## ----setup, cache=FALSE, echo=FALSE-----------------------------------
library(knitr)
options(replace.assign=FALSE,width=72)
opts_chunk$set(fig.path='figs/glm-', cache.path='cache/glm-',
               fig.align='center', dev='pdf', fig.width=3.5,
               fig.height=3.5, fig.show='hold', pars=TRUE,
               tidy=FALSE,  comment=NA)
knit_hooks$set(pars=function(before, options, envir){
if (before && options$fig.show!='none') par(mar=c(4,4,1.6,.1),
              font.main=1, cex.lab=.95,cex.axis=.9,mgp=c(2,.7,0),
              tcl=-.3)
              par(options$pars)
}, crop=hook_pdfcrop)  
pdf.options(pointsize=12)
oldopt <- options(digits=4)

## ----figControl-------------------------------------------------------
# To include the figures, change `showFigs <- FALSE`  
# to `showFigs <- TRUE` in the source `.Rnw` file,
# and regenerate the PDF.
#
showFigs <- FALSE

## ----fig5_1, eval=TRUE, echo=TRUE-------------------------------------
fig5.1 <-
function (){
    ylim <- range(bronchitis$poll)+c(0,2.5)
    par(fig=c(0,.525, 0,1))
    plot(xlab="# cigarettes per day", ylab="Pollution", poll ~ cig,
         col=c(2,4)[r+1], pch=(3:2)[r+1], data=bronchitis, ylim=ylim)
    legend(x="topleft", legend=c("Non-sufferer","Sufferer"), ncol=2,
           pch=c(3,2), col=c(2,4))
    mtext(side=3, line=1.0,
          expression("A: Untransformed "*italic(x)*"-scale"),
          cex=0.95, adj=0)
    par(fig=c(.475,1, 0,1), new=TRUE)
    plot(poll ~ log(cig+1), col=c(2,4)[r+1], pch=(3:2)[r+1],
         xlab="log(# cigarettes per day + 1)", ylab="",
         data=bronchitis, ylim=ylim)
    xy1 <- with(subset(bronchitis, r==0), cbind(x=log(cig+1), y=poll))
    xy2 <- with(subset(bronchitis, r==1), cbind(x=log(cig+1), y=poll))
    est1 <- bkde2D(xy1, bandwidth=c(0.7, 3))
    est2 <- bkde2D(xy2, bandwidth=c(0.7, 3))
    lev <- pretty(c(est1$fhat, est2$fhat),4)
    contour(est1$x1, est1$x2, est1$fhat, levels=lev, add=TRUE, col=2)
    contour(est2$x1, est2$x2, est2$fhat, levels=lev, add=TRUE, col=4,
            lty=2)
    legend(x="topleft", legend=c("Non-sufferer","Sufferer"), ncol=2,
           lty=1:2, col=c(2,4), x.intersp=0.5)
    mtext(side=3, line=1.0,
          expression("B: Log-transformed "*italic(x)*"-scale"),
          cex=0.95, adj=0)
    par(fig=c(0,1,0,1))
}

## ----fig5_2, eval=TRUE, echo=TRUE-------------------------------------
fig5.2 <-
function (plotit=TRUE)
{
    par(mfrow=c(1,2))
    cig2.glm <- glm(r ~ log(cig+1) + poll, family=binomial,
                    data=bronchitis)
    termplot(cig2.glm, se=TRUE, ylim=c(-2,4))
    par(mfrow=c(1,1))
}

## ----fig5_3, eval=TRUE, echo=TRUE-------------------------------------
fig5.3 <-
function ()
{
    nassnew <- subset(nassCDS,
                      !is.na(yearVeh) & yearVeh>=1986 & weight>0)
    nassnew.glm <- glm(dead ~ seatbelt + airbag + dvcat + yearVeh +
                       ageOFocc, weights=weight, family = quasibinomial,
                       data=nassnew)
    par(mfrow=c(1,2))
    termplot(nassnew.glm, terms=c("yearVeh","ageOFocc"),
             smooth=panel.smooth, se=TRUE)
    par(mfrow=c(1,1))
    par(fig=c(0,0.5,0,1), new=TRUE)
    mtext(side=3, line=1.0, "A", adj=0)
    par(fig=c(0.5,1,0,1), new=TRUE)
    mtext(side=3, line=1.0, "B", adj=0)
    par(fig=c(0,1,0,1))
}

## ----fig5_4, eval=TRUE, echo=TRUE-------------------------------------
fig5.4 <-
function (){
    qqnorm(rpois(30, 5), ylab="", main="")
    qqnorm(rpois(30, 5), ylab="", main="")
}

## ----fig5_5, eval=TRUE, echo=TRUE-------------------------------------
fig5.5 <-
function (){
  par(mar=c(3.6,3.6,1.6,0.6), mgp=c(2.25,.5,0), mfrow=c(2,2))
    msg <- "As 'car::spm' is not available, cannot do plot."
    if(!require(car))return(msg)
    if(packageVersion('car') < '3.0.0'){ diag <- "boxplot" 
    car::spm(~ . | habitat, data=moths, cex.labels=1.2,
             col=rep(1,8), var.labels=c("","A","P"), smooth=FALSE, 
             reg.line=NA, diagonal=diag)
    } else {
        diag <- list(method="boxplot")
        car::spm(~ . | habitat, data=moths, cex.labels=1.2,
             col=rep(1,8), var.labels=c("","A","P"), smooth=FALSE, 
             regLine=FALSE, diagonal=diag)
    }
}

## ----fig5_6, eval=TRUE, echo=TRUE-------------------------------------
fig5.6 <-
function ()
{
  par(mar=c(3.6,3.6,1.6,0.6), mgp=c(2.25,.5,0), mfrow=c(2,2))
    P.glm <- glm(P ~ habitat + log(meters), data=moths,
                 family=quasipoisson)
    par(mfrow=c(2,2))
    plot(P.glm, which=1:4)
    par(mfrow=c(1,1))
}

## ----figs5-pkgs, eval=showFigs, message=FALSE, warning=FALSE----------
#  pkgs <- c("DAAG","KernSmooth","car")
#  z <- sapply(pkgs, require, character.only=TRUE, warn.conflicts=FALSE)
#  if(any(!z)){
#    notAvail <- paste(names(z)[!z], collapse=", ")
#    print(paste("The following packages should be installed:", notAvail))
#  }

## ----fig5_1x, eval=showFigs, echo=TRUE, fig.width=6.75, fig.height=4.25, pars=list(mar=c(4,4,2.6,.1)), out.width="0.925\\textwidth"----
#  fig5.1()

## ----fig5_2x, eval=showFigs, echo=TRUE, fig.width=6, fig.height=3.35, out.width="0.675\\textwidth"----
#  fig5.2()

## ----fig5_3x, eval=showFigs, echo=TRUE, fig.width=6, fig.height=3.35, out.width="0.675\\textwidth"----
#  fig5.3()

## ----fig5_4x, eval=showFigs, echo=TRUE, fig.width=6, fig.height=3.5, pars=list(mfrow=c(1,2)), out.width="0.75\\textwidth"----
#  fig5.4()

## ----fig5_5x, eval=showFigs, echo=TRUE, fig.width=6, fig.height=6, out.width="0.97\\textwidth"----
#  if(require(DAAG)) fig5.5() else return("Dataset 'moths' is from 'DAAG', not available")

## ----fig5_6x, eval=showFigs, echo=TRUE, fig.width=6, fig.height=6, out.width="0.75\\textwidth"----
#  if(require(DAAG)) fig5.6() else return("Dataset 'moths' is from 'DAAG', not available")

