Single-Species, Multi-Species, and Integrated Spatial Occupancy Models
Extract Model Fitted Values for svcMsPGOcc Object
Extract Model Fitted Values for svcPGBinom Object
Extract Model Fitted Values for svcPGOcc Object
Extract Model Fitted Values for svcTIntPGOcc Object
Extract Model Fitted Values for svcTMsPGOcc Object
Extract Model Fitted Values for svcTPGBinom Object
Extract Model Fitted Values for svcTPGOcc Object
Extract Model Fitted Values for tIntPGOcc Object
Extract Model Fitted Values for tMsPGOcc Object
Extract Model Fitted Values for tPGOcc Object
Extract spatially-varying coefficient MCMC samples
Detection-nondetection data of 12 foliage gleaning bird species in 201...
Elevation in meters extracted at a 30m resolution across the Hubbard B...
Detection-nondetection data of 12 foliage gleaning bird species from 2...
Function for Fitting Integrated Multi-Species Occupancy Models Using P...
Function for Fitting Single-Species Integrated Occupancy Models Using ...
Function for Fitting a Latent Factor Joint Species Distribution Model
Function for Fitting Latent Factor Multi-Species Occupancy Models
Function for Fitting Multi-Species Occupancy Models Using Polya-Gamma ...
Detection-nondetection data of 12 foliage gleaning bird species in 201...
Function for Fitting Single-Species Occupancy Models Using Polya-Gamma...
Function for Fitting Linear Mixed Models with Previous Model Estimates
Function for performing posterior predictive checks
Function for prediction at new locations for integrated multi-species ...
Function for prediction at new locations for single-species integrated...
Function for prediction at new locations for latent factor joint speci...
Function for prediction at new locations for latent factor multi-speci...
Function for prediction at new locations for multi-species occupancy m...
Function for prediction at new locations for single-species occupancy ...
Function for prediction at new locations for spatial factor joint spec...
Function for prediction at new locations for spatial factor multi-spec...
Function for prediction at new locations for single-species integrated...
Function for prediction at new locations for multi-species spatial occ...
Function for prediction at new locations for single-species spatial oc...
Function for prediction at new locations for multi-season single-speci...
Function for prediction at new locations for multi-season multi-specie...
Function for prediction at new locations for multi-season single-speci...
Function for prediction at new locations for spatially varying coeffic...
Function for prediction at new locations for single-species spatially-...
Function for prediction at new locations for single-species spatially-...
Function for prediction at new locations for multi-season single-speci...
Function for prediction at new locations for multi-season multi-specie...
Function for prediction at new locations for multi-season single-speci...
Function for prediction at new locations for multi-season single-speci...
Function for prediction at new locations for multi-season single-speci...
Function for prediction at new locations for multi-season multi-specie...
Function for prediction at new locations for multi-season single-speci...
Occupancy and detection residuals for PGOcc models
Occupancy and detection residuals for spPGOcc models
Occupancy and detection residuals for svcPGOcc models
Function for Fitting a Spatial Factor Joint Species Distribution Model
Function for Fitting Spatial Factor Multi-Species Occupancy Models
Simulate Single-Species Binomial Data
Simulate Multi-Species Detection-Nondetection Data from Multiple Data ...
Simulate Single-Species Detection-Nondetection Data from Multiple Data...
Simulate Multi-Species Detection-Nondetection Data
Simulate Single-Species Detection-Nondetection Data
Simulate Multi-Season Single-Species Binomial Data
Simulate Single-Species Multi-Season Detection-Nondetection Data from ...
Simulate Multi-Species Multi-Season Detection-Nondetection Data
Simulate Multi-Season Single-Species Detection-Nondetection Data
Function for Fitting Single-Species Integrated Spatial Occupancy Model...
Function for Fitting Multi-Species Spatial Occupancy Models Using Poly...
Single-Species, Multi-Species, and Integrated Spatial Occupancy Models
Function for Fitting Single-Species Spatial Occupancy Models Using Pol...
