lcmm-site

R Code and website for Longitudinal Fecal Calprotectin Profiles Characterize Disease Course Heterogeneity in Crohn’s Disease by Constantine-Cooke et al.

https://github.com/vallejosgroup/lcmm-site

Keywords

Repository

R Code and website for Longitudinal Fecal Calprotectin Profiles Characterize Disease Course Heterogeneity in Crohn’s Disease by Constantine-Cooke et al.

README.Rmd

---
output: github_document
---



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

# lcmm-site

This is the repository for analysis used in Latent Crohn’s Disease Subgroups are
Identified by Faecal Calprotectin Profiles by Constantine-Cooke et al. The
reports generated by this code can be found
[here](http://www.constantine-cooke.com/lcmm-site/).

## Usage

This report requires access to the Crohn's disease inception cohort dataset
hosted by the University of Edinburgh. For access to these data, please
[contact Professor Charlie Lees](mailto:charlie.lees@ed.ac.uk). 

To generate the results, the
[`renv`](https://rstudio.github.io/renv/articles/renv.html) R package and
[Quarto](https://quarto.org) scientific publishing system is
required. 

### `renv`

The `renv` package is used to manage dependency management: ensuring the same R
packages, with their respective versions, are used when the analysis is run. 

Clone this repository. If you have not already, please
[install R](https://cran.r-project.org). Then, from R, install the `renv`
package

```{R, eval = FALSE}
install.packages("renv")
```

Open a project with the working directory of this cloned repository. Then use
the below command to install the R packages required for this project

```{R, eval = FALSE}
renv::restore()
```

### Quarto

Quarto is used to generate the reports. If you have not already, please
[install Quarto](https://quarto.org/docs/get-started/).

### Generating output

Mount `smb://cmvm.datastore.ed.ac.uk/igmm/` to `/Volumes/`. From a terminal, `cd`
into the directory you have cloned this repository into. Finally, run
`quarto render`. Figures used in the paper can be found in the `paper` directory
whilst plots not used in the manuscript can be found in the `plots` directory. 
The generated website files can be found in `docs` and can be served by any
web server, for example by running the below code: 

``` bash
cd docs
python3 -m http.server
```

Owner

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Constantine-Cooke"
  given-names: "Nathan"
  orcid: "https://orcid.org/0000-0002-4437-8713"
- family-names: "Monterrubio-Gómez"
  given-names: "Karla"
  orcid: "https://orcid.org/0000-0001-5617-0074"
- family-names: "Plevris"
  given-names: "Nikolas"
  orcid: "https://orcid.org/0000-0002-3229-8759"
- family-names: "Marioni"
  given-names: "Riccardo E."
  orcid: "https://orcid.org/0000-0003-4430-4260"
- family-names: "Vallejos"
  given-names: "Catalina A."
  orcid: "https://orcid.org/0000-0003-3638-1960"

title: "Analysis for Longitudinal Fecal Calprotectin Profiles Characterize Disease Course Heterogeneity in Crohn's Disease"
version: 1.0.0
date-released: 2023-01-01
url: "https://github.com/vallejosgroup/lcmm-site"
preferred-citation:
  type: article
  authors:
  - family-names: "Constantine-Cooke"
    given-names: "Nathan"
    orcid: "https://orcid.org/0000-0002-4437-8713"
  - family-names: "Monterrubio-Gómez"
    given-names: "Karla"
    orcid: "https://orcid.org/0000-0001-5617-0074"
  - family-names: "Plevris"
    given-names: "Nikolas"
    orcid: "https://orcid.org/0000-0002-3229-8759"
  - family-names: "Derikx"
    given-names: "Lauranne A.A.P."
    orcid: "https://orcid.org/0000-0002-4081-8451"
  - family-names: "Gros"
    given-names: "Beatriz"
    orcid: "https://orcid.org/0000-0002-5628-313X"
  - family-names: "Jones"
    given-names: "Gareth-Rhys"
    orcid: "https://orcid.org/0000-0001-7355-2357"
  - family-names: "Marioni"
    given-names: "Riccardo E."
    orcid: "https://orcid.org/0000-0003-4430-4260"
  - family-names: "Lees"
    given-names: "Charlie W."
    orcid: "https://orcid.org/0000-0002-0732-8215"
  - family-names: "Vallejos"
    given-names: "Catalina A."
    orcid: "https://orcid.org/0000-0003-3638-1960"
  doi: "10.1101/2022.08.16.22278320"
  journal: "Clinical Gastroenterology and Hepatology"
  month: 10
  start: 2918 # First page number
  end: 2927 # Last page number
  title: "Longitudinal Fecal Calprotectin Profiles Characterize Disease Course Heterogeneity in Crohn's Disease"
  issue: 11
  volume: 21
  year: 2023

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