Thierry,
Simon had written some code for this but we never got round to fully
integrate it into the "pscl" package. A file pb.R is attached, but as a
disclaimer: I haven't looked at this code for a while. It still seems to
work (an example is included at the end) but please check.
hth,
Z
On Tue, 16 Dec 2008, ONKELINX, Thierry wrote:
Dear all,
I'm using zeroinfl() from the pscl-package for zero inflated Poisson
regression. I would like to calculate (aproximate) prediction intervals
for the fitted values. The package itself does not provide them. Can
this be calculated analyticaly? Or do I have to use bootstrap?
What I tried until now is to use bootstrap to estimate these intervals.
Any comments on the code are welcome. The data and the model are based
on the examples in zeroinfl().
#aproximate prediction intervals with Poisson regression
fm_pois <- glm(art ~ fem, data = bioChemists, family = poisson)
newdata <- na.omit(unique(bioChemists[, "fem", drop = FALSE]))
prediction <- predict(fm_pois, newdata = newdata, se.fit = TRUE)
ci <- data.frame(exp(prediction$fit + matrix(prediction$se.fit, ncol =
1) %*% c(-1.96, 1.96)))
newdata$fit <- exp(prediction$fit)
newdata <- cbind(newdata, ci)
newdata$model <- "Poisson"
library(pscl)
#aproximate prediction intervals with zero inflated poisson regression
fm_zip <- zeroinfl(art ~ fem | 1, data = bioChemists)
fit <- predict(fm_zip)
Pearson <- resid(fm_zip, type = "pearson")
VarComp <- resid(fm_zip, type = "response") / Pearson
fem <- bioChemists$fem
bootstrap <- replicate(999, {
yStar <- pmax(round(fit + sample(Pearson) * VarComp, 0), 0)
predict(zeroinfl(yStar ~ fem | 1), newdata = newdata)
})
newdata0 <- newdata
newdata0$fit <- predict(fm_zip, newdata = newdata, type = "response")
newdata0[, 3:4] <- t(apply(bootstrap, 1, quantile, c(0.025, 0.975)))
newdata0$model <- "Zero inflated"
#compare the intervals in a nice plot.
newdata <- rbind(newdata, newdata0)
library(ggplot2)
ggplot(newdata, aes(x = fem, y = fit, min = X1, max = X2, colour =
model)) + geom_point(position = position_dodge(width = 0.4)) +
geom_errorbar(position = position_dodge(width = 0.4))
Best regards,
Thierry
------------------------------------------------------------------------
----
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature
and Forest
Cel biometrie, methodologie en kwaliteitszorg / Section biometrics,
methodology and quality assurance
Gaverstraat 4
9500 Geraardsbergen
Belgium
tel. + 32 54/436 185
thierry.onkel...@inbo.be
www.inbo.be
To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to
say what the experiment died of.
~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data.
~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of
data.
~ John Tukey
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## parametric bootstrap
predict.zeroinfl <- function(object, newdata, type = c("response", "prob"),
se=FALSE,MC=1000,level=.95,
na.action = na.pass, ...)
{
type <- match.arg(type)
## if no new data supplied
if(missing(newdata)){
rval <- object$fitted.values
if(!is.null(object$x)) {
X <- object$x$count
Z <- object$x$zero
}
else if(!is.null(object$model)) {
X <- model.matrix(object$terms$count, object$model, contrasts =
object$contrasts$count)
Z <- model.matrix(object$terms$zero, object$model, contrasts =
object$contrasts$zero)
}
else {
stop("no X and/or Z matrices can be extracted from fitted model")
}
if(type == "prob") {
mu <- exp(X %*% object$coefficients$count)[,1]
phi <- object$linkinv(Z %*% object$coefficients$zero)[,1]
}
}
else {
mf <- model.frame(delete.response(object$terms$full), newdata, na.action
= na.action, xlev = object$levels)
X <- model.matrix(delete.response(object$terms$count), mf, contrasts =
object$contrasts$count)
Z <- model.matrix(delete.response(object$terms$zero), mf, contrasts =
object$contrasts$zero)
mu <- exp(X %*% object$coefficients$count)[,1]
phi <- object$linkinv(Z %*% object$coefficients$zero)[,1]
rval <- (1-phi) * mu
}
if(se & !is.null(X) & !is.null(Z)){
require(mvtnorm)
vc <- -solve(object$optim$hessian)
kx <- length(object$coefficients$count)
kz <- length(object$coefficients$zero)
parms <- object$optim$par
if(type!="prob"){
yhat.sim <- matrix(NA,MC,dim(X)[1])
for(i in 1:MC){
cat(paste("MC iterate",i,"of",MC,"\n"))
parms.sim <- rmvnorm(n=1,mean=parms,sigma=vc)
beta <- parms.sim[1:kx]
gamma <- parms.sim[(kx+1):(kx+kz)]
mu.sim <- exp(X%*%beta)[,1]
phi.sim <- object$linkinv(Z%*%gamma)[,1]
yhat.sim[i,] <- (1-phi.sim)*mu.sim
}
}
out <- list()
out$lower <- apply(yhat.sim,2,quantile,(1-level)/2)
out$upper <- apply(yhat.sim,2,quantile,1-((1-level)/2))
out$se <- apply(yhat.sim,2,sd)
}
## predicted probabilities
if(type == "prob") {
if(!is.null(object$y)) y <- object$y
else if(!is.null(object$model)) y <- model.response(object$model)
else stop("predicted probabilities cannot be computed for fits with y =
FALSE and model = FALSE")
yUnique <- min(y):max(y)
nUnique <- length(yUnique)
rval <- matrix(NA, nrow = length(rval), ncol = nUnique)
dimnames(rval) <- list(rownames(X), yUnique)
switch(object$dist,
"poisson" = {
rval[, 1] <- phi + (1-phi) * exp(-mu)
for(i in 2:nUnique) rval[,i] <- (1-phi) * dpois(yUnique[i],
lambda = mu)
},
"negbin" = {
theta <- object$theta
rval[, 1] <- phi + (1-phi) * dnbinom(0, mu = mu, size = theta)
for(i in 2:nUnique) rval[,i] <- (1-phi) * dnbinom(yUnique[i], mu
= mu, size = theta)
},
"geometric" = {
rval[, 1] <- phi + (1-phi) * dnbinom(0, mu = mu, size = 1)
for(i in 2:nUnique) rval[,i] <- (1-phi) * dnbinom(yUnique[i], mu
= mu, size = 1)
})
}
if(se)
rval <- list(rval,out)
rval
}
################################################################
## test this code
require(pscl)
data(bioChemists)
obj <- zeroinfl(art ~ . | .,
data=bioChemists,
dist="negbin",
EM=TRUE)
foo <- predict(obj,se=TRUE,type="response")
indx <- order(foo[[1]])
n <- length(indx)
plot(1:n,
foo[[1]][indx],
type="n",
ylim=range(cbind(foo[[2]]$lower,foo[[2]]$upper)),
xlab="Order Statistic",
ylab="Predicted Value")
segments(x0=1:n,x1=1:n,
y0=foo[[2]]$lower[indx],
y1=foo[[2]]$upper[indx],
col=gray(.45),
lwd=.1)
points(1:n,foo[[1]][indx],cex=.5)
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