---
title: "Model Comparison Using Resampling Methods"
author: "John Maindonald, Statistics Research Associates"
date: '`r format(Sys.Date(),"%d %B %Y")`'
documentclass: article
classoption: b5paper
fontsize: 10pt
output:
  bookdown::html_document2:
    toc: true
    toc_depth: 2
    number_sections: true
    pandoc_args: NULL
    base_format: prettydoc::html_pretty
    link-citations: true
pkgdown:
  as_is: true
vignette: >
  %\VignetteIndexEntry{Model Comparison Using Resampling Methods}
  %\VignetteEncoding{UTF-8}
  %\VignetteEngine{knitr::rmarkdown}
bibliography: mr.bib
header-includes:
- \usepackage{amssymb}
- \usepackage{pifont}
- \usepackage[T1]{fontenc}
- \usepackage[utf8]{inputenc}
- \DeclareUnicodeCharacter{2009}{<}
---

<style type="text/css">
div#TOC li {
    list-style:none;
    background-image:none;
    background-repeat:none;
    background-position:0; 
}
</style>

```{r setup, cache=FALSE, echo=FALSE}
library(knitr)
options(replace.assign=FALSE,width=72)
opts_chunk$set(fig.path='figs/key-', cache.path='cache/key-',
               fig.align='center', fig.width=3.5,
               fig.height=3.5, fig.show='hold', par=TRUE,
               tidy=FALSE,  comment=NA)
knit_hooks$set(par=function(before, options, envir){
if (before && options$fig.show!='none') par(mar=c(4,4,2.6,.1),
              cex.lab=.95,cex.axis=.9,mgp=c(2,.7,0),tcl=-.3)
}, crop=hook_pdfcrop)
oldopt <- options(digits=4)
```

# Handling skew distributions and/or outliers

Figure \@ref(fig:cats-xy) plots heart weight against body weight,
for 97 male cats.  A regression line has been fitted.

```{r cap123}
cap1 <- "Heart weight versus body weight of 97 male cats.
A regression line has been fitted."
cap2 <- "Q-Q plot ('Normal Probability plot') of residuals from
the regression of heart weight on body weight, for the male cats."
cap3 <- "Scatterplot matrix of bootstrap estimates of `Slope`
versus `Intercept`, with boxplots used to summarize the marginal
distributions."
cap4 <- "Bootstrap resampling result, compared with simulation
  resampling."
```

```{r cats-xy, fig.width=4.25, fig.height=4.25, fig.cap=cap1}
library(lattice)
mcats <- subset(MASS::cats, Sex=="M")
xyplot(Hwt ~ Bwt, data=mcats, type=c("p","r"))
```

The fitted regression equation is:
```{r mcats-lm}
mcats.lm <- lm(Hwt~Bwt, data=mcats)
signif(coef(summary(mcats.lm)),3)
```

Figure \@ref(fig:cats-qq) shows the normal Q-Q plot of residuals.
There are clear small and large outliers, though neither are widely
removed from the main body of residuals.  Also, the distribution is
positively skew, as indicated by the bend in the Q-Q plot at a theoretical
quantile of 0.

```{r cats-qq, fig.cap=cap2}
res <- resid(mcats.lm)
qqnorm(res)
```

For later reference, determine the numbers of the rows that
generated the 'outliers':
```{r outlier-num}, eval=TRUE, echo=TRUE}
nout <- (1:nrow(mcats))[c(which.min(res),which.max(res))]
```
Bootstrap methods may be useful when the distribution of residuals is
strongly skew.  The distribution in Figure \@ref(fig:cats-qq) is,
notwithstanding the 'outliers', close enough to symmetric that, 
with 97 data points, the sampling distributions of the regression 
coefficients can fairly safely taken as normal.  Examination of the 
bootstrap distributions will be used to check this claim.

