Occupancy and detection residuals for spPGOcc models

Method for calculating occupancy and detection residuals for single-species spatial occupancy models (spPGOcc) following the approach of Wright et al. (2019).

Usage

# S3 method for spPGOcc
residuals(object, n.post.samples = 100, ...)

Arguments

object

object of class spPGOcc.

n.post.samples

the number of posterior MCMC samples to calculate the residuals for. By default this is set to 100. If set to a value less than the total number of MCMC samples saved for the model, residuals will be calculated for a random subset of the total MCMC samples. Maximum value is the total number of MCMC samples saved.

...

currently no additional arguments

References

Wright, W. J., Irvine, K. M., & Higgs, M. D. (2019). Identifying occupancy model inadequacies: can residuals separately assess detection and presence?. Ecology, 100(6), e02703.

Author

Jeffrey W. Doser doserjef@msu.edu

Value

A list comprised of:

occ.resids

a matrix of occupancy residuals with first dimension equal to n.post.samples and second dimension equal to the number of sites in the data set.

det.resids

a three-dimensional array of detection residuals with first dimension equal to n.post.samples, second dimension equal to the number of sites in the data set, and third dimension equal to the maximum number of repeat visits. Note detection residuals are only calculated for a given site and MCMC iteration when the species is present.