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 |
tPGOcc() |
Single-species multi-season occupancy model |
stPGOcc() |
Single-species multi-season spatio-temporal occupancy model |
ppcOcc() |
Posterior predictive check using Bayesian p-values |
waicOcc() |
Compute Widely Applicable Information Criterion (WAIC) |
simOcc() |
Simulate single-species occupancy data |
simMsOcc() |
Simulate multi-species occupancy data |
simIntOcc() |
Simulate single-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)
sp.names <- dimnames(hbef2015$y)[[1]]
btbwHBEF <- hbef2015
btbwHBEF$y <- btbwHBEF$y[sp.names == "BTBW", , ]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
btbw.occ.formula <- ~ scale(Elevation) + I(scale(Elevation)^2)
btbw.det.formula <- ~ scale(day) + scale(tod) + I(scale(day)^2)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
out <- spPGOcc(occ.formula = btbw.occ.formula,
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): 1.4284
#>
#> Occurrence (logit scale):
#> Mean SD 2.5% 50% 97.5% Rhat ESS
#> (Intercept) 3.9306 0.5843 2.9649 3.8718 5.3272 1.0703 278
#> scale(Elevation) -0.5134 0.2112 -0.9457 -0.5051 -0.1178 1.0070 1110
#> I(scale(Elevation)^2) -1.1388 0.2044 -1.6050 -1.1181 -0.7881 1.0705 466
#>
#> Detection (logit scale):
#> Mean SD 2.5% 50% 97.5% Rhat ESS
#> (Intercept) 0.6663 0.1136 0.4486 0.6656 0.8900 0.9999 5769
#> scale(day) 0.2933 0.0704 0.1531 0.2929 0.4308 1.0000 6000
#> scale(tod) -0.0290 0.0702 -0.1638 -0.0293 0.1070 1.0024 6000
#> I(scale(day)^2) -0.0763 0.0863 -0.2447 -0.0768 0.0910 1.0011 6000
#>
#> Spatial Covariance:
#> Mean SD 2.5% 50% 97.5% Rhat ESS
#> sigma.sq 1.0481 0.9929 0.2094 0.7385 3.8056 1.2883 86
#> phi 0.0085 0.0078 0.0005 0.0053 0.0274 1.1606 53The 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.
ppc.out <- ppcOcc(out, fit.stat = 'freeman-tukey', group = 1)
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: 0.4873
#> Fit statistic: freeman-tukeyThe 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
#> -682.35028 20.86682 1406.43420Alternatively, 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.
out$k.fold.deviance
#> [1] 1496.56Prediction 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
elev.pred <- (hbefElev$val - mean(btbwHBEF$occ.covs[, 1])) / sd(btbwHBEF$occ.covs[, 1])
coords.0 <- as.matrix(hbefElev[, c('Easting', 'Northing')])
X.0 <- cbind(1, elev.pred, elev.pred^2)
out.pred <- predict(out, X.0, coords.0, verbose = FALSE)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 tutoral of multi-season (spatio-temporal)
occupancy models in spOccupancy, see
vignette("spaceTimeModels").
Doser, J. W., Finley, A. O., Kéry, 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.