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Ecological forecasting using Dynamic Generalized Additive Models with R ๐Ÿ“ฆ's {mvgam} and {brms}

Home Page: https://nicholasjclark.github.io/physalia-forecasting-course/

R 0.20% HTML 98.58% Makefile 0.01% CSS 0.92% JavaScript 0.30%
brms ecological-modelling forecasting generalised-additive-models generalised-linear-models mgcv multilevel-models stan time-series-analysis generalized-additive-models

physalia-forecasting-course's Introduction

I'm a Lecturer and research fellow at the University of Queensland's School of Veterinary Science. I am broadly interested in exploring new ways to (1) understand how ecological communities are formed and (2) predict how they will change over time.

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I'm actively seeking Honours and PhD students to work in the areas of ecological forecasting, multivariate model evaluation, hierarchical GAMs and development of {mvgam}. Please reach out if you are interested

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physalia-forecasting-course's Issues

Updates for 2024 version

In all tutorials and relevant lecture slides, provide links to mvgam vignettes

Day 1

  • Link to the ESA talk rather than the Stat Rethinking Categories and Curves
  • Skip over ETS and ARMA slides in lecture
  • Skip through the Beta example as well
  • Introduce the portal example when first talking about random effects; then pause, switch to live coding and show how to do this in mgcv (provide syntax to do it in brms, mvgam and glm as well); show how to use marginaleffects to make hindcast predictions; emphasize how to create smooth plots; emphasize how to take realisations of fitted functions so they can be used for more custom plots or analyses
  • Create an extra exercise script that shows how to handle nested and crossed random effects in mgcv: https://stats.stackexchange.com/questions/618715/building-the-right-gam-model-struggling-with-the-jump-from-lmer/618760#618760
  • Switch to live coding for the yearly smooth, again showing in mgcv; use gratia to show the basis; extract residuals and plot against another predictor to start building in the idea of a workflow
  • Link to Nishan's paper in the tutorial and include the cheatsheet pdf in the supplied files

Day 2

  • Link to the Oceania EcoForecasting seminar
  • Skip over the tscount AR example slides
  • For the dynamic Beta GAM, pause and switch to live coding; show how to do something similar in mgcv with the RW MRF basis; talk about tensor products and introduce the idea of ti() decompositions to help build strategies (link to some of Gavin's Stackoverflow descriptions and the gam.models help page as well)
  • Skip over the enforcing stationarity Student T example
  • In the dynamic coefficient example, switch to live coding; show how to do something similar in mgcv with the RW MRF basis; mention how one could use the same principles for spatially varying coefficients
  • Use Hilbert GP in dynamic coefficient mvgam example
  • In tutorial fix typo: "except the length scale was changed to 3" should be "except the length scale was changed to 4"
  • Subtitles should use "GAM" rather than "GLM"; i.e. "A standard Poisson GLM" should be "A standard Poisson GAM"
  • Link to MRFtools
  • Include the cheatsheet pdf in the supplied files

Day 3

  • Link to the forecasting vignette and to Juniper's paper on forecast evaluation
  • Skip over expectations entirely and reduce down the conditional predictions part
  • At the types of predictions, switch to live coding and show something cool / interesting (distributed lags in mgcv)
  • Same at probabilistic forecast evaluation; perhaps show a strategy to estimate a decaying effect of some treatment (time since treatment example, or time-varying dispersion with a distributional model)
  • Remove stochastic trend extrapolation completely, and talk about loo_compare instead; relate back to the cheatsheet
  • Include the cheatsheet pdf in the supplied files

Day 4

  • At hierarchical dist lags, switch to live coding and show something cool / interesting (phylogenetically informed intercepts and nonlinear functions in mgcv; illustrate prediction by excluding certain terms to show how the trend is built of additive functions)
  • At multivariate forecast evaluation, switch to live coding and show time-varying seasonality in mvgam

Day 5

  • Pick a more simple and useful dataset for groups to analyse

Be sure to create PDFs of all lectures again, once finalised

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