Calculations use the functions `simreg()` and `bootreg()`
respectively, from the {\em gamclass} package.   Both sets of calculations
start by fitting a regression, then calculating fitted values and
residuals.  Then the following calculation is repeated 1000 times:

* For simulation take a sample of 97 values from a normal
  distribution with the same standard deviation as the residuals.  For
  bootstrap sampling take a bootstrap sample of the residuals.
* Add simulated residuals (bootstrap residuals) on to the fitted
  values, thus generating a new set of simulated (bootstrapped) $y$-values.
* Using the new simulated  (bootstrapped) $y$-values fit a
  regression and record the coefficients.

Figure \@ref(fig:boot-regcoefs) shows the bootstrap results:
Notice the strong correlation between `Slope` and `Intercept`.
The marginal boxplots give a rough summary of the distributions:
      


```{r boot-regcoefs, fig.cap=cap3, fig.width=2.85, fig.height=3}
library(gamclass, quietly=TRUE)
library(car, quietly=TRUE)
mcats <- subset(MASS::cats, Sex=="M")
bootmat <- bootreg(Hwt ~ Bwt,
                   data = mcats,
                   nboot = 1000)
bootdf <- as.data.frame(bootmat)
names(bootdf) <- c("Intercept",
                   "Slope")
colr <- adjustcolor(rep("black",3),
                    alpha.f=0.25)
scatterplot(Slope ~ Intercept,
            col=colr, data=bootdf,
            boxplots="xy",
            regLine=NA,
            smooth=FALSE)
```

Now calculate 95% confidence intervals for the intercept and slope:
```{r 95CI}
sapply(bootdf, quantile, prob=c(.025, .975))
```

Bootstrap samples can include 0, 1, 2 or more repeats of row 97 that
as identified as an outlier.

It is then instructive to compare Figure \@ref(fig:boot-regcoefs) with
Figure \@ref(fig:alt-resamp), which shows the equivalent plots when
the outlier is omitted:

* In Figure \@ref(fig:alt-resamp)A the range of values, both on the
  `Intercept` and on the `Slope` scale, is reduced
  relative to Figure \@ref(fig:boot-regcoefs).
* Figure \@ref(fig:alt-resamp)B shows the counterpart of Figure
  \@ref(fig:boot-regcoefs), from the use of simulation.  The
  simulation process assumes a normal distribution, without outliers.
  The standard deviation used is however for the data that included the
  outlier.  The range of values, on both axes, is accordingly greater
  than in \@ref(fig:alt-resamp)A.

```{r alt-boot-omitOutlier}
library(lattice)
bootmat <- bootreg(formula = Hwt ~ Bwt,
                   data = mcats[-97, ],
                   nboot = 1000)
bootdf0 <- as.data.frame(bootmat)
names(bootdf0) <- c("Intercept","Slope")
gphA <- xyplot(Slope ~ Intercept, data=bootdf0, alpha=0.25)
```


```{r alt-sim}
simmat <- simreg(formula = Hwt ~ Bwt,
                 data=mcats[-97, ], nsim=1000)
simdf <- as.data.frame(simmat)
names(simdf) <- c("Intercept","Slope")
gphB <- xyplot(Slope ~ Intercept, data=simdf, alpha=0.25)
```

```{r alt-resamp, out.width='47%', fig.show='hold', fig.width=3.85, fig.height=3.85, fig.cap=cap4}
update(gphA, main=grid::textGrob("A: Bootstrap (outlier omitted)",
       x=grid::unit(.05, "npc"),
       y = grid::unit(.25, "npc"), just="left",
       gp=grid::gpar(cex=1)))
update(gphB, main=grid::textGrob("B: Simulation",
       x = grid::unit(.05, "npc"),
       y = grid::unit(.25, "npc"), just="left",
       gp=grid::gpar(cex=1)))
```


# Use tree-based methods appropriately!

```{r cap5}
cap5 <- "Regression tree for predicting `Mileage` given
`Weight`. At each node, observations for which the
criterion is satisfied take the branch to the left.  Thus,
at the first node, `tonsWt$>=$1.218` chooses the branch to
the left, while `tonsWt$<$1.218` chooses the branch to the
right.  Panel B plots `Mileage` versus `tonsWt`, with
fitted values from the `rpart` model shown as horizontal 
grey lines."
```

