README.Rmd

---
output: github_document
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

#### 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

```{r fig_sims, echo = FALSE, out.width = '75%'}
knitr::include_graphics("outputs/examp_sims.png")
```