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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VARsim-infer #59

Closed Fontanapink closed 5 months ago

Fontanapink commented 5 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:

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