spOccupancy fits single-species, multi-species, and integrated
spatial occupancy models using Markov Chain Monte Carlo (MCMC). Models
are fit using Póly-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. As of v0.4.0, `spOccupancy`

provides functions for
multi-season (i.e., spatio-temporal) single-species occupancy models.
Below we provide a very brief introduction to some of the package’s
functionality, and illustrate just one of the model fitting funcitons.
For more information, see the resources referenced at the bottom of this
page.

You can install the released version of `spOccupancy`

from
CRAN with:

`install.packages("spOccupancy")`

`spOccupancy` Function |
Description |
---|---|

`PGOcc()` |
Single-species occupancy model |

`spPGOcc()` |
Single-species spatial occupancy model |

`intPGOcc()` |
Single-species occupancy model with multiple data sources |

`spIntPGOcc()` |
Single-species spatial occupancy model with multiple data sources |

`msPGOcc()` |
Multi-species occupancy model |

`spMsPGOcc()` |
Multi-species spatial occupancy model |

`lfJSDM()` |
Joint species distribution model without imperfect detection |

`sfJSDM()` |
Spatial joint species distribution model without imperfect detection |

`lfMsPGOcc()` |
Multi-species occupancy model with species correlations |

`sfMsPGOcc()` |
Multi-species spatial occupancy model with species correlations |

`intMsPGOcc()` |
Multi-species occupancy model with multiple data sources |

`tPGOcc()` |
Single-species multi-season occupancy model |

`stPGOcc()` |
Single-species multi-season spatio-temporal occupancy model |

`svcPGBinom()` |
Single-species spatially-varying coefficient GLM |

`svcPGOcc()` |
Single-species spatially-varying coefficient occupancy model |

`svcTPGBinom()` |
Single-species spatially-varying coefficient multi-season GLM |

`svcTPGOcc()` |
Single-sepcies spatially-varying coefficient multi-season occupancy model |

`postHocLM()` |
Fit a linear (mixed) model using estimates from a previous model fit |

`ppcOcc()` |
Posterior predictive check using Bayesian p-values |

`waicOcc()` |
Compute Widely Applicable Information Criterion (WAIC) |

`simOcc()` |
Simulate single-species occupancy data |

`simTOcc()` |
Simulate single-species multi-season occupancy data |

`simBinom()` |
Simulate detection-nondetection data with perfect detection |

`simTBinom()` |
Simulate multi-season detection-nondetection data with perfect detection |

`simMsOcc()` |
Simulate multi-species occupancy data |

`simIntOcc()` |
Simulate single-species occupancy data from multiple data sources |

`simIntMsOcc()` |
Simulate multi-species occupancy data from multiple data sources |

To get started with `spOccupancy`

we load the package and
an example data set. We use data on twelve foliage-gleaning birds from
the Hubbard Brook Experimental
Forest, which is available in the `spOccupancy`

package
as the `hbef2015`

object. Here we will only work with one
bird species, the Black-throated Blue Warbler (BTBW), and so we subset
the `hbef2015`

object to only include this species.

```
library(spOccupancy)
data(hbef2015)
<- dimnames(hbef2015$y)[[1]]
sp.names <- hbef2015
btbwHBEF $y <- btbwHBEF$y[sp.names == "BTBW", , ] btbwHBEF
```

`spPGOcc()`

Below we fit a single-species spatial occupancy model to the BTBW
data using a Nearest Neighbor Gaussian Process. We use the default
priors and initial values for the occurrence (`beta`

) and
regression (`alpha`

) coefficients, the spatial variance
(`sigma.sq`

), the spatial range parameter (`phi`

),
the spatial random effects (`w`

), and the latent occurrence
values (`z`

). We assume occurrence is a function of linear
and quadratic elevation along with a spatial random intercept. We model
detection as a function of linear and quadratic day of survey and linear
time of day the survey occurred.

```
# Specify model formulas
<- ~ scale(Elevation) + I(scale(Elevation)^2)
btbw.occ.formula <- ~ scale(day) + scale(tod) + I(scale(day)^2) btbw.det.formula
```

We run the model using an Adaptive MCMC sampler with a target
acceptance rate of 0.43. We run 3 chains of the model each for 10,000
iterations split into 400 batches each of length 25. For each chain, we
discard the first 6000 iterations as burn-in and use a thinning rate of
4 for a resulting 3000 samples from the joint posterior. We fit the
model using 5 nearest neighbors and an exponential correlation function.
We also specify the `k.fold`

argument to perform 2-fold
cross-validation after fitting the full model. Run `?spPGOcc`

for more detailed information on all function arguments.

```
# Run the model
<- spPGOcc(occ.formula = btbw.occ.formula,
out det.formula = btbw.det.formula,
data = btbwHBEF, n.batch = 400, batch.length = 25,
accept.rate = 0.43, cov.model = "exponential",
NNGP = TRUE, n.neighbors = 5, n.burn = 2000,
n.thin = 4, n.chains = 3, verbose = FALSE, k.fold = 2)
```

