BRIEF-IBS

LAST UPDATED: Arvid Lundervold, 2023-05-31

Code and data accompanying the paper: A.J. Lundervold, ..., A. Lundervold. "Assessment of self-reported executive function in irritable bowel syndrome using a machine learning framework" Journal of Clinical Medicine 2023;12:3771

Website: https://www.mdpi.com/2077-0383/12/11/3771
PDF Version: https://www.mdpi.com/2077-0383/12/11/3771/pdf
Overleaf Version: https://www.overleaf.com/project/64633e1ad925e61795ca94f4 (restricted access)

The conda environment:

• pycaret3

The notebooks:

• 1-eda-brief.ipynb - Exploratory Data Analysis of the BRIEF-A data
• 2-ml-brief.ipynb - Analysis using Machine Learning (PyCaret 3.0)

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Installation and maintenence

# To clone the repository (once)
git clone git@github.com:MMIV-ML/BRIEF-IBS.git

# To install environment (once)
conda env update -f environment.yml
conda activate pycaret3

# back to (base)
conda deactivate   # back to (base)

# To update the pycaret3 environment (if new versions become available):
conda update -n pycaret3 --all      # To update all packages in the named environment

# To remove and reinstall the pycaret environment (if installation problems):
conda deactivate
conda env remove -n pycaret3
#   <fix iinstallation>
# e.g. pip install --upgrade pycaret
# Then, recreate the conda environment pycaret3 as above:
conda env update -f environment.yml
conda activate pycaret3

## OPTIONAL: To install a jupyter kernel PYCARET3
python -m ipykernel install --user --name pycaret3 --display-name "PYCARET3"