The example now considered uses data, from the dataset `rpart::cars`,
that are not well suited to the approaches implemented in the `rpart` 
and `randomForest` packages.  Figure \@ref(fig:deftree)A, shows the
regression tree from an `rpart` model that fits car `Mileage` as a
function of `tonsWt`. The gray horizontal lines in Figure 
\@ref(fig:deftree)B show predictions from the model.

```{r rpart}
library(rpart)
Car90 <- na.omit(car90[, c("Mileage","Weight")])
## Express weight in metric tonnes
Car90 <- within(Car90, tonsWt <- Weight/2240)
car90.rpart <- rpart(Mileage ~ tonsWt, data=Car90)
```

```{r deftree, out.width='48%', fig.cap=cap5,fig.width=5.25, fig.height=5.25, fig.show='hold'}
## Code for Panel A
plot(car90.rpart)
text(car90.rpart, xpd=TRUE, digits=3)
mtext(side=3, line=1.25, "A: Regression tree", adj=0, cex=1.25)
## Code for Panel B
plot(Mileage ~ tonsWt, data=Car90, fg='gray')
wt <- with(Car90, tonsWt)
hat <- predict(car90.rpart)
gamclass::addhlines(wt, hat, lwd=2, col="gray")
mtext(side=3, line=1.25, "B: Predicted values from tree", adj=0, cex=1.25)
```

The fitted values change in discrete units, where they should
change smoothly.  Least squares regression, fitting a line or 
curve is a much preferable tool for the task.

## Choosing the split point

```{r cap6}
cap6 <- "Between group sum of squares for `Mileage`, as a
function of the value of `tonsWt` at which the split is
made. The choice $c = 1.218$ maximizes the between groups
sum of squares."
```

In the example used here, with just the one variable `tonsWt`,
all splits are on a value of that variable.
For each cutpoint $c$, with observations for values with $x < c$
placed in the first group, and observations for values of $x >= c$
placed in the second group, the split will partition the observations
into two sets, with subscripts that we write ${j1}$ and ${j2}$. The
between group sum of of squares for $y$ = `Mileage` is then:
\[
BSS = n_1 (\bar{y_1} - \bar{y})^2 + n_2 (\bar{y_2} - \bar{y})^2
\]
where $\bar{y_1}$ is the mean for the $n_1$ values in the first
group, $\bar{y_2}$ is the mean for the $n_2$ values in the second
group, and $\bar{y}$ is the overall mean.  The cutpoint $c$
that maximizes the $BSS$ is then chosen for the first split.

Figure \@ref(fig:bss-plot) calculates and plots $BSS$ for all 
choices of cutpoint $c$, making it clear that the first split 
should be at `tonsWt>=1.218`.


```{r bss-plot, fig.width=5, h=4.25, out.width="60%", fig.cap=cap6}
## Code
BSS <- bssBYcut(tonsWt, Mileage, Car90)
with(BSS, plot(xOrd, bss, xlab="Cutpoint", fg='gray', ylab=""))
mtext(side=2, line=1.5, "Between groups\nsum of squares")
abline(v=1.218, lty=2)
```

# Random forest fit to residuals from a trend surface

```{r cap7, out.width='80%'}
cap7 <- "Scatterplot matrix of accuracies for the several models.
         The line $y=x$ is shown in each panel.
         Note that `rfOOB` is out-of-bag accuracy, i.e., calculated from
         the set of 95 observations, and that `rfTest` is accuracy on the
         test data, again for a random forest model with no preliminary
         smoothing. Results from hybrid models are labeled according to
         the name of the formula for the smooth.   The final accuracy,
         evaluated on the test data, is for a random forest model
         fitted to residuals from the smooth"
```

A hybrid model may do better than, as investigated here,
separate random forest or generalized additive models.
The function `gamclass::gamRF()` fits a randomForest model
for use as baseline, then also a hybrid model that follows
use of the `mgcv::gam()` to fit a trend surface followed by
use of  `randomForest()` to fit to the residuals.  

