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Course syllabus

Overview

This is a 3-session, one-day workshop. It was developed with the goal of giving you enough GAM knowledge to feel comfortable fitting and working with GAMs in your day-to-day modelling practice, with just enough of more advanced applications to give a flavour of what GAMs can do. I will be covering a basic intro to GAM theory, with the rest focused on practical applications and a few advanced topics that I think might be interesting.

Learning Goals

  • Understand the basic GAM model, basis functions, and penalties
  • Fit 1D, 2D, and tensor-product GAMs to normal and non-normal data
  • Plot GAM fits, and understand how to explain GAM outputs
  • Diagnose common mispecification problems when fitting GAMs
  • Use GAMs to make predictions about new data, and assess model uncertainty
  • See how more complicated GAM models can be used as part of a modern workflow

Syllabus

1. What is a GAM, and 1d smoothers

  • Example data: temperature with depth

  • refresher on GLMs (regression, parameters, link functions)

  • why smooth?

  • simple models with s()

  • introduction to the data

  • adding more than one smooth to your model

  • summary and plot

2. "twiddling knobs in gam"

  • moving beyond normal data (richness, shrimp biomass)

    • exponential family and conditionally exp family (i.e., family + tw + nb)

  • more dimensions (Shrimp biomass)

    • thin-plate 2d (Shrimp biomass with space)

    • what are tensors? (Shrimp biomass as a function of depth and temperature)

      • ti vs te

    • spatio-temporal modelling

      • te(x,y,t) constructions

  • centering constraints

    • what does the intercept mean?

3. prediction, uncertainty, model checking, and selection

  • using predict to calculate confidence intervals

  • posterior simulation

  • gam.check for model checking

  • quantile residuals

  • diagnostic: DHARMa

  • fitting to the residuals

  • AIC etc.

  • shrinkage and select=TRUE

Other useful resources

3-day GAM workshop for DFO, a longer version of this workshop

Our ESA GAM workshop

Our paper on Hierarchical Generalized Additive Models

Noam Ross's GAMs in R tutorial

Noam Ross's Short talk on many types of models that can fit with mgcv

Gavin Simpson's Blog: From the Bottom of the Heap

Gavin Simpson's Online GAM workshop

David Miller's NOAA workshop based on the ESA workshop

David Miller's Distance DSM workshop

Other useful GAM resources:

  • Simon Wood's book "Generalized Additive Models: An Introduction with R, Second Edition", is an incredibly useful tool for learning about GAMs, and covers all of this material in depth.

  • Hefley et al. (2017). "The basis function approach for modeling autocorrelation in ecological data". This is a great paper laying out how basis functions are used to model complex spatially structured systems.

  • The mgcVis package has more tools for plotting GAM model outputs. See Fasiolo et al.'s paper 2019 "Scalable visualization methods for modern generalized additive models".