predict.abund {spAbundance} | R Documentation |
Function for prediction at new locations for univariate GLMMs
Description
The function predict
collects posterior predictive samples for a set of new locations given an object of class 'abund'.
Usage
## S3 method for class 'abund'
predict(object, X.0, ignore.RE = FALSE, z.0.samples, ...)
Arguments
object |
an object of class abund |
X.0 |
the design matrix of covariates at the prediction locations. This should be a three-dimensional array, with dimensions corresponding to site, replicate, and covariate, respectively. Note that the first covariate should consist of all 1s for the intercept if an intercept is included in the model. If random effects are included in the abundance portion of the model, the levels of the random effects at the new locations/time periods should be included as an element of the three-dimensional array. The ordering of the levels should match the ordering used to fit the data in |
ignore.RE |
logical value that specifies whether or not to remove unstructured random effects from the subsequent predictions. If |
z.0.samples |
a matrix with rows corresponding to MCMC samples and columns corresponding to prediction locations containing the full posterior samples of the predicted binary portion of a zero-inflated Gaussian model. In the context of abundance models, this typically corresponds to estimates of the presence or absence of the species at the location. When using |
... |
currently no additional arguments |
Value
A list object of class predict.abund
. The list consists of:
mu.0.samples |
a three-dimensional object of posterior predictive samples for the
expected abundance values with dimensions corresponding to posterior predictive
sample, site, and replicate. When there is no replication, this will be a two-dimensional
matrix. Note if an offset was used when fitting the model with |
y.0.samples |
a three-dimensional object of posterior predictive samples for the
abundance values with dimensions corresponding to posterior predictive sample, site,
and replicate. When there is no replication, this will be a two-dimensional matrix.
These will be in the same units as |
The return object will include additional objects used for standard extractor functions.
Note
When ignore.RE = FALSE
, both sampled levels and non-sampled levels of random effects are supported for prediction. For sampled levels, the posterior distribution for the random effect corresponding to that level of the random effect will be used in the prediction. For non-sampled levels, random values are drawn from a normal distribution using the posterior samples of the random effect variance, which results in fully propagated uncertainty in predictions with models that incorporate random effects.
Author(s)
Jeffrey W. Doser doserjef@msu.edu,
Examples
set.seed(1010)
J.x <- 15
J.y <- 15
J <- J.x * J.y
n.rep <- sample(1, J, replace = TRUE)
beta <- c(0, -1.5, 0.3, -0.8)
p.abund <- length(beta)
mu.RE <- list()
kappa <- 0.5
sp <- FALSE
family <- 'NB'
dat <- simAbund(J.x = J.x, J.y = J.y, n.rep = n.rep, beta = beta,
kappa = kappa, mu.RE = mu.RE, sp = sp, family = 'NB')
# 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, , , drop = FALSE]
# Prediction covariates
X.0 <- dat$X[pred.indx, , ]
coords <- as.matrix(dat$coords[-pred.indx, ])
coords.0 <- as.matrix(dat$coords[pred.indx, ])
abund.covs <- list(int = X[, , 1],
abund.cov.1 = X[, , 2],
abund.cov.2 = X[, , 3],
abund.cov.3 = X[, , 4])
data.list <- list(y = y, covs = abund.covs)
# Priors
prior.list <- list(beta.normal = list(mean = 0, var = 100),
kappa.unif = c(0.001, 10))
# Starting values
inits.list <- list(beta = 0, kappa = kappa)
n.batch <- 5
batch.length <- 25
n.burn <- 0
n.thin <- 1
n.chains <- 1
out <- abund(formula = ~ abund.cov.1 + abund.cov.2 + abund.cov.3,
data = data.list,
n.batch = n.batch,
batch.length = batch.length,
inits = inits.list,
priors = prior.list,
accept.rate = 0.43,
n.omp.threads = 1,
verbose = TRUE,
n.report = 1,
n.burn = n.burn,
n.thin = n.thin,
n.chains = n.chains)
# Predict at new locations ------------------------------------------------
colnames(X.0) <- c('intercept', 'abund.cov', 'abund.cov.2', 'abund.cov.3')
out.pred <- predict(out, X.0)
mu.0.quants <- apply(out.pred$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])