The dataset `sp::meuse` holds data on heavy metal
concentrations at 155 locations near the village of Stein in
the Netherlands, in the floodplain of the river Meuse.  The
best candidates for the initial trend surface will in general be
variables that may plausibly have similar effects irrespective of
geographical location, i.e., the variables `dist`, `elev`,
`ffreq` and `soil`.  The usefulness of including also
`x` and `y` in the initial smooth can be checked.  All
variables from this set of five will then be used for the
`randomForest()` fit to the residuals. The following model
formulae for the initial smooth canvass a range of possibilities:

Repeated random subsets will be taken that comprise 95 of the
155 observations.  For each such sample, the remaining 60
observations will be used for testing.  These form just under 
39% of the total, which is close to the just under the
average 37% of the observations that each \txtt{randomForest} 
tree, from the fit to the total dataset, sets aside as test 
or ``out-of-bag'' (OOB) data.
```{r meuse-setup}
data("meuse", package="sp")
meuse <- within(meuse, {levels(soil) <- c("1","2","2")
                        ffreq <- as.numeric(ffreq)
                        loglead <- log(lead)
})
```

```{r gam-formulae}
form1 <- ~ dist + elev + soil + ffreq
form3 <- ~ s(dist, k=3) + s(elev,k=3) + soil +ffreq
form3x <- ~ s(dist, k=3) + s(elev,k=3) + s(x, k=3) + soil+ffreq
form8x <- ~ s(dist, k=8) + s(elev,k=8) + s(x, k=8) + soil+ffreq
formlist <- list("Hybrid1"=form1, "Hybrid3"=form3, "Hybrid3x"=form3x,
                 "Hybrid8x"=form8x)
```

```{r rfgam-setup}
rfVars <- c("dist", "elev", "soil", "ffreq", "x", "y")
nrep <- 100
errsmat <- matrix(0, nrep, length(formlist)+2)
dimnames(errsmat)[[2]] <- c(names(formlist), "rfTest", "rfOOB")
```

```{r rfgam-many}
n <- 95
for(i in 1:nrep){
sub <- sample(1:nrow(meuse), n)
meuseOut <- meuse[-sub,]
meuseIn <- meuse[sub,]
errsmat[i, ] <- gamclass::gamRF(formlist=formlist, yvar="loglead",
                                rfVars=rfVars, data=meuseIn,
                      newdata=meuseOut, printit=FALSE)
}
```

```{r cf-models-rfgam, fig.cap=cap7, fig.width=7.5, fig.height=7.5, out.width='65%'}
## Code for scatterplot of results
ran <- range(errsmat)
at <- round(ran+c(0.02,-0.02)*diff(ran),2)
lis <- list(limits=ran, at=at, labels=format(at, digits=2))
lims=list(lis,lis,lis,lis,lis,lis)
library(lattice)
splom(errsmat,
      pscales=lims,
      par.settings=simpleTheme(cex=0.75),
      col=adjustcolor("black", alpha=0.5),
      panel=function(x,y,...){lpoints(x,y,...)
      panel.abline(0,1,col="gray")}
)
```

```{r cf-accs-rfgam}
errdf <- stack(as.data.frame(errsmat[,-6]))
names(errdf) <- c("errs","model")
errdf$model <- relevel(errdf$model, ref="rfTest")
errdf$sample <- factor(rep(1:nrow(errsmat),5))
errors.aov <- aov(errs ~ model+sample, data=errdf)
round(coef(summary.lm(errors.aov))[1:5,], 4)
```

```{r cf-accs-rfgam-ests}
model.tables(errors.aov, type="mean", cterms='model')
```

# Linear and quadratic discriminant analysis

Comparisons are made with other methods also.

```{r cuckoos-caps}
cap8 <- "Length versus breadth, compared between cuckoo eggs laid in
        the different host nests. Axes for the scores are overlaid."
cap9 <- "Plot of length versus breadth of cuckoo eggs, now showing
a boundary line for distinguishing `wren` from `not-wren`,
based on the `lda()` analysis."
```

The dataset `DAAG::cuckoos` has measurements,
from museum collections in the UK, of the length and breadth of eggs of
each of six host species.  What support
does the data provide for the suggestion that, in nests of some
host species at least, cuckoos match the dimensions of their eggs
to those of the host species?

