Analysis for Longitudinal Fecal Calprotectin Profiles Characterize Disease Course Heterogeneity in Crohn’s Disease


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 where data obtained from clinicians are reformatted and any data quality issues are dealt with.
  2. Model selection where latent class mixed models are fitted with differing numbers of assumed clusters and the most appropriate model is selected.
  3. Association testing 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 version 4.2.1. 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.

This website has been generated using the Quarto scientific publishing system built on pandoc.


BibTeX citation:
  author = {Nathan Constantine-Cooke and Karla Monterrubio-Gómez and
    Nikolas Plevris and Lauranne A.A.P. Derikx and Beatriz Gros and
    Gareth-Rhys Jones and Riccardo E. Marioni and Charlie W. Lees and
    Catalina A. Vallejos},
  publisher = {Elsevier},
  title = {Longitudinal {Fecal} {Calprotectin} {Profiles} {Characterize}
    {Disease} {Course} {Heterogeneity} in {Crohn’s} {Disease}},
  journal = {Clinical Gastroenterology and Hepatology},
  url = {},
  doi = {10.1016/j.cgh.2023.03.026},
  issn = {1542-3565},
  langid = {en}
For attribution, please cite this work as:
Nathan Constantine-Cooke, Karla Monterrubio-Gómez, Nikolas Plevris, Lauranne A.A.P. Derikx, Beatriz Gros, Gareth-Rhys Jones, Riccardo E. Marioni, Charlie W. Lees, and Catalina A. Vallejos. n.d. “Longitudinal Fecal Calprotectin Profiles Characterize Disease Course Heterogeneity in Crohn’s Disease.” Clinical Gastroenterology and Hepatology.