This is the repository for analysis used in Longitudinal Fecal Calprotectin Profiles Characterize Disease Course Heterogeneity in Crohn’s Disease by Constantine-Cooke et al. The reports generated by this code can be found here.
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.
To generate the results, the
renv R package
and Quarto scientific publishing system is
required.
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. Then, from R, install the renv package
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
renv::restore()Quarto is used to generate the reports. If you have not already, please install Quarto.
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:
cd docs
python3 -m http.server