Because there are just two measurements, a
two-dimensional representation provides a complete description of the
results of the analysis. Any plot of scores will be a rotated version
of the plot of `length` versus `breadth`.

The following uses \code{MASS::lda()} to fit a model:

```{r cuckoos-lda}
cuckoos <- within(DAAG::cuckoos,
    levels(species) <- abbreviate(levels(species), 8))
cuckoos.lda <- MASS::lda(species ~ length + breadth, data=cuckoos)
```

The list element `cuckoos.lda$scaling` gives the coefficients
that are used in calculating the discriminant scores.  The entries in the
column headed `LD1` are the coefficients of `length` and
`breadth` that give the first set of discriminant scores.
Those in the column headed `LD2` give the second set of
discriminant scores:

Code that can be used to give the scores is then:
<<calc-scores, eval=TRUE, echo=TRUE>>=
@ %
The scores can be obtained directly from the calculation
`predict(cuckoos.lda)\$x`.

The following uses leave-one-out cross-validation to give
accuracy assessments for `lda()`:

```{r cuckoo-basic-gph}
gph <- xyplot(length ~ breadth, groups=species, data=cuckoos,
              type=c("p"), auto.key=list(space="right"), aspect=1,
              scales=list(tck=0.5), par.settings=simpleTheme(pch=16))
```

```{r cuckoos-sc, fig.cap=cap8,out.width='70%', fig.width=6.25, fig.height=4.75}
## library(latticeExtra)  # This package has the function layer()
LDmat <- cuckoos.lda$scaling
ld1 <- LDmat[,1]
ld2 <- LDmat[,2]
gm <- sapply(cuckoos[, c("length", "breadth")], mean)
av1 <- gm[1] + ld1[2]/ld1[1]*gm[2]
av2 <- gm[1] + ld2[2]/ld2[1]*gm[2]
addlayer <- latticeExtra::layer(panel.abline(av1, -ld1[2]/ld1[1], lty=1),
                                panel.abline(av2, -ld2[2]/ld2[1], lty=2))
gph + addlayer
```

```{r calc-scores}
gm <- apply(cuckoos.lda$means*cuckoos.lda$prior,2,sum)
  # Grand 'means'
## Sweep out grand 'means'
centered <- sweep(as.matrix(cuckoos[,1:2]), 2, gm)
```

```{r loo-cv-acc}
## Leave-one-out cross-validation
## Accuracies for linear discriminant analysis
cuckooCV.lda <- MASS::lda(species ~ length + breadth,
                    data=cuckoos, CV=TRUE)
confusion(cuckoos$species, cuckooCV.lda$class,
          gpnames=abbreviate(levels(cuckoos$species), 8))
## Post-multiply by scaling matrix
scores <- centered %*% cuckoos.lda$scaling
```

Here for comparison are accuracy assessments, again based on leave-one-out
cross-validation, for `qda()`.  The code is an obvious modification
of that for `lda():

```{r qda-loo-cv-acc}
## Accuracies for quadratic discriminant analysis
cuckooCV.qda <- MASS::qda(species ~ length + breadth,
                    data=cuckoos, CV=TRUE)
acctab <-confusion(cuckoos$species, cuckooCV.qda$class,
                   gpnames=levels(cuckoos$species),
                   printit=FALSE)$confusion
tab <- table(cuckoos$species)
##
## Overall accuracy
cat("Overall accuracy =",
    sum(diag(acctab)*tab)/sum(tab), "\n")
## Confusion matrix
round(acctab, 3)
```

Notice that accuracy is slightly reduced, relative to the use of `lda()`.

