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Ben Augustine

@bencaugustine.bsky.social
217 followers 146 following 293 posts

Ecological Statistics. I came for the charismatic megafauna and stayed for the problematic megamodels. Skeptic. github.com/benaug

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Reposted by Ben Augustine
Aimee M. Van Tatenhove @full-o-fulmars.bsky.social · 22/09/2026
Two acoustic integration #postdoc positions at @cornellbirds.bsky.social: Statistical integration of eBird and acoustic data academicjobsonline.org/ajo/jobs/32523 Acoustic abundance estimation with eBird data academicjobsonline.org/ajo/jobs/32728 Please share and reach out with any questions!
academicjobsonline.org
Cornell University, Lab of Ornithology
Job #AJO32523, WDR-00061235 Postdoc Associate eBird-acoustic statistical integration, Cornell University, Ithaca NY, Cornell Lab of Ornithology, Lab of Ornithology, Cornell University, Ithaca, New Yor...
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Ben Augustine @bencaugustine.bsky.social · 22/09/2026
On one hand, I don't like hiding most of the model in a custom distribution, but on the other hand, the model runs 228x faster here, so.....
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Ben Augustine @bencaugustine.bsky.social · 04/09/2026
Refactored this Royle-Young model for search encounter surveys of individuals. Between this and a joint N/density intercept update, runs 12x faster on an real world data set.
github.com
GitHub - benaug/RoyleYoung: Royle Young models for area or transect searches where you detect individuals (not their sign). Density and resource selection. Data simulators and files to fit models in ...
Royle Young models for area or transect searches where you detect individuals (not their sign). Density and resource selection. Data simulators and files to fit models in nimble. Known ID versions...
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Ben Augustine @bencaugustine.bsky.social · 19/08/2026
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.com
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
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Ben Augustine @bencaugustine.bsky.social · 07/08/2026
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.
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Ben Augustine @bencaugustine.bsky.social · 25/06/2026
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.
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Reposted by Ben Augustine
Sarah B. Bassing, PhD @sbassing.bsky.social · 24/06/2026
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.
sites.google.com
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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Ben Augustine @bencaugustine.bsky.social · 24/06/2026
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
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Ben Augustine @bencaugustine.bsky.social · 23/06/2026
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
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Ben Augustine @bencaugustine.bsky.social · 23/06/2026
Data simulators/model fitting code for marginal version of SCR random thinning model here github.com/benaug/Rando...
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Ben Augustine @bencaugustine.bsky.social · 22/06/2026
New random thinning SCR paper
besjournals.onlinelibrary.wiley.com
Making the most of hard‐won data: Incorporating commonly discarded information from unidentifiable samples improves precision and cost‐effectiveness in wolf population monitoring
RT-SCR provides a principled and cost-effective way to recover information from samples that are usually discarded, improving both precision and the reliability of parameter estimates without extra f...
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Ben Augustine @bencaugustine.bsky.social · 12/06/2026
Friday code fuel genghistron.bandcamp.com/album/signal...
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Ben Augustine @bencaugustine.bsky.social · 05/06/2026
Spatial mark resight is coming out of my ears
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Ben Augustine @bencaugustine.bsky.social · 21/05/2026
This postdoc looks awesome recruit.visma.com/spa/public/a...
recruit.visma.com
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Ben Augustine @bencaugustine.bsky.social · 18/05/2026
Smithsonian Ecological Data Scientist ad reposted. Sounds more strictly like data science now, less quantitative ecology/statistics?
trustcareers.si.edu
Data Scientist, IS-1560-12
Job Opening: Data Scientist, IS-1560-12 at National Zoo and Conservation Biology Institute in Front Royal, VA.
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Ben Augustine @bencaugustine.bsky.social · 17/05/2026
Cluster SCR model for perfectly aggregated and cohesive groups where you observe individual ID but not group ID. Pretty sure. 😆 github.com/benaug/Group...
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Ben Augustine @bencaugustine.bsky.social · 06/05/2026
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.
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Reposted by Ben Augustine
Philip Patton @ptpatton.bsky.social · 20/04/2026
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...
trustcareers.si.edu
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.
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Ben Augustine @bencaugustine.bsky.social · 11/04/2026
I never understand what the bots are up to
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Ben Augustine @bencaugustine.bsky.social · 10/04/2026
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.
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Ben Augustine @bencaugustine.bsky.social · 05/04/2026
Hey, open population SMR works after all. First stab. github.com/benaug/Spati...
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Ben Augustine @bencaugustine.bsky.social · 04/04/2026
Saturday code fuel thecallousdaoboys.bandcamp.com/album/gigant...
thecallousdaoboys.bandcamp.com
Gigantic Parasite Tongue, by The Callous Daoboys
1 track album
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Ben Augustine @bencaugustine.bsky.social · 27/03/2026
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.
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Ben Augustine @bencaugustine.bsky.social · 20/03/2026
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
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Ben Augustine @bencaugustine.bsky.social · 19/03/2026
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.
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Ben Augustine @bencaugustine.bsky.social · 19/03/2026
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
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Ben Augustine @bencaugustine.bsky.social · 13/03/2026
