2025 R Workshops @ UQ

I have recently joined the R Workshops @ UQ team, which has been conducting several R Workshops at the University of Queensland each year since 2012. The team is composed of a wonderful group of quantitative ecologists who have learnt data analysis and data science through application to real-world problems in R. Because we are self-taught, we want to help others avoid some of the mistakes we made when we were setting out to learn and use R. We have now taught >1,500 students at these workshops, and we look forward to helping the next generation of R programmers and applied statisticians learn the skills they need to meet the demands of the modern research environment. The 2025 workshops, happening over 5 days in February, will cover the tidyverse, ggplot2, linear models, Generalized Linear Models, Generalized Additive Models, spatial and spatiotemporal modelling, multivariate modelling and much more!

Harnessing the power of ecological forecasting

Rapidly changing climates and landscape modification are impacting global ecosystems at all micro- and macroecological levels, incurring significant economic and environmental costs. Human encroachment into bushland and habitat alterations are magnifying risks of zoonotic diseases and shifting key conservation targets. Changing temperatures are altering food distributions and influencing reproductive cycles for important fishery species, introducing major uncertainties for vulnerable economies. There is broad consensus among scientists, parliamentarians and decision-makers that anticipating probable future states is vital to mitigate these impacts of environmental change. Ecological forecasting is a fundamental representation of hypothesis-driven science that aims to address this gap by (1) using theory-driven models and observational data to make near-term forecasts (2) falsifying these forecasts against future data to identify critical data / model limitations (3) refining hypotheses and model structures and (4) repeating. This iterative cycle can accelerate learning, drive model improvement and emphasize outputs that are immediately useful for effective planning and resource management. It is no surprise then that ecological forecasting is becoming a key focus in diverse fields including evolutionary biology, ecosystem services and epidemiology. In this talk, I introduce the near-term forecasting cycle and motivate its importance to ecology by providing a set of simple but thought-provoking questions we can ask ourselves whenever we seek to build biologically relevant models and deliver predictions that are more useful to relevant end-users.

Time series modeling with Bayesian Dynamic Generalized Additive Models

In this talk I introduce Bayesian Dynamic Generalized Additive Models (DGAMs) and illustrate their advantages for analyzing and forecasting real-world time series. I discuss mvgam, an open-source R package that can fit DGAMs with nonlinear effects, hierarchical effects and dynamic processes to data from a wide variety of observation distributions. These models are especially useful for analysing multiple series, as they can estimate hierarchical smooth functions while learning complex temporal associations with latent vector autoregressive processes or dimension-reduced dynamic factor processes. Because the package uses Hamiltonian Monte Carlo inference through Stan, it is straightforward to create Stan code and all necessary data structures so that additional stochastic elements can be added to suit the user’s bespoke needs. Other key features of {mvgam} are functions to critique models using rolling window forecasts and posterior predictive checks, online data augmentation via a recursive particle filter and graphical tools to visualise probabilistic uncertainties for smooth functions and predictions. I hope show how models that describe real-world complexity, both through nonlinear covariate functions and multi-series dependence, are useful to ask targeted questions about drivers of change.

Ecological forecasting with dynamic GAMs

Time series analysis and forecasting are standard goals in applied ecology. But ecological forecasting is difficult because ecology is complex. The abundances of species, for example, fluctuate for many reasons. Food and shelter availability limit survival. Biotic interactions affect colonization and vital rates. Severe weather events and climate variation alter habitat suitability. These sources of variation make it difficult to understand, let alone predict, ecosystem change. Moreover, most available time series software cannot handle features that dominate ecological data, including overdispersion, clustering, missingness, discreteness and nonlinear effects. In this talk, I will introduce Dynamic Generalized Additive Models (DGAMs) as one solution to meet this complexity. I illustrate a number of models that can be tackled with the mvgam R package, which builds Stan code to specify probabilistic Bayesian models that include nonlinear smooth functions, random effects and dynamic processes, all with a simple interface that is familiar to most R users.

Ecological forecasting with dynamic Generalized Additive Models (DGAMs)

Time series analysis and forecasting are standard goals in applied ecology. But ecological forecasting is difficult because ecology is complex. The abundances of species, for example, fluctuate for many reasons. Food and shelter availability limit survival. Biotic interactions affect colonization and vital rates. Severe weather events and climate variation alter habitat suitability. These sources of variation make it difficult to understand, let alone predict, ecosystem change. Moreover, most available time series software cannot handle features that dominate ecological data, including overdispersion, clustering, missingness, discreteness and nonlinear effects. In this talk, I will introduce Dynamic Generalized Additive Models (DGAMs) as one solution to meet this complexity. I illustrate a number of models that can be tackled with the mvgam R package, which builds Stan code to specify probabilistic Bayesian models that include nonlinear smooth functions, random effects and dynamic processes, all with a simple interface that is familiar to most R users.

Ascertainment and near-term forecasting of tick paralysis admissions

Tick paralysis is a leading cause of emergency veterinary admissions for Australian companion animals, often resulting in death if left untreated. Availability of timely information on periods of increased risk can help modulate behaviours that reduce exposures to ticks and improve awareness of owners for the need of preventative ectoparasite treatment. However, detection of trends in risk is hampered by the lack of clearly annotated historical records of tick paralysis. Natural Language Processing (NLP) of clinical records is required to first ascertain historical cases. Here we describe a platform to perform NLP on VetCompass Australia’s veterinary clinical records to accurately identify historical cases of canine tick paralysis where we make use of combine bespoke spellchecking and tokenization routines with a domain-expertise inspired clinical dictionary to identify important terms in free text indicative of a tick paralysis diagnosis. Resulting time series of tick paralysis cases are then analysed using Dynamic Generalised Additive Models to jointly estimate nonlinear distributed lag effects of environmental predictors and dynamic latent temporal processes that facilitate probabilistic near-term forecasts of tick paralysis risk. Our models forecast tick paralysis cases with exceptional accuracy while preserving epidemiological interpretability. We have designed an interactive online dashboard to showcase our data and modelling results so that we can refine the way we present probabilistic predictions to meet end-user requirements. We expect our data acquisition / modelling pipeline to act as a platform for developing early warning systems that can notify clinicians and pet owners about heightened risks of environmentally driven veterinary conditions.

Rapid winter warming associated with major shifts in coastal fish communities

Marine ecosystems are under increasing threat from warming waters. Winter warming is occurring at a faster rate than summer warming for ecosystems around the world, but most studies focus on the summer. Here, we show that winter warming could affect coastal fish community compositions in the Mediterranean Sea using a model that captures how biotic associations change with sea surface temperature to influence species’ distributions for 215 fish species. Species’ associations control how communities are formed, but the effect of winter warming on associations will be on average four times greater than that of summer warming. Projections using future climate scenarios show that 60% of coastal Mediterranean grid cells are expected to lose fish species by 2040. Heavily fished areas in the west will experience diversity losses that exacerbate regime shifts linked to overexploitation. Incorporating seasonal differences will therefore be critical for developing effective coastal fishery and marine ecosystem management. Clark, N.J., Kerry, J.T. & Fraser, C.I. Rapid winter warming could disrupt coastal marine fish community structure. Nature Climate Change 10, 862–867 (2020). https://doi.org/10.1038/s41558-020-0838-5