R: Predictions from a model at new data values

predict.merMod {lme4}

R Documentation

Predictions from a model at new data values

Description

The predict method for merMod objects, i.e. results of lmer(), glmer(), etc.

Usage

## S3 method for class 'merMod'
predict(object, newdata = NULL, newparams = NULL,
    re.form = NULL, ReForm, REForm, REform,
    random.only=FALSE, terms = NULL,
    type = c("link", "response"), allow.new.levels = FALSE,
    na.action = na.pass,
    se.fit = FALSE,
    ...)

Arguments

`object`	a fitted model object
`newdata`	data frame for which to evaluate predictions.
`newparams`	new parameters to use in evaluating predictions, specified as in the `start` parameter for `lmer` or `glmer` – a list with components `theta` and/or (for GLMMs) `beta`.
`re.form`	(formula, `NULL`, or `NA`) specify which random effects to condition on when predicting. If `NULL`, include all random effects; if `NA` or `~0`, include no random effects.
`ReForm`, `REForm`, `REform`	allowed for backward compatibility: `re.form` is now the preferred argument name.
`random.only`	(logical) ignore fixed effects, making predictions only using random effects?
`terms`	a `terms` object - unused at present.
`type`	character string - either `"link"`, the default, or `"response"` indicating the type of prediction object returned.
`allow.new.levels`	logical if new levels (or NA values) in `newdata` are allowed. If FALSE (default), such new values in `newdata` will trigger an error; if TRUE, then the prediction will use the unconditional (population-level) values for data with previously unobserved levels (or NAs).
`na.action`	`function` determining what should be done with missing values for fixed effects in `newdata`. The default is to predict `NA`: see `na.pass`.
`se.fit`	(Experimental) A logical value indicating whether the standard errors should be included or not. Default is FALSE.
`...`	optional additional parameters. None are used at present.

Details

If any random effects are included in re.form (i.e. it is not ~0 or NA), newdata must contain columns corresponding to all of the grouping variables and random effects used in the original model, even if not all are used in prediction; however, they can be safely set to NA in this case.
There is no option for computing standard errors of predictions because it is difficult to define an efficient method that incorporates uncertainty in the variance parameters; we recommend bootMer for this task.

Value

a numeric vector of predicted values

Examples

(gm1 <- glmer(cbind(incidence, size - incidence) ~ period + (1 |herd), cbpp, binomial))
str(p0 <- predict(gm1))            # fitted values
str(p1 <- predict(gm1,re.form=NA))  # fitted values, unconditional (level-0)
newdata <- with(cbpp, expand.grid(period=unique(period), herd=unique(herd)))
str(p2 <- predict(gm1,newdata))    # new data, all RE
str(p3 <- predict(gm1,newdata,re.form=NA)) # new data, level-0
str(p4 <- predict(gm1,newdata,re.form= ~(1|herd))) # explicitly specify RE
stopifnot(identical(p2, p4))

[Package lme4 version 1.1-35.3 Index]