The code in this repository reproduces display items of the Machine Learning section of the Fecal Microbiota Transplantation Meta-Analysis conducted by Ianiro, Punchochar, Karcher et al. (2022, Nature Medicine). Specifically, it reproduces main text figure 4 and accompanying supplementary figures.
To obtain all data required for reproducing this code, please contact [email protected] and [email protected]
In order to set up your environment to be able to run this code, start by installing conda (as described under this link https://conda.io/projects/conda/en/latest/user-guide/install/index.html). Then create a fresh conda environment using the .yml file in this repository like so
conda env create -f FMT.yml
This will create a new environment called FMT which you can activate by typing conda activate FMT after the environment was succesfully set up.
Also create necessary folders
mkdir data; mkdir figures; mkdir tmp
and make sure to put raw data into the data (see above) folder.
Reproduce the display items by typing Rscript FMT.r. It will take around a day to finish.