How do I calculate the R squared metric for a Bayesian model? A good friend I met on a field trip long ago, Dominique Roche, recently emailed me to ask about evaluation of Bayesian models. He has been delving into generalized linear models, using Ba... [Read more...]

General Linear Models: The Basics General linear models are one of the most widely used statistical tool in the biological sciences. This may be because they are so flexible and they can address many different problems, that they provide useful output... [Read more...]

Checking residual distributions for non-normal GLMs Quantile-quantile plots If you are fitting a linear regression with Gaussian (normally distributed) errors, then one of the standard checks is to make sure the residuals are approximately normally d... [Read more...]

Stay motivated with R programming by knowing your emotions We don’t usually think of programming as an ‘emotional’ experience. It is all code and computer logic and if using R, probably statistics. But recognising the emotions you face when pro... [Read more...]

Some thoughts about Bayesian Kriging in INLA I have been playing around with spatial modelling in the R INLA package. This blog just records a few thoughts I have had about using INLA for kriging (spatial interpolation). I am keen to discuss these ide... [Read more...]

seascapemodels.org version 2 I just (8-8-2017) updated my webpage to version 2 styling. If something is missing that you use, please let me know. Hope you enjoy the new page. [Read more...]

Impact of the conservation optimism hashtag The hashtag #conservationoptimism became popular during the recent International Congress for Conservation Biology symposium. Michael Burgass asked me what its twitter impact was, so here is a quick analysi... [Read more...]

What analysis programs drive conservation science? With the International Congress for Conservation Biology on at the end of July I was wondering, what analysis programs are supporting conservation science? And, what programs support spatial analysis ... [Read more...]

“Memorable dataviz with the R program” awarded people’s choice prize For the past two years Dr Nick Hamilton has invited me to give a talk on creating data visuals with the R program at the wonderful UQ Winterschool in Bioinformatics. This year... [Read more...]

What are people saying about International Congress for Conservation Biology 2017 on Twitter? Here’s a brief analysis of tweets from the International Congress for Conservation Biology to date. The conference started on the starting 23rd July I was ... [Read more...]

International Congress for Conservation Biology: What analysis program do conservation scientists use? With the International Congress for Conservation Biology starting 23rd July I was wondering, what analysis programs are most commonly used by conser... [Read more...]

Data visuals: notes for my talks in 2017 Supplementary notes for CJ Brown’s talks on dataviz in 2017 for Griffith University’s honours students and the UQ Winterschool in Bioinformatics. Skip to the quiz Visualsing sexual dimorphism in elephant ... [Read more...]

Data visuals 2017 Supplementary notes for CJ Brown’s talks on dataviz in 2017 for Griffith University’s honours students and the UQ Winterschool in Bioinformatics. Skip to the quiz Structure of this talk Tools for dataviz Eleven principles... [Read more...]

What does under or over-dispersion look like? One issue that often comes up in analysis with linear models is under or over dispersion. For instance, if you are fitting a linear regression model, you are assuming the residuals (difference between the... [Read more...]

Smoothing a time-series with a Bayesian model Recently I looked at fitting a smoother to a time-series using Bayesian modelling. Now I will look at how you can control the smoothness by using more or less informative priors on the precision (1/varianc... [Read more...]

Quantifying the magnitude of a population decline with Bayesian time-series modelling Population abundances tend to vary year to year. This variation can make it make it hard detect a change and hard to quantify exactly what that change is. Bayesian ... [Read more...]

Visualising uncertainty in time-series using animations I was reading an example of visualising election outcome uncertainty using a wobbly needle and wondered, could animating uncertainty help communicate for the kind of work I do on population model... [Read more...]

Choosing R packages for mixed effects modelling based on the car you drive There are many roads you can take to fit a mixed effects model (sometimes termed hierarchical models) in R. There are numerous packages that each deploy different engines to fi... [Read more...]

A fast method to add annotations to a plot Making professional looking plots in R can be fiddly. One task that I often spend ages doing is manually finding coordinates to add labels. Wouldn’t it be nice if you could just send the coordinates directl... [Read more...]

Mean trophic levels of a genera from FishBase How would you selectively aggregate observations using R? For instance, say you have a table of trophic level estimates by fish species, but many species are missing values. For those species missing a val... [Read more...]