predict.clm: Predict Method for CLM fits

Description

Obtains predictions from a cumulative link (mixed) model.

Usage

## S3 method for class 'clm':
predict(object, newdata, ...)

Arguments

object

a fitted object of class inheriting from clm including clmm objects.

newdata

optionally, a data frame in which to look for variables with which to predict. Observe that the response variable should also be present.

...

further arguments passed to or from other methods.

Value

A vector of predicted probabilities.

Details

This method does not duplicate the behavior of predict.polr in package MASS which produces a matrix instead of a vector of predictions. The behavior of predict.polr can be mimiced as shown in the examples. If newdata is not supplied, the fitted values are obtained. For clmm fits this means predictions that are controlled for the observed value of the random effects. If the predictions for a random effect of zero, i.e. an average 'subject', are wanted, the same data used to fit the model should be supplied in the newdata argument. For clm fits those two sets of predictions are identical.

Examples

Run this code

options(contrasts = c("contr.treatment", "contr.poly"))
data(soup)

## More manageable data set for less voluminous printing:
(tab26 <- with(soup, table("Product" = PROD, "Response" = SURENESS)))
dimnames(tab26)[[2]] <- c("Sure", "Not Sure", "Guess", "Guess", "Not Sure", "Sure")
dat26 <- expand.grid(sureness = as.factor(1:6), prod = c("Ref", "Test"))
dat26$wghts <- c(t(tab26))
dat26

m1 <- clm(sureness ~ prod, scale = ~prod, data = dat26,
          weights = wghts, link = "logistic")
predict(m1)

mN1 <-  clm(sureness ~ 1, nominal = ~prod, data = dat26,
            weights = wghts)
predict(mN1)

predict(update(m1, scale = ~.-prod))

## Fit model from polr example:
data(housing, package = "MASS")
fm1 <- clm(Sat ~ Infl + Type + Cont, weights = Freq, data = housing)
predict(fm1)

#################################
## Mimicing the behavior of predict.polr:
set.seed(123)
nlev <- 3
y <- gl(nlev, 5)
x <- as.numeric(y) + rnorm(15)
fm.clm <- clm(y ~ x)
fm.polr <- polr(y ~ x)

## The equivalent of predict.polr(object, type = "probs"):
(pmat.polr <- predict(fm.polr, type = "probs"))
ndat <- expand.grid(y = gl(nlev,1), x = x)
(pmat.clm <- matrix(predict(fm.clm, newdata = ndat), ncol=nlev,
                    byrow = TRUE))
all.equal(c(pmat.clm), c(pmat.polr), tol = 1e-5) # TRUE

## The equivalent of predict.polr(object, type = "class"):
(class.polr <- predict(fm.polr))
(class.clm <- factor(apply(pmat.clm, 1, which.max)))
all.equal(class.clm, class.polr) ## TRUE