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.
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Ben Augustine @bencaugustine.bsky.social · 08/03/2026
17 years ago. Today, I have to simulate my own bears.
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Reposted by Ben Augustine
gavin jones @ecologyofgavin.bsky.social · 05/12/2025
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/
gavinmjones.com
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…
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Ben Augustine @bencaugustine.bsky.social · 07/03/2026
Saturday code fuel moeldk.bandcamp.com/album/dreamc...
moeldk.bandcamp.com
DREAMCRUSH, by MØL
11 track album
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Ben Augustine @bencaugustine.bsky.social · 05/03/2026
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!
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Ben Augustine @bencaugustine.bsky.social · 04/03/2026
Hypothesis: data aug can screw up RJMCMC for Dcov selection in SCR because of the z=0 individuals that still have likelihoods for their activity centers. You can actually have z=0 individuals not have ACs and simulate them when proposing to turn them on. I bet you'd get different inclusion probs.
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Ben Augustine @bencaugustine.bsky.social · 03/03/2026
Just saw this group SMR paper and was wondering how they did it without using the Emmett approach with double data augmentation! I got it wrong in my first attempt. This works because of the "using data twice" approach where you model marked data as marked and then combine with unmarked.
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Ben Augustine @bencaugustine.bsky.social · 26/02/2026
From ChatGPT 😆 "The space of “people who would want to do this” ∩ “people willing to implement extremely complex custom samplers” is small."
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Ben Augustine @bencaugustine.bsky.social · 14/02/2026
Modified the Royle-Young supermodel to do sign searches (e.g., scat transects). Lets you retain the continuous det locs instead of snapping to effective detector centroid. Assumes perfect compensatory heterogeneity. Within home range resource selection. Seems like an improvement.
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Ben Augustine @bencaugustine.bsky.social · 08/02/2026
🤔🧐 Some of the better fits. Used dirichlet-multinomial model for telemetry counts in cells, within cell location informs avail sigma. Random RSF slopes for individuals. Need better covariates or spatial random effects, but seems pretty cool. Daily locs, probably need to thin more.
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Ben Augustine @bencaugustine.bsky.social · 06/02/2026
Not sure who this Ben is, but they freak me out weekly--what did i agree to, and who is asking me questions!?
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Ben Augustine @bencaugustine.bsky.social · 04/02/2026
Nothing new here, but inference about landscape connectivity and resource selection could differ a lot depending on how availability is defined. Here, decay is halfnormal, hazard, annular-normal (territorial sps?)
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Ben Augustine @bencaugustine.bsky.social · 31/01/2026
Simulation of home range placement and within home range resource selection with connectivity constraints for availability. Assuming the road is narrow relative to grid res and animals can spend time in road cells if they contain good habitat, just are less likely to cross them.
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Ben Augustine @bencaugustine.bsky.social · 27/01/2026
Multivariate Probit occupancy model explored recently by Dorazio et al. works much better than initially presented. besjournals.onlinelibrary.wiley.com/doi/10.1111/...
besjournals.onlinelibrary.wiley.com
Correction to ‘An evaluation of multi‐species occupancy models with correlated species occurrences’
Click on the article title to read more.
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Ben Augustine @bencaugustine.bsky.social · 20/01/2026
Exploring impact of search effort resolution for Royle-Young model. How accurate does it need to be? In this scenario, probably 1sigma or less. 2sigma only -4% bias, not bad. 4sigma -8%
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Ben Augustine @bencaugustine.bsky.social · 13/01/2026
One thing regular SCR does not account for is if you have a hard boundary like hab mask, detection probability should generally go up inside the hab mask if the detection function extends beyond it. Ignoring this can introduce false individual heterogeneity in p. Proper RSF model is one solution.
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Reposted by Ben Augustine
Chris Sutherland @chrissuthy.bsky.social · 28/12/2025
We are recruiting several PhD students. If you are interested in conservation conflicts, population ecology, quantitative ecology, or biodiversity, check these projects out (links in the thread, feel free to reach out):
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Ben Augustine @bencaugustine.bsky.social · 24/11/2025
Passing those posterior predictive checks
media.tenor.com
a man wearing 3d glasses and a hard hat says " like a boss "
ALT: a man wearing 3d glasses and a hard hat says " like a boss "
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Ben Augustine @bencaugustine.bsky.social · 19/11/2025
Recently came across this Dorazio et al. paper showing that parameter expansion can make probit multispecies occupancy models much more efficient to sample. besjournals.onlinelibrary.wiley.com/doi/full/10.... I wanted to learn a new trick so I made a nimble version. github.com/benaug/Probi...
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Ben Augustine @bencaugustine.bsky.social · 19/11/2025
Today I learned that people will just remove individuals with large home range sizes from their SCR analyses and not tell anyone
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Ben Augustine @bencaugustine.bsky.social · 05/11/2025
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Reposted by Ben Augustine
Sara Beery @sarameghanbeery.bsky.social · 03/11/2025
COME WORK WITH ME!!! Very exciting open faculty position at MIT, with ecosystem and biodiversity modeling as a focus! cee.mit.edu/people/share...
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Ben Augustine @bencaugustine.bsky.social · 31/10/2025
TIL that the slice sampler in jags can't handle unbounded support so jags uses MH that adds/subtracts 1 integer at a time to update latent poisson RVs etc. 🤯 Nimble FTW again.
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Ben Augustine @bencaugustine.bsky.social · 29/10/2025
added a more rigorous explanation of my N-prior data augmentation approach
github.com
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