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Getting Started
Why High-Dimensional Statistics?
Atacama Soil Microbiome
Download the Tutorial Data
End-to-End Tutorial
Prerequisites & Installation
Installing q2-gglasso
Installing q2-classo
Verifying Your Installation
Start small: a 13-ASV network
Graphical Lasso Models
Data Preparation
Single Graphical Lasso
Sparse + Low-Rank (Latent Variables)
Adaptive Graphical Lasso
Regularization Paths & Model Selection
Multiple Graphical Lasso (GGL / FGL)
Latent-Component PCA
Summarizing a Solution
Interpretation
Log-Contrast Models
Synthetic Data with Known Truth
Data Preparation
Regression
Log-Contrast
With trac
Classification
Log-Contrast
With trac
Advanced: Concomitant Formulation
Advanced: Choosing a Model
Predict & Summarize
Interpretation
Scale up: hundreds of features
Overview
The 300-ASV Dataset
Selecting lambda
Choosing the Latent Rank
Latent Components & Covariates
Log-Contrast Models at Scale
Interpretation
Shotgun: mOTUs Profiles
Reference
Command Coverage Matrix
q2-gglasso Parameter Reference
q2-classo Parameter Reference
Troubleshooting & Known Failure Modes
Appendix: Mathematical Background
Appendix: Shotgun Metagenomics (MOSHPIT cocoa)
References
Index
