Modelling and Inference of MICrobiomes Project (MIMIC)

Contents:

• Modelling and Inference of MICrobiomes Project (MIMIC)
  • Overview
  • Structure
  • Installation
    • Prerequisites
    • Installation Steps
    • Alternative Installation Using Pip Only
  • Usage
  • Contributing
  • License
  • Acknowledgements
  • Contact
• Installation
  • Prerequisites
  • Installation Steps
    • For macOS and Ubuntu
    • For Windows
  • Alternative Installation Using Pip Only
    • Compilers
• Usage
• mimic
  • mimic package
    • Subpackages
    • Module contents
• Examples
  • Jupyter Notebook Examples by Model
  • CRM
    • Simulate some time course data from the CRM
  • GP
    • Imputing Missing Values using Gaussian Process
    • Using the Data Imputator on a Real Public Dataset - Stein et al. (2013)
  • MVAR
    • MVAR Simulation for Microbiota and Metabolites
    • MVAR Simulation for Microbiota and Metabolites
  • MultiModel
    • VAR inference on a Real Public Dataset, Herold et al. (2020)
    • Sparse VAR on a Real Public Dataset, Herold et al. (2020)
    • Data imputation on a Real Public Dataset, Herold et al. (2020)
  • VAR
    • Bayesian Inference for Vector AutoRegression (VAR) Models
    • Vector AutoRegression (VAR) Simulation
  • gLV
    • Repeat Rutter & Dekker et al 2024 analysis
    • Perform Bayesian inference with shrinkage
    • Repeat Stein et al. 2013 analysis
    • Used Bayesian inference to infer the parameters of a (linearised) gLV model
    • Example Lasso gLV model
    • Simulate some time course data and perform ridge regression as in Stein et al. 2013
    • Simulate some time course data from the gLV
  • gMLV
    • Run ridge regression and lasso for the gMLV model
    • Simulate some time course data from the gMLV
• Credits
  • Development Lead
  • Contributors
• Contributing to MIMIC
  • Getting Started
  • Making Changes
  • Pull Request Checklist
  • Development Workflow
  • Code Review Process
  • Reporting Bugs
  • Suggesting Enhancements
  • Common Issues:
  • Additional Notes
• History
  • 0.1.0 (2024-01-30)

Indices and tables

• Index

• Module Index

• Search Page