Function for Fitting Multi-Season Single-Species Spatial Integrated Oc...
Function for Fitting Multi-Species Multi-Season Spatial Occupancy Mode...
Function for Fitting Multi-Season Single-Species Spatial Occupancy Mod...
Methods for intMsPGOcc Object
Methods for intPGOcc Object
Methods for lfJSDM Object
Methods for lfMsPGOcc Object
Methods for tPGOcc Object
Function for Fitting Multi-Species Spatially-Varying Coefficient Occup...
Function for Fitting Single-Species Spatially-Varying Coefficient Bino...
Function for Fitting Single-Species Spatially-Varying Coefficient Occu...
Function for Fitting Multi-Season Single-Species Spatially-varying Coe...
Function for Fitting Multi-Species Multi-Season Spatially-Varying Coef...
Function for Fitting Multi-Season Single-Species Spatially-Varying Coe...
Function for Fitting Multi-Season Single-Species Spatially-Varying Coe...
Function for Fitting Multi-Season Single-Species Integrated Occupancy ...
Function for Fitting Multi-Species Multi-Season Occupancy Models
Function for Fitting Multi-Season Single-Species Occupancy Models Usin...
Update a spOccupancy or spAbundance model run with more MCMC iteration...
Compute Widely Applicable Information Criterion for spOccupancy Model ...
Extract Model Fitted Values for sfMsPGOcc Object
Extract Model Fitted Values for spIntPGOcc Object
Extract Model Fitted Values for spMsPGOcc Object
Extract Model Fitted Values for spPGOcc Object
Extract Model Fitted Values for stIntPGOcc Object
Extract Model Fitted Values for stMsPGOcc Object
Extract Model Fitted Values for stPGOcc Object
Extract Model Fitted Values for PGOcc Object
Extract Model Fitted Values for sfJSDM Object
Extract Model Fitted Values for intPGOcc Object
Extract Model Fitted Values for lfJSDM Object
Extract Model Fitted Values for lfMsPGOcc Object
Extract Model Fitted Values for msPGOcc Object
Methods for msPGOcc Object
Methods for PGOcc Object
Methods for postHocLM Object
Methods for ppcOcc Object
Methods for sfJSDM Object
Methods for svcTIntPGOcc Object
Methods for sfMsPGOcc Object
Methods for spIntPGOcc Object
Methods for spMsPGOcc Object
Methods for spPGOcc Object
Methods for stIntPGOcc Object
Methods for stMsPGOcc Object
Methods for stPGOcc Object
Methods for svcMsPGOcc Object
Methods for svcPGBinom Object
Methods for svcPGOcc Object
Methods for svcTMsPGOcc Object
Methods for svcTPGBinom Object
Methods for svcTPGOcc Object
Methods for tIntPGOcc Object
Methods for tMsPGOcc Object
Fits single-species, multi-species, and integrated non-spatial and spatial occupancy models using Markov Chain Monte Carlo (MCMC). Models are fit using Polya-Gamma data augmentation detailed in Polson, Scott, and Windle (2013) <doi:10.1080/01621459.2013.829001>. Spatial models are fit using either Gaussian processes or Nearest Neighbor Gaussian Processes (NNGP) for large spatial datasets. Details on NNGP models are given in Datta, Banerjee, Finley, and Gelfand (2016) <doi:10.1080/01621459.2015.1044091> and Finley, Datta, and Banerjee (2022) <doi:10.18637/jss.v103.i05>. Provides functionality for data integration of multiple single-species occupancy data sets using a joint likelihood framework. Details on data integration are given in Miller, Pacifici, Sanderlin, and Reich (2019) <doi:10.1111/2041-210X.13110>. Details on single-species and multi-species models are found in MacKenzie, Nichols, Lachman, Droege, Royle, and Langtimm (2002) <doi:10.1890/0012-9658(2002)083[2248:ESORWD]2.0.CO;2> and Dorazio and Royle <doi:10.1198/016214505000000015>, respectively.
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