README.Rmd

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output: github_document
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knitr::opts_chunk$set(
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# 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
```