spAbundance (version 0.1.3)

predict.DS: Function for prediction at new locations for single-species hierarchical distance sampling models

Description

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

Usage

# S3 method for DS
predict(object, X.0, ignore.RE = FALSE, type = 'abundance', ...)

Value

A list object of class predict.DS. When type = 'abundance', the list consists of:

mu.0.samples

a coda object of posterior predictive samples for the expected abundance values, or expected abundance per unit area (i.e., density) values when an offset was used when fitting the model with DS().

N.0.samples

a coda object of posterior predictive samples for the latent abundance values. These will be in the same units as mu.0.samples.

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

sigma.0.samples

a coda object of posterior predictive samples for sigma (the parameter controlling detection probability).

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

Arguments

object

an object of class DS

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 abundance (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 DS. Columns should correspond to the order of how covariates were specified in the corresponding formula argument of DS. Column names of all variables must match the names of variables used when fitting the model (for the intercept, use '(Intercept)').

ignore.RE

logical value that specifies whether or not to remove random abundance (or detection if type = 'detection') effects from the subsequent predictions. If TRUE, random effects will be included. If FALSE, random effects will be set to 0 and predictions will only be generated from the fixed effects.

type

a quoted keyword indicating what type of prediction to produce. Valid keywords are 'abundance' to predict latent abundance and expected abundance 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 ,

Examples

set.seed(123)
J.x <- 10
J.y <- 10 
J <- J.x * J.y
# Number of distance bins from which to simulate data. 
n.bins <- 5
# Length of each bin. This should be of length n.bins
bin.width <- c(.10, .10, .20, .3, .1)
# Abundance coefficients
beta <- c(1.0, 0.2, 0.3, -0.2)
p.abund <- length(beta)
# Detection coefficients
alpha <- c(-1.0, -0.3)
p.det <- length(alpha)
# Detection decay function
det.func <- 'halfnormal'
mu.RE <- list()
p.RE <- list()
sp <- FALSE 
family <- 'NB'
kappa <- 0.1
offset <- 1.8
transect <- 'point'

dat <- simDS(J.x = J.x, J.y = J.y, n.bins = n.bins, bin.width = bin.width,
             beta = beta, alpha = alpha, det.func = det.func, kappa = kappa, 
             mu.RE = mu.RE, p.RE = p.RE, sp = sp, family = family, 
             offset = offset, transect = transect)

# Split into fitting and prediction data set
pred.indx <- sample(1:J, round(J * .25), replace = FALSE)
y <- dat$y[-pred.indx, ]
# Abundance covariates
X <- dat$X[-pred.indx, ]
# Prediction covariates
X.0 <- dat$X[pred.indx, ]
# Detection covariates
X.p <- dat$X.p[-pred.indx, ]
dist.breaks <- dat$dist.breaks

covs <- cbind(X, X.p)
colnames(covs) <- c('int.abund', 'abund.cov.1', 'abund.cov.2', 'abund.cov.3', 
                    'int.det', 'det.cov.1')

data.list <- list(y = y, 
                  covs = covs,
                  dist.breaks = dist.breaks, 
                  offset = offset)

# Priors
prior.list <- list(beta.normal = list(mean = 0, var = 10),
                   alpha.normal = list(mean = 0,
                                       var = 10), 
                   kappa.unif = c(0, 100)) 
# Starting values
inits.list <- list(alpha = 0,
                   beta = 0,
                   kappa = 1)
# Tuning values
tuning <- list(beta = 0.1, alpha = 0.1, beta.star = 0.3, alpha.star = 0.1, 
               kappa = 0.2) 

out <- DS(abund.formula = ~ abund.cov.1 + abund.cov.2 + abund.cov.3,
          det.formula = ~ det.cov.1,
          data = data.list, 
          n.batch = 10, 
          batch.length = 25, 
          inits = inits.list, 
          family = 'NB',
          det.func = 'halfnormal', 
          transect = 'point', 
          tuning = tuning,
          priors = prior.list, 
          accept.rate = 0.43, 
          n.omp.threads = 1, 
          verbose = TRUE, 
          n.report = 100,
          n.burn = 100,
          n.thin = 1,
          n.chains = 1) 
summary(out)

# Predict at new locations ------------------------------------------------
colnames(X.0) <- c('intercept', 'abund.cov.1', 'abund.cov.2', 'abund.cov.3')
out.pred <- predict(out, X.0)
mu.0.quants <- apply(out.pred$mu.0.samples, 2, quantile, c(0.025, 0.5, 0.975))
plot(dat$mu[pred.indx], mu.0.quants[2, ], pch = 19, xlab = 'True', 
     ylab = 'Fitted', ylim = c(min(mu.0.quants), max(mu.0.quants)))
segments(dat$mu[pred.indx], mu.0.quants[1, ], dat$mu[pred.indx], mu.0.quants[3, ])
lines(dat$mu[pred.indx], dat$mu[pred.indx])