Add a vignette with plots and summaries

- vignette template in Rmarkdown.
- see the buildPkg.R about how render it.

vignettes/vignette-01.Rmd

+---
+title: "Multivariate Covariance Generalized Linear Models"
+author: "Wagner Hugo Bonat"
+date: "`r paste('mcglm', packageVersion('mcglm'), Sys.Date())`"
+output:
+  rmarkdown::html_vignette:
+    fig_width: 6
+    fig_height: 6
+    toc: true
+    toc_dep: 3
+vignette: >
+  %\VignetteIndexEntry{Multivariate Covariance Generalized Linear Models}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+<style type="text/css">
+body, td, caption {
+    font-family: "Palatino Linotype", "Book Antiqua", Palatino, serif;
+    background-color: white;
+    font-size: 16px;
+}
+
+tt, code, pre {
+    font-family: "Inconsolata", "Andale Mono", monospace;
+}
+
+code {
+    font-size: 16px;
+}
+
+pre code {
+    font-size: 14px;
+}
+
+pre:not([class]) code {
+    background-color: #92BFB1;
+}
+pre, code {
+    background-color: #62BFB1;
+    border-radius: 3px;
+    color: #333;
+}
+
+/* R output */
+pre:not([class]) code {
+    background-color: #D4D4D4;
+}
+pre:not([class]), code {
+    background-color: #D4D4D4;
+}
+
+/* R input */
+pre, code {
+    border-radius: 3px;
+    background-color: #EDEDED;
+    color: #333;
+}
+
+img {
+    max-width: 100% !important;
+    display: block;
+    margin: auto;
+}
+
+.MathJax {
+    font-size: 80% !important;
+}
+
+</style>
+
+```{r setup, include=FALSE}
+##----------------------------------------------------------------------
+
+library(knitr)
+
+opts_chunk$set(
+    dev.args=list(family="Palatino"))
+
+options(width=68)
+
+##----------------------------------------------------------------------
+
+library(latticeExtra)
+rm(list=ls())
+
+## Color palette.
+mycol <- c("#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00",
+           "#FFFF33")
+dput(mycol)
+
+## Trellis graphical style.
+ps <- list(
+    box.rectangle=list(col=1, fill=c("gray70")),
+    box.umbrella=list(col=1, lty=1),
+    dot.symbol=list(col=1, pch=19),
+    dot.line=list(col="gray50", lty=3),
+    plot.symbol=list(col=1, cex=0.8),
+    plot.line=list(col=1),
+    plot.polygon=list(col="gray95"),
+    superpose.line=list(col=mycol, lty=1),
+    superpose.symbol=list(col=mycol, pch=1),
+    superpose.polygon=list(col=mycol),
+    strip.background=list(col=c("gray80","gray50"))
+    )
+trellis.par.set(ps)
+## show.settings()
+
+```
+
+****
+
+To install the stable version of [`mcglm`][], use
+`devtools::install_git()`. For more information, visit [mcglm/README].
+
+```{r, eval=FALSE}
+library(devtools)
+install_git("http://git.leg.ufpr.br/wbonat/mcglm.git")
+```
+
+```{r, eval=FALSE, error=FALSE, message=FALSE, warning=FALSE}
+library(mcglm)
+packageVersion("mcglm")
+```
+
+```{r, echo=FALSE, error=FALSE, message=FALSE, warning=FALSE}
+library(mcglm)
+packageVersion("mcglm")
+```
+
+****
+## The Australian Health Survey
+
+```{r}
+##----------------------------------------------------------------------
+## Loadin the Australian Health Survey data.
+
+data(ahs)
+
+## Object structure.
+str(ahs)
+
+## Descriptive measures.
+summary(ahs)
+
+##----------------------------------------------------------------------
+## Frequency tables.
+
+names(ahs)[c(1, 4:7, 10)]
+
+par(mfrow=c(2,3))
+## sapply(ahs[, c(1, 4:7, 10)],
+##        FUN=function(x){
+##            ## pie(table(x))
+##            barplot(prop.table(table(x)))
+##        })
+
+barplot(prop.table(xtabs(~sex, data=ahs)),
+        ylab="Sample proportion",
+        xlab="Sex")
+
+barplot(prop.table(xtabs(~levyplus, data=ahs)),
+        ylab="Sample proportion",
+        xlab="levyplus")
+
+barplot(prop.table(xtabs(~freepoor, data=ahs)),
+        ylab="Sample proportion",
+        xlab="freepoor")
+
+barplot(prop.table(xtabs(~freerepa, data=ahs)),
+        ylab="Sample proportion",
+        xlab="freerepa")
+
+barplot(prop.table(xtabs(~illness, data=ahs)),
+        ylab="Sample proportion",
+        xlab="illness")
+
+barplot(prop.table(xtabs(~chcond, data=ahs)),
+        ylab="Sample proportion",
+        xlab="chcond")
+layout(1)
+
+xt <- xtabs(~age+sex, data=ahs)
+mosaicplot(xt)
+
+xt <- xtabs(~age+chcond, data=ahs)
+mosaicplot(xt)
+
+xt <- xtabs(~sex+chcond, data=ahs)
+mosaicplot(xt)
+
+##----------------------------------------------------------------------
+
+library(lattice)
+library(latticeExtra)
+
+useOuterStrips(
+    combineLimits(
+        xyplot(Ndoc+Nndoc+Nadm+Nhosp+Nmed~age|sex,
+               outer=TRUE, data=ahs,
+               jitter.x=TRUE, amount=0.01,
+               type=c("p", "a"),
+               scales=list(y=list(relation="free")),
+               ylab="Number or occurences",
+               xlab="Age (years/100)")
+    )
+)
+
+useOuterStrips(
+    combineLimits(
+        xyplot(Ndoc+Nndoc+Nadm+Nhosp+Nmed~income|sex,
+               outer=TRUE, data=ahs,
+               jitter.x=TRUE, amount=0.01,
+               type=c("p", "a"),
+               scales=list(y=list(relation="free")),
+               ylab="Number or occurences",
+               xlab="Income")
+    )
+)
+
+useOuterStrips(
+    combineLimits(
+        xyplot(Ndoc+Nndoc+Nadm+Nhosp+Nmed~age|chcond,
+               groups=sex, outer=TRUE, data=ahs,
+               jitter.x=TRUE, amount=0.01,
+               type=c("p", "a"),
+               scales=list(y=list(relation="free")),
+               ylab="Number or occurences",
+               xlab="Age (years/100)")
+    )
+)
+
+```
+
+<!---------------------------------------------------------------------- -->
+
+[`mcglm`]: http://git.leg.ufpr.br/wbonat/mcglm
+[mcglm/README]: http://git.leg.ufpr.br/wbonat/mcglm/blob/master/README.md