Who am I? Chris is a Senior Lecturer at Griffith University and an Australian Research Council Future Fellow. Chris and his team in the Seascapemodels lab work on the conservation of ocean ecosystems and sustainable management of fisheries. His team uses advances in statistical modelling approaches to synthesize ecological data and inform environmental decision making.

Chris’ career was built with R’s open-source tools. He is paying forwards that favour by creating free R resources and teaching workshops far and wide.

Introduction

(QUICK LINK TO GET THE DATA)

R is the leading programming language for ecological modelling for good reason. Being free and open-source certainly helps. Having strengths in dataviz also helps. And because of these traits, R now has a huge ecosystem of user-contributed packages that enable sophisticated modelling applications.

This ecosystem of R packages is created by a huge community of R users, many of whom are leaders in their field developing cutting edge statistical models and data science tools. This means if you know R, you can access cutting edge tools and combine them in new ways.

While there are other languages that excel for scientific computing, R owns the market in species distribution modelling (SDMs), the topic of this course.

Until quite recently most R users would prepare their data outside of R (e.g. in Arc GIS) and then read it into R for the SDM. But R now also has efficient and user friendly GIS and mapping packages. This means you can create your entire SDM workflow, from data download to visualization, in R.

But starting an SDM project in R can be daunting for new users. There is a steep learning curve for coding, and there are so many options for packages it is easy to get decision paralysis.

So in this course we are going to provide an introduction to some common SDMs in R. We will also learn how to build an efficient workflow. Our goals today are:

  1. Overview R’s capability for GIS and spatial dataviz

  2. Learn how to build efficient and repeatable workflows for SDMs

  3. Learn how to run some SDMs

  4. Learn how to visualize spatial data and SDM results

This course is suitable for people who have some R experience. It is not a beginners course, but users with a little bit of R experience can follow through the first few sections.

Methods we will cover

In this course we’ll overview:

  • GIS in R with shapefiles and rasters (using the modern packages sf and terra)

  • Generalized linear models

  • Generalized least squares and models of spatial autocorrelation

  • Generalized additive models

  • Spatial prediction and interpolation

What you’ll need

Make sure you have a recent version of R (available at the CRAN website) and Rstudio installed (free desktop version is fine).

You will need to install these packages:

install.packages(c("tmap", "tidyverse", "terra",
                   "sf", "nlme",
                   "patchwork", "visreg"))

You will also need to download the data for the course.

Case-study: Bumphead parrotfish, ‘Topa’ in Solomon Islands

Bumphead parrotfish (Bolbometopon muricatum) are an enignmatic tropical fish species. Adults of these species are characterized by a large bump on their forehead that males use to display and fight during breeding. Sex determination for this species is unknown, but it is likely that an individual has the potential to develop into either a male or female at maturity.

Adults travel in schools and consume algae by biting off chunks of coral and in the process they literally poo out clean sand. Because of their large size, schooling habit and late age at maturity they are susceptible to overfishing, and many populations are in decline.

Their lifecycle is characterized by migration from lagoonal reef as juveniles (see image below) to reef flat and exposed reef habitats as adults. Early stage juveniles are carnivorous and feed on zooplankton, and then transform into herbivores at a young age.