spOccupancy (version 0.8.0)

predict.spMsPGOcc: Function for prediction at new locations for multi-species spatial occupancy models

Description

The function predict collects posterior predictive samples for a set of new locations given an object of class `spMsPGOcc`. Prediction is possible for both the latent occupancy state as well as detection.

Usage

# S3 method for spMsPGOcc
predict(object, X.0, coords.0, n.omp.threads = 1, verbose = TRUE, 
                            n.report = 100, ignore.RE = FALSE, type = 'occupancy', ...)

Value

An list object of class predict.spMsPGOcc. When type = 'occupancy', the list consists of:

psi.0.samples

a three-dimensional array of posterior predictive samples for the latent occurrence probability values.

z.0.samples

a three-dimensional array of posterior predictive samples for the latent occurrence values.

w.0.samples

a three-dimensional array of posterior predictive samples for the latent spatial random effects.

run.time

execution time reported using proc.time().

When type = 'detection', the list consists of:

p.0.samples

a three-dimensional array of posterior predictive samples for the detection probability values.

run.time

execution time reported using proc.time().

The return object will include additional objects used for standard extractor functions.

Arguments

object

an object of class spMsPGOcc

X.0

the design matrix of covariates at the prediction locations. This should include a column of 1s for the intercept if an intercept is included in the model. If random effects are included in the occupancy (or detection if type = 'detection') portion of the model, the levels of the random effects at the new locations should be included as a column in the design matrix. The ordering of the levels should match the ordering used to fit the data in spMsPGOcc. Columns should correspond to the order of how covariates were specified in the corresponding formula argument of spMsPGOcc. Column names of the random effects must match the name of the random effects, if specified in the corresponding formula argument of spMsPGOcc.

coords.0

the spatial coordinates corresponding to X.0. Note that spOccupancy assumes coordinates are specified in a projected coordinate system.

n.omp.threads

a positive integer indicating the number of threads to use for SMP parallel processing. The package must be compiled for OpenMP support. For most Intel-based machines, we recommend setting n.omp.threads up to the number of hyperthreaded cores. Note, n.omp.threads > 1 might not work on some systems.

verbose

if TRUE, model specification and progress of the sampler is printed to the screen. Otherwise, nothing is printed to the screen.

n.report

the interval to report sampling progress.

ignore.RE

a logical value indicating whether to include unstructured random effects for prediction. If TRUE, unstructured random effects will be ignored and prediction will only use the fixed effects and the spatial random effects. If FALSE, random effects will be included in the prediction for both observed and unobserved levels of the unstructured random effects.

type

a quoted keyword indicating what type of prediction to produce. Valid keywords are 'occupancy' to predict latent occupancy probability and latent occupancy values (this is the default), or 'detection' to predict detection probability given new values of detection covariates.

...

currently no additional arguments

Author

Jeffrey W. Doser ,
Andrew O. Finley

Examples

set.seed(400)

# Simulate Data -----------------------------------------------------------
J.x <- 7
J.y <- 7
J <- J.x * J.y
n.rep <- sample(2:4, size = J, replace = TRUE)
N <- 5
# Community-level covariate effects
# Occurrence
beta.mean <- c(0.2, -0.15)
p.occ <- length(beta.mean)
tau.sq.beta <- c(0.6, 0.3)
# Detection
alpha.mean <- c(0.5, 0.2, -.2)
tau.sq.alpha <- c(0.2, 0.3, 0.8)
p.det <- length(alpha.mean)
# Draw species-level effects from community means.
beta <- matrix(NA, nrow = N, ncol = p.occ)
alpha <- matrix(NA, nrow = N, ncol = p.det)
for (i in 1:p.occ) {
  beta[, i] <- rnorm(N, beta.mean[i], sqrt(tau.sq.beta[i]))
}
for (i in 1:p.det) {
  alpha[, i] <- rnorm(N, alpha.mean[i], sqrt(tau.sq.alpha[i]))
}
phi <- runif(N, 3/1, 3/.4)
sigma.sq <- runif(N, 0.3, 3)
sp <- TRUE

dat <- simMsOcc(J.x = J.x, J.y = J.y, n.rep = n.rep, N = N, beta = beta, alpha = alpha,
		phi = phi, sigma.sq = sigma.sq, sp = TRUE, cov.model = 'exponential')

# Number of batches
n.batch <- 30
# Batch length
batch.length <- 25
n.samples <- n.batch * batch.length

# Split into fitting and prediction data set
pred.indx <- sample(1:J, round(J * .25), replace = FALSE)
y <- dat$y[, -pred.indx, ]
# Occupancy covariates
X <- dat$X[-pred.indx, ]
# Coordinates
coords <- as.matrix(dat$coords[-pred.indx, ])
# Detection covariates
X.p <- dat$X.p[-pred.indx, , ]
# Prediction values
X.0 <- dat$X[pred.indx, ]
coords.0 <- as.matrix(dat$coords[pred.indx, ])
psi.0 <- dat$psi[, pred.indx]

# Package all data into a list
occ.covs <- X[, 2, drop = FALSE]
colnames(occ.covs) <- c('occ.cov')
det.covs <- list(det.cov.1 = X.p[, , 2], 
		 det.cov.2 = X.p[, , 3]
		 )
data.list <- list(y = y, 
		  occ.covs = occ.covs,
		  det.covs = det.covs, 
		  coords = coords)

# Priors 
prior.list <- list(beta.comm.normal = list(mean = 0, var = 2.72), 
		   alpha.comm.normal = list(mean = 0, var = 2.72), 
		   tau.sq.beta.ig = list(a = 0.1, b = 0.1), 
		   tau.sq.alpha.ig = list(a = 0.1, b = 0.1),
		   phi.unif = list(a = 3/1, b = 3/.1), 
		   sigma.sq.ig = list(a = 2, b = 2)) 
# Starting values
inits.list <- list(alpha.comm = 0, 
		      beta.comm = 0, 
		      beta = 0, 
		      alpha = 0,
		      tau.sq.beta = 1, 
		      tau.sq.alpha = 1, 
		      phi = 3 / .5, 
		      sigma.sq = 2,
		      w = matrix(0, nrow = N, ncol = nrow(X)),
		      z = apply(y, c(1, 2), max, na.rm = TRUE))
# Tuning
tuning.list <- list(phi = 1) 
# Note that this is just a test case and more iterations/chains may need to 
# be run to ensure convergence.
out <- spMsPGOcc(occ.formula = ~ occ.cov, 
                 det.formula = ~ det.cov.1 + det.cov.2, 
                 data = data.list,
                 inits = inits.list, 
                 n.batch = n.batch, 
                 batch.length = batch.length, 
                 accept.rate = 0.43, 
                 priors = prior.list, 
                 cov.model = "exponential", 
                 tuning = tuning.list, 
                 n.omp.threads = 1, 
                 verbose = TRUE, 
                 NNGP = TRUE, 
                 n.neighbors = 5, 
                 search.type = 'cb', 
                 n.report = 10, 
                 n.burn = 500, 
                 n.thin = 1)

summary(out, level = 'both')

# Predict at new locations ------------------------------------------------
out.pred <- predict(out, X.0, coords.0, verbose = FALSE)