At the start of 2024 Brian Gerber, Kadambari Devarajan, Zach Farris and I released the Diel.Niche R package and companion paper in the Journal of Animal Ecology. In this R package, we provide a way to quantify a species diel phenotype (e.g.…
When you flip a fair coin, the probability that you get heads at least once increases with the number of times you flip the coin. This makes intuitive sense. More chances means you are more likely to succeed at least once. If you wanted to
When fitting complex models in NIMBLE or JAGS you can end up with hundreds or even thousands of parameters. Take, for example, a multi-species occupancy model. In NIMBLE that would look something like this: From this model we would want to
In the past few years I have had the opportunity to either review a decent number of papers that have used the Rota et al. (2016) occupancy model or talk to graduate students that are interested in applying that model (or other offshoots of…
When cleaning data for different analyses one of the first things you need to do is determine if there are any data entry errors present. For spatial coordinate data, this would mean plotting the points out on a map to determine if they fal…
I have to be honest. It’s been a while since I’ve actually thought about fitting a static, or single season, occupancy model. Why? The lab I am part of has been camera trapping in Chicago for over a decade. So naturally, we generally use di…
Okay, so I’m finally starting to make the move from JAGS to NIMBLE. The reason I’ve decided to do this is mostly because of all the customization you can do with NIMBLE in terms of easily specifying different samplers. JAGS uses a slice sam…
This is the second post in a series I am writing on multistate occupancy models. I will be building off my previous example of a static multistate model, so if you’ve not read the first post be sure to check it out here. Likewise, if want m…
Let’s say we have two curves, there is some overlap between them, and we want to calculate the amount of area of overlap. One way we can do this is with some numerical integration (assuming we have a sufficient number of points for both cur…
I’ve got a little bone to pick with the term multistate occupancy model. As the name implies, multistate occupancy models estimate multiple states across space and sometimes through time (e.g., species absent, species present but not breedi…
Species distribution models (SDMs) are useful tools in ecology and conservation biology. As the name implies, SDMs are used to estimate species presence or abundance across geographic space and through time. At their core, SDMs are a way to…
There are a lot of different ways to algebraically write out a statistical model, and as such there are an equally large number of ways to write a model in Nimble, JAGS, or Stan. One technique that I see in introductory text books on Bayesi…