predict.manyglm: Predict Method for MANYGLM Fits

In mvabund: Statistical Methods for Analysing Multivariate Abundance Data

Predict Method for MANYGLM Fits

Description

Obtains predictions and optionally estimates standard errors of those predictions from a fitted manyglm object.

Usage

## S3 method for class 'manyglm'
predict(object, newdata, type = c("link", "response",
    "terms"), se.fit = FALSE, dispersion = NULL, terms = NULL,
    na.action = na.pass, ...)

Arguments

object	a fitted object of class inheriting from "manyglm".
newdata	optionally, a data frame in which to look for variables with which to predict. If omitted, the fitted linear predictors are used.
type	the type of prediction required. The default is on the scale of the linear predictors; the alternative "response" is on the scale of the response variable. Thus for a default binomial model the default predictions are of log-odds (probabilities on logit scale) and type = "response" gives the predicted probabilities. The "terms" option returns a matrix giving the fitted values of each term in the model formula on the linear predictor scale. The value of this argument can be abbreviated.
se.fit	logical switch indicating if standard errors are required.
dispersion	the dispersion of the MANYGLM fit to be assumed in computing the standard errors. If omitted, that returned by summary applied to the object is used.
terms	with type="terms" by default all terms are returned. A character vector specifies which terms are to be returned
na.action	function determining what should be done with missing values in newdata. The default is to predict NA.
...	further arguments passed to or from other methods.

Details

predict.manyglm refits the model using glm before making predictions. In rare (usually pathological) cases this may lead to differences in predictions as compared to what would be expected if using the manyglm coefficients directly.

If newdata is omitted the predictions are based on the data used for the fit. In that case how cases with missing values in the original fit is determined by the na.action argument of that fit. If na.action = na.omit omitted cases will not appear in the residuals, whereas if na.action = na.exclude they will appear (in predictions and standard errors), with residual value NA. See also napredict.

Value

If se = FALSE, a matrix of predictions or an array of predictions and bounds. If se = TRUE, a list with components

fit	the predictions
se.fit	estimated standard errors
residual.scale	a scalar giving the square root of the dispersion used in computing the standard errors.

Author(s)

Ulrike Naumann, Yi Wang and David Warton <[e-mail]>.

See Also

manyglm.

Examples

data(spider)
spiddat <- mvabund(spider$abund)
Y <- spiddat[1:20,]
X <- spider$x[1:20,]
glm.spid.poiss <- manyglm(Y~soil.dry+bare.sand, family="poisson", data=X)
glm.spid.poiss$data = X
newdata <- spider$x[21:28,]
predict(glm.spid.poiss, newdata)
pred.w.plim <- predict(glm.spid.poiss, newdata, interval="prediction")
pred.w.clim <- predict(glm.spid.poiss, newdata, interval="confidence")

mvabund documentation built on March 18, 2022, 7:25 p.m.