ucl-cssb / MIMIC

Modelling and Inference of MICrobiomes Project (MIMIC) is a Python package dedicated to simulate, model, and predict microbial communities interactions

MIT License

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MVAR inference methods and examples #58

Closed Fontanapink closed 3 months ago

Fontanapink commented 3 months ago

Pull Request To-Do List

Description of the changes:

This PR brings mainly the ability to do sparce VAR inferene between abundances and metabolites. It adds:

run_inference_xs() and run_inference_large_xs() to do MVAR inference
modifications to have sim_VARM to simulate data for abundances AND metabolites
added a real-dataset example using VAR infer (Herold et al. 2020)
the ability to download calculated posteriors
the ability to plot posterior calculations
the ability to plot inferred parameters with a heatmap
name changes to make it more consistent with the rest of the package
All documentation examples to reflect the latest changes
All example modifications to make everything running with the latest changes

I have done the following to make this PR ready for review:

[x] I have re-based my branch on the latest master branch
[x] I have added necessary documentation (if appropriate)
[x] I have commented my code, particularly in hard-to-understand areas
[x] I have assigned a reviewer to this PR

For the reviewer, make sure this PR meets these criteria before merging:

[ ] New code has comments
[ ] New code has tests (if appropriate)
[ ] New code has documentation (if appropriate)
[ ] New code has been reviewed by at least one other person

Fontanapink commented 3 months ago

problems with GitHub Actions