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occStan: Occupancy models with RStan

November 16, 2021

occStan is an R package (R Core Team 2021) providing a collection of occpuancy Bayesian models written in the Stan language as called through RStan (Stan Development Team 2021). The package is a USGS software software release.

The purpose of the package is to document these models for use in USGS projects and allow easy discrimination. The package assumes the user is familiar with R and occupancy models including Bayesian modeling. Furthermore, occStan assumes the user has advanced level-knowledge of these areas. The package is easier to use than compiling RStan models on ones own,
but requires more technical skill than using functions such as lm() or glm(). occStan users would also befit from understanding how RStan works because it relies upon that package and users may use RStan tools for model diagnostics (and would benefit from doing so!) such as rstan::traceplot() to understand if their model converged.

Currently, the project includes multiple models including

A 2-level occupancy model
A 3-level occupancy model

The R package contains vignettes providing an overview of the package and how to use the models. To access these, type browseVignettes("occStan") in R.

Publication Year 2021
Title occStan: Occupancy models with RStan
DOI 10.5066/P9YUC2EB
Authors Richard A Erickson, Laura L Peterman
Product Type Software Release
Record Source USGS Digital Object Identifier Catalog
USGS Organization Upper Midwest Environmental Sciences Center