The calculations that follow will require an `lda()` model
with `CV=FALSE`, which is the default:

```{r CVfalse}
cuckoos.lda <- MASS::lda(species ~ length + breadth, data=cuckoos)
```

```{r calc-discrim}
x <- pretty(cuckoos$breadth, 20)
y <- pretty(cuckoos$length, 20)
Xcon <- expand.grid(breadth=x, length=y)
cucklda.pr <- predict(cuckoos.lda, Xcon)$posterior
```

Figure \@ref(fig:cuckoos-contour) shows contours for distinguishing
`wren` from `not-wren`, for the `lda()` analysis
(gray line).

```{r cuckoos-contour, fig.cap=cap9,out.width='70%', fig.width=6.25, fig.height=4.75}
m <- match("wren", colnames(cucklda.pr))
ldadiff <- apply(cucklda.pr, 1, function(x)x[m]-max(x[-m]))
addlayer1 <- latticeExtra::as.layer(contourplot(ldadiff ~ breadth*length,
                                  at=c(-1,0,1), labels=c("", "lda",""),
                                  label.style="flat", col='gray',
                                  data=Xcon), axes=FALSE)
gph + addlayer1
```

\subsection{Accuracy comparisons}

The function `gamclass::compareModels()` can be used
to compare the accuracies of alternative model fits, checking for
consistency over the data as a whole.  Two model fits will be
compared -- the `lda()` fit above, and a variation on the
`lda()` fit that includes terms in
`length^2`, `breadth^2 and `length*breadth`.

```{r cf-acc-lda-qda}
library(gamclass, quietly=TRUE)
cucklda.pr <- cuckooCV.lda$posterior
cucklda.pr2 <- MASS::lda(species ~ length + breadth + I(length^2)
                   + I(breadth^2) + I(length*breadth), CV=TRUE,
                   data=cuckoos)$posterior
compareModels(groups=cuckoos$species,
              estprobs=list(lda=cucklda.pr,
                            "lda plus"=cucklda.pr2),
              gpnames=abbreviate(levels(cuckoos$species),8))
```

The fit using `qda()`, which could also be included, has for
simplicity been left out.

# Tree-based methods

The dataset `spam`, from the `kernlab` package, was put
together in 1999, with information on 2788 non-spam emails and
1813 spam emails. The emails are not dated.  In the absence of
more recent data from comparable sources that uses the same
measures, there is no ready way to test how any model that might
be developed would perform as one moves forward in time from 1999.
Use of a holdout data set against which to assess results is the
best that we can do.

A first step is to divide the dataset into 3 parts, thus:

```{r getdata-spam}
data(spam, package='kernlab')
spam[,-58] <- scale(spam[,-58])
nr <- sample(1:nrow(spam))
spam0 <- spam[nr[1:2601],]      ## Training
spam1 <- spam[nr[2602:3601],]   ## Holdout
spam01 <- spam[nr[1:3601],]     ## Use for training,
                                ## if holdout not needed
spam2 <- spam[nr[3602:4601],]   ## Test
```

<!-- ```{r lda-spam01} to be omitted -->
<!-- ldaErr <- function(train.lda=spam01.lda, train=spam01, test=spam2, -->
<!--                    traingp=spam01[,'type'], testgp=spam2[,'type']){ -->
<!--     trainCV.lda <- update(train.lda, CV=TRUE) -->
<!--     prior01 <- train.lda$prior -->
<!--     ldaRates <- c(loo=1-confusion(traingp, -->
<!--                             trainCV.lda$class, -->
<!--                             printit=NULL)$overall, -->
<!--               trainerr=1-confusion(traingp, -->
<!--                                  predict(train.lda)$class, -->
<!--                                  printit=NULL)$overall, -->
<!--               testerr=1-confusion(testgp, -->
<!--                                 predict(train.lda, -->
<!--                                         newdata=test)$class, -->
<!--                                 prior=prior01, printit=NULL)$overall) -->
<!--      ldaRates -->
<!-- } -->
<!-- ``` -->

```{r lda-rates}
library('MASS')
spam01.lda <- lda(type~., data=spam01)
ldaRates <- ldaErr(train.lda=spam01.lda, train=spam01, test=spam2,
                   group='type')
```

For calculation of the test error rate, the prior is set to the proportions
in the training data `spam01`.  This ensures that accuracies are
for the same population mix of non-spam and spam.

