Ben Augustine
@bencaugustine.bsky.social
Ecological Statistics. I came for the charismatic megafauna and stayed for the problematic megamodels. Skeptic. github.com/benaug
OK, I think this is done cooking for now. Added examples of fitting several other jolly-seber data augmentation models using Gibbs updates for latent states instead of updating them conditionally. Read to of readme and then scroll down to "alternative data augmentation approaches". So fast!
GitHub - benaug/Jolly-Seber-N-Prior-DA: Jolly-Seber MCMC samplers using N-prior data augmentation
Jolly-Seber MCMC samplers using N-prior data augmentation - benaug/Jolly-Seber-N-Prior-DA
github.com
Three ways to fit the Schwarz-Arnason data augmentation model from Royle and Dorazio (2008). Original approach, marginalized, and (i think new) entry probabilities approach. Third was most efficient in limited comparison. It gets you a conjugate update for pi that marginalization breaks.
Me: Can you evaluate this via MCMC? ChatGPT: yes (thinks for 5 minutes), here are the results! Me: Did you actually run the MCMC? ChatGPT: No, I lied. I made the numbers up.
Yea, OK, mixing can be fine with conditional version of SMR, too, with abundant telemetry data. Runs faster, so you can run more iterations per unit time. Poor mixing in conditional model more of an issue for abundance, survival, recruitment. Negbin obsmod here.
Ben Augustine@bencaugustine.bsky.social · 2mo agoWith abundant telemetry data and patience, you can get acceptable (but still not good) mixing for yearly RSF movement parameters in open population SMR. At least when marginalizing out individual ID. Not sure if it's worth making a version for the conditional model where mixing already is not great
Just over one week left to apply for the Biometric Working Group’s student travel grant. If you’re a student presenting at The Wildlife Society annual conference this fall, consider applying! No need to be a BWG member. Application deadline is July 3. Details in the link.
TWS Biometrics Working Group - Student Travel Grants
The purpose of the student travel grants is to promote and support student interest in biometrics and the Biometrics Working Group by attending The Wildlife Society annual conference. The number of gr...
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With abundant telemetry data and patience, you can get acceptable (but still not good) mixing for yearly RSF movement parameters in open population SMR. At least when marginalizing out individual ID. Not sure if it's worth making a version for the conditional model where mixing already is not great
What do people think are the least well understood aspects about spatial mark resight? Things people often get wrong? Assumptions that are hard to meet in practice? etc etc
Data simulators/model fitting code for marginal version of SCR random thinning model here github.com/benaug/Rando...
Ben Augustine@bencaugustine.bsky.social · 2mo agoNew random thinning SCR paper
Smithsonian Ecological Data Scientist ad reposted. Sounds more strictly like data science now, less quantitative ecology/statistics?
Data Scientist, IS-1560-12
Job Opening: Data Scientist, IS-1560-12 at National Zoo and Conservation Biology Institute in Front Royal, VA.
trustcareers.si.edu
Cluster SCR model for perfectly aggregated and cohesive groups where you observe individual ID but not group ID. Pretty sure. 😆 github.com/benaug/Group...
Dusted off this model for group SCR with unknown group IDs. It is difficult to determine which updates are needed to fully explore the posterior, but currently works well with higher group D and smaller group sizes. But posterior bottlenecks otherwise. Need to see if I can alleviate those.
Job Alert: Smithsonian's National Zoo and Conservation Biology Institute is hiring a Data Scientist with robust quantitative skills, knowledge of best practices with data management, and an ability to collaborate across units. Based in Front Royal, VA. trustcareers.si.edu/postings/c63...
Ecological Data Scientist, IS-1560-12
Job Opening: Ecological Data Scientist, IS-1560-12 at National Zoo and Conservation Biology Institute in Front Royal, VA.
trustcareers.si.edu
Open population SMR scenario with marking effort only in years 1 and 3 out of 6. 60% of marks stay on until following year, 40% make it to 2nd year (unless animal dies), so marks persist into sighting only years.
Hey, open population SMR works after all. First stab. github.com/benaug/Spati...
Messing around with Open SCR + telemetry survival. Here, Method A is live capture to deploy a collar, assumed to stay on for 2 years or until they die (starting simple). Method B is some generic capture recapture method, say hair snares. So hair snare in years 1,3,5, live cap in years 2,4.
Leveled up this OpenPopSCR model with density covs in year 1 and RSF activity center relocation--runs faster, mixes better. Ran this in 1.5 hours. M=225, 5 years, 144 traps/year, 1156 habitat cells. Effective sample sizes: D.beta1 rsf.beta sigma.move 779.5270 397.6123 368.2466
Looking for candidate motivating data sets for open population SCR methods. Need multiple years of capture-recapture data with concurrent telemetry collars where you have capture recapture data to explain how they were marked. Spatial IPM where telemetry informs survival.
Still not great mixing, but finding that open pop SCR dispersal scale parameters mix better if you don't keep the activity centers in the model for augmented individuals are not in the population and just propose a new s trajectory when proposing to turn them on
The Chandler Clark Jolly Seber parameterization implies Poisson entries as M goes to infinity, but in practice we want to set M as low as we can get away with. This causes the variance in recruits to be less than Poisson variance and it shrinks through time. Here "slack" is M - N.super.
17 years ago. Today, I have to simulate my own bears.
I’m recruiting a PhD and MSC student for fall 2026 working on the movement ecology and conservation of Mexican spotted owls in SW forests and rocky canyonlands. Exciting partnership with Los Alamos National Laboratory. Great vibrant lab group, high impact research! 🦉 gavinmjones.com/opportunities/
Opportunities
***PhD and MSc openings – Movement ecology and conservation*** I will periodically support graduate students, postdocs, and other staff through the Biology Department at the University of New…
gavinmjones.com
If anyone goes through my phone after I die, they'll find a bunch of random pictures of code. I bet they will be baffled. Who would guess that I look for bugs in my code while falling asleep and email myself if I figure it out so I don't forget. When I do some of my best work!
