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 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...]

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...]

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...]

Make your R simulation models 20 times faster R can be frustratingly slow if you use its loops. However, you can speed it up significantly (e.g. 20 times!) using the Rcpp package. That could turn a day long simulation into an hour long simulation. I ... [Read more...]

Part 3: Spatial analysis of geotagged data See the other parts in this series of blog posts. In parts 1 and 2 we extracted spatial coordinates from our photos and then made an interactive web map that included data associate with those photos. Here I... [Read more...]

Part 2: Create an interactive web map with geotagged photos See the other parts in this series of blog posts. In part 1 we looked at making a simple interactive map using locations from our geotagged photos. Those photos have data associated with the... [Read more...]

Part 1: Extracting exif data from photos using R See the other parts in this series of blog posts. My camera comes with an inbuilt GPS allowing you to geo-reference photos you take. Here is a simple example for how we can use this feature to create a... [Read more...]

From geotagged photos to species distribution models My camera comes with an inbuilt GPS allowing you to geotag photos. I was on a family holiday on the beautiful Hornby Island (near Vancouver) and started wondering why the oysters growing on the rock... [Read more...]

A ‘tidyverse’ approach to simulation models I am a big fan of Rstudio’s (mainly led by Hadley Wickham) series of R packages known as the ‘tidyverse’. The packages modernise much of R’s functionality to better deal with moderately large da... [Read more...]

How to inset a plot on another plot in R The difficulty of plotting one plot over the top of another in R has always frustrated me. I often end up opening some photo editing software (like Gimp, which is free) and doing it manually. However, manual ed... [Read more...]