---
title: "CARWatch examples"
description: "Executable end-to-end walkthroughs and focused R Markdown examples for CARWatch."
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{CARWatch examples}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

This catalogue lists the executable R Markdown examples in the
[carwatch-r repository](https://github.com/carwatch-tools/carwatch-r/tree/main/examples).
Each example creates its inputs below `tempdir()` unless it explicitly asks
for an interactive action.

To run an example locally, clone or download the repository, open
`examples/examples.Rproj` in RStudio, and open the linked `.Rmd` file. Use
**Run All** to work through it step by step or **Knit** to create an HTML
report. Install `pkgload`, `rmarkdown`, `shiny`, and `DT` as described in the
[tutorial guide](tutorials.html).

## End-to-end walkthroughs

| If you want to… | Start here |
| --- | --- |
| Import app logs, review issues, submit decisions, and save Study Results | [`01-log-processing.Rmd`](https://github.com/carwatch-tools/carwatch-r/blob/main/examples/01-log-processing.Rmd) |
| Merge cortisol data, assess compliance, and compute response features | [`02-saliva-analysis.Rmd`](https://github.com/carwatch-tools/carwatch-r/blob/main/examples/02-saliva-analysis.Rmd) |
| Create sampling timelines, compliance, deviation, and saliva-response plots | [`03-plotting.Rmd`](https://github.com/carwatch-tools/carwatch-r/blob/main/examples/03-plotting.Rmd) |
| Generate synthetic data and try the Shiny tools | [`04-synthetic-study-interactive-log-processing.Rmd`](https://github.com/carwatch-tools/carwatch-r/blob/main/examples/04-synthetic-study-interactive-log-processing.Rmd) |

## Focused research workflows

1. [Load participant folders and check imported files](https://github.com/carwatch-tools/carwatch-r/blob/main/examples/gallery/01-research-workflow/01-load-carwatch-logs.Rmd)
2. [Resolve conversion issues through a CSV report](https://github.com/carwatch-tools/carwatch-r/blob/main/examples/gallery/01-research-workflow/02-resolve-conversion-issues-in-spreadsheet.Rmd)
3. [Resolve conversion issues interactively](https://github.com/carwatch-tools/carwatch-r/blob/main/examples/gallery/01-research-workflow/03-resolve-conversion-issues-interactively.Rmd)
4. [Assess and filter sampling compliance](https://github.com/carwatch-tools/carwatch-r/blob/main/examples/gallery/01-research-workflow/04-assess-and-filter-sampling-compliance.Rmd)
5. [Inspect individual sampling timing](https://github.com/carwatch-tools/carwatch-r/blob/main/examples/gallery/01-research-workflow/05-inspect-individual-sampling-timing.Rmd)
6. [Merge positional saliva measurements](https://github.com/carwatch-tools/carwatch-r/blob/main/examples/gallery/01-research-workflow/06-merge-saliva-measurements.Rmd)
7. [Compute cortisol response features](https://github.com/carwatch-tools/carwatch-r/blob/main/examples/gallery/01-research-workflow/07-compute-cortisol-features.Rmd)

## Protocol variants and example data

- [Reconstruct a multi-registration protocol](https://github.com/carwatch-tools/carwatch-r/blob/main/examples/gallery/02-protocol-variants/01-reconstruct-multi-registration-protocol.Rmd)
- [Generate local CARWatch example data](https://github.com/carwatch-tools/carwatch-r/blob/main/examples/gallery/03-example-data/01-generate-local-example-data.Rmd)

The examples are rendered and smoke-tested in continuous integration. The
developer workflow is documented in [Development](development.html).