Beginner's questions (figures, bibliography) with Sweave/R/LaTeX---my first document

Question

I am just starting with Sweave and with R. Here I am using R to output some data and I am also trying to include a plot. The code does not sweave. I have one Sweave example from the web that compiles well in RStudio with LaTeX.

\documentclass[a4paper]{article}
\begin{document}
<<echo=TRUE>>=
x <- rnorm(100)
xm <- mean(x)
xm
@

<<echo=FALSE>>=
x <- rnorm(100)
xm <- mean(x)
xm
@

<<echo=TRUE>>= 
test.frame<-read.table(file="apples.d",header=T,sep= "")
names(test.frame)
head(test.frame)
class(test.frame)
@
\begin{figure}[htbp]
\begin{center}
\setkeys{Gin}{width=0.5\textwidth}
<<echo=FALSE,fig=TRUE,width=4,height=4>>=
plot(year,value)
@
\end{center}
\end{document}

and the file apples.d contains:

#Number of apples I ate
year value
8   12050  #year 2008  
9   15292  #year 2009 
10  23907  #year 2010 
11  33997  #year 2011

What am I doing wrong?

Other related question:

Does a Sweave document support normal LaTeX bibliography file. How to do the compilation?

Thanks a lot...

Answer 1

Several problems corrected, marked by %%%% or ####

\documentclass[a4paper]{article}
\begin{document}
<<echo=TRUE>>=
x <- rnorm(100)
xm <- mean(x)
xm
@

<<echo=FALSE>>=
x <- rnorm(100)
xm <- mean(x)
xm
@

<<echo=TRUE>>= 
##### Remove all comments from your data file 
test.frame<-read.table(file="apples.d",header=T,sep= "")
names(test.frame)
head(test.frame)
class(test.frame)
@

\begin{figure}[htbp]
\begin{center}
\setkeys{Gin}{width=0.5\textwidth}
<<echo=FALSE,fig=TRUE,width=4,height=4>>=
#### Must tell plot where to get the data from. Could also use test.frame$year
with(test.frame,plot(year,value))
@
\end{center}
\end{figure}
\end{document}

Answer 2

Sweave does not take care of your bibliography, so you have to compile it by yourself; I believe some people have automated this job in their R scripts, but I would recommend you to use LyX if you are an experienced LaTeX user. LyX has official support to Sweave, and it takes care of everything you want in LaTeX intelligently (including bibliography). See the manual: https://github.com/downloads/yihui/lyx/sweave.pdf