ubms is an R package for fitting Bayesian hierarchical models of
animal occurrence and abundance. The package has a formula-based
interface compatible with
unmarked,
but the model is fit using MCMC with Stan
instead of using maximum likelihood. Currently there are Stan versions
of unmarked functions occu, occuRN, colext, occuTTD, pcount,
distsamp, and multinomPois. These functions follow the stan_
prefix naming format established by
rstanarm.
For example, the Stan version of the unmarked function occu is
stan_occu.
Advantages compared to unmarked:
- Obtain posterior distributions of parameters and derived parameters
- Include random effects in parameter formulas (same syntax as
lme4) - Assess model fit using WAIC and LOO via the loo package
Disadvantages compared to unmarked:
- MCMC is slower than maximum likelihood
- Not all model types are supported
- Potential for convergence issues
ubms is on
CRAN:
install.packages("ubms")Alternatively, the latest development version can be installed from Github:
# install.packages("devtools")
devtools::install_github("biodiverse/ubms")A detailed vignette for the package is available here.
