index.qmd

---
title: "Analysis for Longitudinal Fecal Calprotectin Profiles Characterize Disease Course Heterogeneity in Crohn's Disease"
format:
  html:
    code-tools: false
date: ""
date-format: ""
title-block-banner: false
author:
  - name: "Nathan Contantine-Cooke" 
    url: https://scholar.google.com/citations?user=2emHWR0AAAAJ&hl=en&oi=ao
    corresponding: true
    affiliations:
      - ref: HGU
      - ref: CGEM
---

## About

This website presents the analytical reports developed for
*Longitudinal Faecal Calprotectin Profiles Characterize Disease Course Heterogeneity in Crohn's Disease*
by Constantine-Cooke et al. In this work, we use latent class mixed models to
identify clusters within the Crohn's disease patient population based
upon the longitudinal profiles of a biomarker, faecal calprotectin. 

The analysis pipeline for this project consists of three stages:

1. [Data cleaning](data-cleaning.qmd) where data obtained from clinicians are
   reformatted and any data quality issues are dealt with.
2. [Model selection](selection.qmd) where latent class mixed models are fitted
   with differing numbers of assumed clusters and the most appropriate model is
   selected.
3. [Association testing](associations.qmd) where potentially significant
   associations between cluster membership for the optimal model and either
   data available at diagnosis, treatments, or outcomes are tested for. 
   
## Using this website

The navigation menu at the top of the page will allow you to navigate through
the steps of the analysis pipeline.  The code button at the top of each page can
be used to show all code blocks instead of clicking on the code buttons for each
individual block of code. Moving the mouse pointer over any citations in a
report will produce a pop up box with reference details. Clicking on the
citation will link to the bibliography at the bottom of the page. 

## Software versions

All analyses have been generated using
[`r strsplit(R.version$version.string, " (", fixed = TRUE)[[1]][1]`](https://www.r-project.org).
See the Session Information sections at the bottom of each report to see the R
packages used for that particular analysis and the respective package versions. 

## {.appendix}

This website has been generated using the [Quarto](https://quarto.org)
scientific publishing system built on [pandoc](https://pandoc.org).