Published in @jappliedecology.bsky.social!😀
We show how (Hierarchical) Hidden Markov Models ((H)HMMs) can be tailored to different epidemiological scenarios to infer disease status directly from animal movement data.
🔗 ttps://besjournals.onlinelibrary.wiley.com/doi/10.1111/1365-2664.70323
Also similar: step selection functions where Pr(move) = movement model * resource selection.
But still challenging: still need to choose form of availability model; interpretation of "resource selection" changes for different models of movement/availability, etc.
Is this similar to weighted distributions where selection + availability estimated jointly?
Lele & Keim 2006. Weighted distributions and estimation of resource selection probability functions.
Johnson et al 2013. Estimating animal resource selection from telemetry data using point process models.
Periodically stationary distribution (probability that the fly is active) as a function of the time of day. True stationary distribution is compared to biased approximation, and we see a substantial difference.
Our paper on #HMMs with periodically ⏰ varying transition probabilities is published! 🎉 @carlinafeldmann.bsky.social, Sina Mews, @rmichels.bsky.social @rolandlangrock.bsky.social
doi.org/10.1214/25-AOAS2107
We derive the periodically #stationary distribution and the implied dwell-time distribution
Figure with two panels. Left panel: visualisation of a 3D movement track. Right panel: visualisation of the 3D direction of movement as two angles (one horizontal angle and one vertical angle).
We have a preprint about modelling three-dimensional movement tracks, led by @njklappstein.bsky.social.
The model takes the form of a step selection function and, just like in 2D, it can include directional persistence, attraction to targets, and habitat selection.
doi.org/10.1101/2025...
We've got a great plenary speaker lineup -- covering theoretical ecology, statistics, AI, conservation, disease ecology, animal movement, Bayesian stats, machine learning & more!
Deadline for workshops + round tables on Nov 15: statisticalecology.org (in English o en español)
Come join us!
In hindsight, we might have been able to avoid a few bugs if we had been discussing this in a meeting room rather than yelling at each other, 30 meters apart in a field... But it was well worth it!
Version history of moveHMM R package, showing version 1.0 dated 2015-10-23
moveHMM version 1.0 turns 10 today 🎉 Such a fun 10 years; exchanging with folks who use the package (and its extensions) has been one of the best parts of my job!
The next International Statistical Ecology Conference (ISEC) will take place in Mérida, México, on January 8-15, 2027. Very exciting!
The organisers are inviting submissions for workshops and round table discussions: statisticalecology.org (Deadline: November 15th)
🚨 New preprint!
Have you ever wondered if we can detect disease in wildlife just by looking at their movement?
We show how hidden Markov models can link animal trajectories to infection states — tested on reintroduced scimitar-horned oryx and simulated data.
👉 arxiv.org/abs/2509.21132
The hmmTMB paper is finally out in the Journal of Statistical Software!
An R package for hidden Markov models with random effects, flexible spline-based covariate effects, and fast inference using TMB or Stan.
Check out the GIthub repository for more examples.
doi.org/10.18637/jss...
Like to develop spatio-temporal models? Interested in Arctic marine mammals 🦭🐳 and their susceptibility to oil spills? You may be the postdoctoral fellow Dr. Mariane Marcoux and I are looking for! See the details in the job ad: tinyurl.com/spatiostatamm
History-changing day for labour relations at @dalhousieu.bsky.social. Lockout of faculty could begin as early as Wed morning. Rest assured, DFA members are ready for what is about to happen. #keepdalstrong @cupe3912.bsky.social @nsgeu.bsky.social @ansut.bsky.social @caut.bsky.social
New PhD position in our group! Join us to study gull foraging ecology at sea using GPS and accelerometry data! You will be working here Amsterdam Movement Ecology group under supervision of @judyshamounb.bsky.social, @rooskentie.bsky.social and me. Apply here werkenbij.uva.nl/en/vacancies...
The world is on 🔥 -- and here's my first publication in an astronomy journal: iopscience.iop.org/article/10.3...
We combine Gaussian processes + hidden Markov models to efficiently detect stellar flares in one modelling step. 🧪
All my ecology peeps slinging the GAM(M)s might find this paper interesting. I was surprised to learn there is a frequentist interpretation of GAM(M)s! (jk) besjournals.onlinelibrary.wiley.com/doi/full/10....
Sina Mews, Roland Langrock, and I have updated 🆕 our review paper!
It offers a comprehensive overview on choosing the right time ⏰ and space 📏 formulation for latent Markov models, providing a unifying perspective on discrete- and continuous-time HMMs, SSMs and MMPPs.
👉 arxiv.org/abs/2406.19157
Animal movement workshop alert! A line of speakers difficult to beat with John Fieberg, Marie Auger-Méthé, Brett McClintock & Inês Silva and the location is definitely a place that makes you "move" for it: lovely Madeira. 19-23 May 2025. Just after the ECS in Azores. It's PT islands 2025. See you?
Posterior sampled for relationship between transition probabilities and covariates in a 2-state hidden Markov model. The posterior samples allow for convenient visualisation of the uncertainty.
Updated vignette on Bayesian inference for hidden Markov models with hmmTMB: specifying priors, extracting posterior samples, visualising posterior uncertainty for estimated distributions and covariate-parameter relationships, etc.
Based on Stan, so it's pretty fast too!
github.com/TheoMichelot...
Recently discovered a fun webpage called Probability Playground where you can interactively explore probability distributions.
It’s helpful especially for distributions with parameters that are not immediately intuitive. Very cool!
www.acsu.buffalo.edu/~adamcunn/pr...
Here are some thoughts on teaching #statistics to non-statistical students, specifically those in #applied #ecology degrees. Thanks to Will Kay and Tiago Marques for an enjoyable (and not last) collaboration.
You can access the PDF here 👉 tinyurl.com/33keh22s
Going to test out the power of new followers! Does anyone here (or do you know anyone who) teach statistics (specifically GLMs) to primarily ecology/evolution/bio students and would be willing to potentially review a book proposal?