This will produce a large output object, and you can use
`str(out)`

to get an overview of what’s in there. Here we use
the `summary()`

function to print a concise but informative
summary of the model fit.

```
summary(out)
#>
#> Call:
#> spPGOcc(occ.formula = btbw.occ.formula, det.formula = btbw.det.formula,
#> data = btbwHBEF, cov.model = "exponential", NNGP = TRUE,
#> n.neighbors = 5, n.batch = 400, batch.length = 25, accept.rate = 0.43,
#> verbose = FALSE, n.burn = 2000, n.thin = 4, n.chains = 3,
#> k.fold = 2)
#>
#> Samples per Chain: 10000
#> Burn-in: 2000
#> Thinning Rate: 4
#> Number of Chains: 3
#> Total Posterior Samples: 6000
#> Run Time (min): 1.4416
#>
#> Occurrence (logit scale):
#> Mean SD 2.5% 50% 97.5% Rhat ESS
#> (Intercept) 3.9738 0.6010 3.0092 3.9023 5.3748 1.0144 164
#> scale(Elevation) -0.5209 0.2194 -0.9778 -0.5152 -0.0984 1.0003 1101
#> I(scale(Elevation)^2) -1.1552 0.2118 -1.6305 -1.1370 -0.7892 1.0070 238
#>
#> Detection (logit scale):
#> Mean SD 2.5% 50% 97.5% Rhat ESS
#> (Intercept) 0.6642 0.1146 0.4413 0.6634 0.8821 1.0014 5474
#> scale(day) 0.2939 0.0712 0.1524 0.2939 0.4335 0.9999 6000
#> scale(tod) -0.0301 0.0697 -0.1698 -0.0302 0.1063 1.0010 6435
#> I(scale(day)^2) -0.0747 0.0862 -0.2410 -0.0755 0.1033 1.0027 6000
#>
#> Spatial Covariance:
#> Mean SD 2.5% 50% 97.5% Rhat ESS
#> sigma.sq 1.1194 1.0085 0.2165 0.7676 4.1197 1.0419 88
#> phi 0.0072 0.0075 0.0007 0.0039 0.0270 1.1564 58
```

The function `ppcOcc`

performs a posterior predictive
check on the resulting list from the call to `spPGOcc`

. For
binary data, we need to perform Goodness of Fit assessments on some
binned form of the data rather than the raw binary data. Below we
perform a posterior predictive check on the data grouped by site with a
Freeman-Tukey fit statistic, and then use the `summary`

function to summarize the check with a Bayesian p-value.

```
<- ppcOcc(out, fit.stat = 'freeman-tukey', group = 1)
ppc.out summary(ppc.out)
#>
#> Call:
#> ppcOcc(object = out, fit.stat = "freeman-tukey", group = 1)
#>
#> Samples per Chain: 10000
#> Burn-in: 2000
#> Thinning Rate: 4
#> Number of Chains: 3
#> Total Posterior Samples: 6000
#>
#> Bayesian p-value: 0.4917
#> Fit statistic: freeman-tukey
```

The `waicOcc`

function computes the Widely Applicable
Information Criterion (WAIC) for use in model selection and assessment
(note that due to Monte Carlo error your results will differ
slightly).

```
waicOcc(out)
#> elpd pD WAIC
#> -681.52155 21.21463 1405.47236
```

Alternatively, we can perform k-fold cross-validation (CV) directly
in our call to `spPGOcc`

using the `k.fold`

argument and compare models using a deviance scoring rule. We fit the
model with `k.fold = 2`

and so below we access the deviance
scoring rule from the 2-fold cross-validation. If we have additional
candidate models to compare this model with, then we might select for
inference the one with the lowest value of this CV score.

```
$k.fold.deviance
out#> [1] 1412.951
```

Prediction is possible using the `predict`

function, a set
of occurrence covariates at the new locations, and the spatial
coordinates of the new locations. The object `hbefElev`

contains elevation data across the entire Hubbard Brook Experimental
Forest. Below we predict BTBW occurrence across the forest, which are
stored in the `out.pred`

object.

```
# First standardize elevation using mean and sd from fitted model
<- (hbefElev$val - mean(btbwHBEF$occ.covs[, 1])) / sd(btbwHBEF$occ.covs[, 1])
elev.pred .0 <- as.matrix(hbefElev[, c('Easting', 'Northing')])
coords.0 <- cbind(1, elev.pred, elev.pred^2)
X<- predict(out, X.0, coords.0, verbose = FALSE) out.pred
```

The `vignette("modelFitting")`

provides a more detailed
description and tutorial of the core functions in
`spOccupancy`

. For full statistical details on the MCMC
samplers for core functions in `spOccupancy`

, see
`vignette("mcmcSamplers")`

. In addition, see our recent paper that
describes the package in more detail (Doser et al. 2022a). For a
detailed description and tutorial of joint species distribution models
in `spOccupancy`

that account for residual species
correlations, see `vignette("factorModels")`

, as well as
`vignette("mcmcFactorModels")`

for full statistical details.
For a description and tutorial of multi-season (spatio-temporal)
occupancy models in `spOccupancy`

, see
`vignette("spaceTimeModels")`

. For a tutorial on
spatially-varying coefficient models in `spOccupancy`

, see
`vignette("svcUnivariateHTML")`

and take a look at our recent pre-print that
presents a series of guidelines and recommendations for using
spatially-varying coefficients in species distribution models.

Doser, J. W., Finley, A. O., Kery, M., and Zipkin, E. F. (2022a). spOccupancy: An R package for single-species, multi-species, and integrated spatial occupancy models. Methods in Ecology and Evolution. https://doi.org/10.1111/2041-210X.13897.

Doser, J. W., Finley, A. O., and Banerjee, S. (2022b). Joint species distribution models with imperfect detection for high-dimensional spatial data. arXiv preprint arXiv:2204.02707.

Doser, J. W., Kery, M., Finley, A. O., Saunders, S. P., Weed, A. S., Zipkin, E. F. (2023). Guidelines for the use of spatially-varying coefficients in species distribution models. arXiv preprint arXiv:2301.05645.