How to use large language models to assist in systematic literature reviews In the near future, we will all be doing systematic lit reviews by getting LLMs to gather data from papers. Below is an example of how to extract text data from a study. Once ... [Read more...]

Setting up VScode for R and Cline Cline lets you create and run entire workflows via using prompts to a large language model. Its not widely used in the R community yet, but I expect it will be soon. You can create your entire R project, interpret the... [Read more...]

Probability intervals with GAMs A neat trick with GAMs (generalized additive models) fit using the mgcv package is that you can use simulation to get Bayesian credible intervals. This is handy because it means you can easily calculate probabilities fo... [Read more...]

Introduction to structural causal modelling A primary goal of science is to understand causes. Structural causal modelling is a framework for developing causal hypotheses to test with data. I taught a workshop at the Australian Marine Sciences Associ... [Read more...]

Bayesian structural equation model tutorial Structural equation modelling (SEM) is a tool for exploring relationships among multiple variables. lavaan and piecewiseSEM are too of the most widely used and accessible packages for latent variable modelli... [Read more...]

Why GLMs should be a priority when teaching statistics There is often debate over the best place to start when teaching students inferential statistics. The teaching of statistics should start with basic understanding of what data are, probability and... [Read more...]

Tips for using chatGPT to learn R ChatGPT can help you learn R code. Here are some tips my team and I have worked out for ways to use the model to help with learning R. There is also an askgpt package now that is meant to integrate ChatGPT directly ... [Read more...]

Making predictions from GAMs in R explained by an 18th century author As explained by ChatGPT with some minor edits by me. This post is an example for my post “Tips for using chatGPT to learn R” Pray, let us first summon the mgcv package, that we may... [Read more...]

Organising R scripts Here’s some key points for how I organise my R projects. Folder structure I use the folder structure from the excellent collaboration framework Max Campbell created for my lab. This allows us to share and backup code via github,... [Read more...]

R workshops Brisbane February 2023 Hands-on R training! February 14th-17th 2023 Presenters Professor Anthony J. Richardson (UQ CARM) Professor David Schoeman (University Sunshine Coast) Associate Professor Chris Brown (Griffith University) Dr Christ... [Read more...]

Rules of thumb for the design of ecological experiments Are you planning an experiment in the lab or field, or an observational study? Its a good idea to talk to a statistician before you start. Students often ask me for help with statistics after th... [Read more...]

Running R code for all combinations of some parameters with lapply karate Sometimes we want to run the same bit of code many times for different parameters. Then if we have multiple parameters, we may want to run the code for all combinations of those... [Read more...]

Current approaches to Species Distribution Modelling in R My course notes for “Current approaches to Species Distribution Modelling in R “ for World Fisheries Congress 2021 are now free online. The course covers tidyverse and sf workflows for models,... [Read more...]

Comparison of terra and stars packages The other day I wrote a comparison of raster and terra packages. The other newish raster package on the block is stars. So I go through the same code here. If you are starting out with stars, read their manual f... [Read more...]

A comparison of terra and raster packages The terra package looks designed to replace an old favourite raster. It is made by a similar team. The terra documentation states “can do more, is simpler to use, and it is faster.” So should you make the swi... [Read more...]

How to solve common problems with GAMs Here I’ll provide solutions to some common problems I run into when fitting GAMs with mgcv and ways to solve them. The four problems are: Categorical variables should be input to gam() as factors ... [Read more...]

When interpolation doesn’t work with GAMs GAMs shouldn’t be used for extrapolation, and they can give strange results for interpolation too. Here I’ll explain why and we’ll look at a solution that involves changing the order a smoother’s penalty. Gaps... [Read more...]

Fast functions with pipes Pipes are becoming popular R syntax, because they help make code more readable and can speed up coding. You can even use pipes to create functions. This is handy if you want to repeat a piped process for several different dat... [Read more...]

R workshops in Brisbane 2021 Our annual series of popular R workshops is on again between 5th and 12th February 2021, in person at the University of Queensland. Over the past 5 years we’ve successfully trained hundreds of academics, researchers and s... [Read more...]

New course on preparation and graphing of biological data in R We’re running a short online introduction to data preparation and graphing. The course will cover the basics of pre-processing data, including common data wrangling routines. We will use r... [Read more...]