figures.
  • This project uses the targets package to create its analysis pipeline. The steps are defined in the _targets.R file and the workflow can be executed by running targets::tar_make().

A coverage plot from some initial simulations

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