Quantitative Ecologist and Consultant @realQuantecol | 🇳🇱 in 🇦🇺 | Field Herping and Wildlife Tours
Ballina, New South Wales
Joined January 2019
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occARU: Bayesian (multispecies) occupancy models for ARU data using @mcmc_stan. Automated recording units (ARUs) like camera traps produce rich time series which warrant going beyond occupancy and focusing on detection rates. 1/n
mhollanders.github.io/occARU…
occARU now supports multiseason occupancy. The package (1) detects which sites were sampled in each season and then (2) fits a continuous time dynamic occupancy model for repeatedly sampled sites. 1/n
mhollanders.github.io/occARU…
The ecological parameters are recovered as:
logit(psi) = alpha[1] + lambda[1] * eta
log(gamma) = alpha[2] + lambda[2] * eta
log(epsilon) = alpha[3] + lambda[3] * eta
Maybe not everyone's cup of tea, but drastically reduces model complexity; nice for multispecies models! 5/n
As for the single season model, posterior inference on underlying occupancy states is done with the forward-backward sampling algorithm, in occARU_rng() here: 6/6
github.com/mhollanders/occAR…
occARU accommodates site-level predictors for occupancy and detection and additionally site-by-survey level predictors for detection rates. Continuous, categorical, and ordinal predictors are currently supported. Model complexity is handled via global-local shrinkage priors. 4/n
Single season models are currently supported for single- and multispecies analyses. Dynamic occupancy models, where sites are surveyed over several disjuct periods, are currently under development. To read more about the model, see the model vignette. 5/5
mhollanders.github.io/occARU…
New pre-print! I cover a range of open capture-recapture models (single survey/robust design, multistate/multievent, in (Cormack-)Jolly-Seber variants) in Stan, and provide efficient log likelihood functions... 1/n
ecoevorxiv.org/repository/vi…
I am once again trying to submit a manuscript to a journal that only accepts PDF submissions. Wish me luck.
Matthijs Hollanders retweeted
I'm going to repeat my concluding takeaway: science is hard. And the profession should be constructed in such a way – taking replication and reproducibility seriously, and institutionalizing it, rather than punishing it – to reflect that reality.
Matthijs Hollanders retweeted
Me: Decimal points are missing, and please check the identical data.
Correction: Decimal points added. Identical numbers are identical numbers.
Scientific Reports: Cool.
Me: Bro......
pubpeer.com/publications/757…
