Software

spAbundance fits univariate (i.e., single-species) and multivariate (i.e., multi-species) spatial N-mixture models, hierarchical distance sampling models, and generalized linear mixed models using Markov chain Monte Carlo (MCMC). Spatial models are fit using Nearest Neighbor Gaussian Processes (NNGPs) to facilitate model fitting to large spatial datasets.

spOccupancy fits single-species, multi-species, and integrated spatial occupancy models using Markov chain Monte Carlo (MCMC). Models are fit using Pólya-Gamma data augmentation. Spatial models are fit using either Gaussian processes or Nearest Neighbor Gaussian Processes (NNGP) for large spatial datasets. The package provides functionality for data integration of multiple single-species occupancy data sets using a joint likelihood framework. For multi-species models, spOccupancy provides functions to account for residual species correlations in a joint species distribution model framework while accounting for imperfect detection. spOccupancy also provides functions for multi-season (i.e., spatio-temporal) occupancy models.