<!-- ```{r rpartErr} to be omitted -->
<!-- rpartErr <- function(train.rp=spam01.rp, train=spam01, test=spam2, -->
<!--                      group='type'){ -->
<!--     cptab <- train.rp$cptable -->
<!--     nbest <- which.min(cptab[,"xerror"]) -->
<!--     rnprop <- prop.table(table(train.rp$y)) -->
<!--     xcv <- cptab[nbest,"xerror"] * min(rnprop) -->
<!--     trainerr <- cptab[nbest,"rel error"] * min(rnprop) -->
<!--     class2 <- predict(train.rp, newdata=test, type="class") -->
<!--     testerr <- 1-confusion(test[, outcome], class2, printit=FALSE, -->
<!--                          prior=rnprop)$overall -->
<!--     c(cverror=xcv, trainerror=trainerr, testerror=testerr) -->
<!-- } -->
<!-- ``` -->

Now use the function `rpartErr()` for a similar exercise for 
an `rpart()` model, and `gamclass::rfErr()` for a `randomForest()`
model.

```{r rpart-dofun}
set.seed(29)   ## Make results precisely reproducible
spam01.rp <- rpart::rpart(type~., data=spam01, cp=0.0001)
rpRates <- rpartErr(train.rp=spam01.rp, train=spam01, test=spam2,
                    group='type')
```

<!-- ```{r rfErr} to be omitted -->
<!-- rfErr <- function(train.rf=spam01.rf, train=spam01, test=spam2, -->
<!--                   outcome='type'){ -->
<!--     trainClass <- predict(train.rf, newdata=spam01, type="class") -->
<!--     testClass <- predict(train.rf, newdata=test, type="class") -->
<!--     rnprop <- prop.table(table(train[, outcome])) -->
<!--     OOBerr <- as.vector(train.rf$err.rate[train.rf$ntree, "OOB"]) -->
<!--     rfRates <- c(OOBerr=OOBerr, -->
<!--              trainerr=1-confusion(train$type, trainClass, -->
<!--                                   printit=FALSE)$overall, -->
<!--              testerr=1-confusion(spam2$type, testClass, printit=FALSE, -->
<!--                                  prior=rnprop)$overall) -->
<!--     rfRates -->
<!-- } -->
<!-- ``` -->

```{r rf-dofun}
set.seed(29)   ## Make results precisely reproducible
spam01.rf <- randomForest::randomForest(type ~ ., data=spam01)
rfRates <- rfErr(train.rf=spam01.rf, train=spam01, test=spam2,
                 group='type')
```

The following table summarizes results:
```{r acctable}
lda_main <- c(round(ldaRates['loo'], 3), round(ldaRates['trainerr'], 3),'-',
              round(ldaRates['testerr'], 3))
rpartAcc <- c('-',round(rpRates['cverror'], 3),round(rpRates['trainerror'], 3),
           round(rpRates['testerror'], 3))
rfAcc <- c('-',round(rfRates['trainerr'], 3),round(rfRates['OOBerr'], 3),
                  round(rfRates['testerr'], 3))
accmat <- rbind(lda_main,rpartAcc,rfAcc)
rownames(accmat) <- c('lda (main effects)','rpart','randomForest')
kable(accmat, col.names=c("Leave One Out CV","Training",
                          "Out of Bag","Test rate"), align=rep('r',4))
```
Calculation of a ten-fold cross-validation error rate for linear
discriminant analysis is left as an exercise for the user.  As the 
test data are a random sample from the total dataset, it should be
similar to the test error rate.

## Inclusion of interaction terms, with `lda()`

Can we improve model performance by including first order interaction terms? Factor by factor interaction terms allow a different estimate for each different combination of factor levels. Factor by variable interaction terms allow for a different slope for each different factor level. Variable by variable interaction terms create variables that are elementwise multiples of the two individual variables. The separate linear effects of variables `x1` and `x2` are increased or decreased by an amount that depends on the extent to which `x1` and `x2` increase or decrease together.  In this example, with 57 explanatory variables, the effect is to generate a model matrix with 1653 columns.  Main effects account for 57 columns, to which is added the `choose(57,2) =` `r choose(57,2)` ways of choosing combinations of two of the columns.  The model matrix that results is (pretty much inevitably) multicollinear, over-fitting is likewise likely, higher order interactions are not accounted for,
and calculations take a long time.

