predict,occumbFit-method {occumb}

Predict method for occumbFit class.

Description

Obtain predictions of parameters related to species occupancy and detection from an occumbFit model object.

Usage

## S4 method for signature 'occumbFit'
predict(
  object,
  newdata = NULL,
  parameter = c("phi", "theta", "psi"),
  scale = c("response", "link"),
  type = c("quantiles", "mean", "samples")
)

Arguments

object

An occumbFit object.

newdata

An optional occumbData object with covariates to be used for prediction. If omitted, the fitted covariates are used.

parameter

The parameter to be predicted.

scale

The scale on which the prediction is made. type = "response" returns the prediction on the original scale of the parameter. type = "link" returns the prediction on the link scale of the parameter.

type

The type of prediction. type = "quantiles" returns 50% quantile as the posterior median of the prediction in addition to 2.5 and 97.5% quantiles as the lower and upper limits of the 95% credible interval of the prediction. type = "mean" returns the posterior mean of the prediction. type = "samples" returns the posterior samples of the prediction.

Details

Applying predict() to an occumbFit object generates predictions for the specified parameter (phi, theta, or psi) based on the estimated effects and the given covariates. It is important to recognize that the predictions are specific to the individual species being modeled since they depend on the estimated species-specific effects (i.e., alpha, beta, and gamma; see the package vignette for details). When providing newdata, it must thus be assumed that the set of species contained in newdata is the same as that of the data being fitted.

Value

Predictions are obtained as a matrix or array that can have dimensions corresponding to statistics (or samples), species, sites, and replicates. The dimension and label attributes are added to the output object to inform these dimensions. If the sequence read count data y has species, site, or replicate names appended as the dimnames attribute (see Details in occumbData()), they will be copied into the label attribute of the returned object.