It is nevertheless insightful to proceed with the (time-consuming) 
fit, and note the results:
```{r lda-x, eval=FALSE}
mm01x <- model.matrix(type ~ 0+.^2, data=spam01)
mm2x <- model.matrix(type ~ 0+.^2, data=spam2)
spam01x.lda <- lda(x=mm01x, grouping=spam01[,'type'])
ldaRatesx <- ldaErr(train.lda=spam01x.lda, train=mm01x, test=mm2x,
                    group=spam01[,'type'])
round(ldaRatesx,3)
```
Results obtained were:
```{r errRates, echo=FALSE}
c(loo=0.291,  trainerr=0.027,  testerr=0.164)
```

The test error rate is the standard against which the other two rates should be compared. The leave-one-out estimate is wildly astray. A training rate that is highly over-optimistic is not surprising, given the large number of explanatory terms.

The big advantage of `randomForest()` is its ability to accommodate 
what, using classical approaches, would require the incorporation
of high order interaction terms.

## Multiple Levels of variation -- the `Vowel` dataset

The discussion that follows is designed to illustrate the important 
point that estimates of prediction error must, to be useful, reflect 
the  intended generalization.  For inference from the data considered 
here, prediction for one of the 15 speakers represented in the data 
is an inherently easier task than prediction for a new speaker.

The dataset `Vowel` (in the `mlbench` package) has data on 15 different 
speakers, each tested 6 times on each of 11 different vowels.  
Information additional to the dataset's help page can be found at
http://archive.ics.uci.edu/datasets.

```{r data-Vowel}
data('Vowel', package='mlbench')
Vowel$V1 <-  factor(Vowel$V1)
```

The first data column identifies the speaker/vowel combination.
The next 9 columns of the data are measures derived from auditory
signal processing.  The final column identifies the vowel sound.
The `V1` identifies the speaker. For prediction for a
new speaker, `V1` is not a useful explanatory factor.

We will compare the following:

* `lda()`, without and with first order interactions
* `qda()`
* `randomForest()`

Except for `randomForest()`, we will use cross-validation with
subjects as clusters to assess accuracy, i.e., subjects will be left
out one at a time.\^[Very similar results are obtained if they
  are left out three at a time, i.e., 5 folds].  For
`randomForest()`, 500 bootstrap samples of subjects will be
taken.  For each bootstrap sample, a single tree will be found, and
predictions made for the out-of-bag subjects.  This is a clumsy use of
`randomForest()`, necessary however because
`randomForest()` does not have provision for sampling the data
in a manner that reflects the intended generalization.  For prediction
to new speakers, each tree must be based on a bootstrap sample of
speakers, with estimated error rates based on performance for OOB
speakers.

```{r vowel-qda}
vowelcv.qda <- qda(Class ~ ., data=Vowel, CV=TRUE)
accqda <- confusion(Vowel$Class, vowelcv.qda$class,
                    printit=FALSE)$overall
print(round(accqda,3))
## Compare with CV performance
accspqda <- CVcluster(Class ~ ., id=V1,
                      data=Vowel, nfold=15, FUN=qda,
                      printit=FALSE)$CVaccuracy
print(round(accspqda,3))
```

```{r vowel-rf}
data('Vowel', package='mlbench')
Vowel$V1 <-  factor(Vowel$V1)
vowel.rf <- randomForest::randomForest(Class ~ ., data=Vowel)
print("OOB accuracy estimate")
accOOB <- 1-sum(rep(1/11,11)*vowel.rf$confusion[,"class.error"])
print(round(accOOB,3))
## Compare with performance based on OOB choice of speakers
accspOOB <- RFcluster(Class ~ ., id=V1,
                      data=Vowel, ntree=500,
                      progress = FALSE)$OOBaccuracy
print(round(accspOOB),3)
```