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\title{Miscellaneous \R\ notes}
\author{\copyright 2005 Ben Bolker}

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\begin{enumerate}
\item{\textbf{installing packages without administrative privileges:}
The following commands install \R\ packages
(in this case the
\code{plotrix}, \code{gplots}, \code{gtools}
and \code{gdata} packages) into a working
folder and then attach them.
First go to the file menu, and \code{Change dir} to your Desktop or My Documents
or something.  Then:
<<eval=FALSE>>=
desktop=getwd()
options(repos="http://cran.us.r-project.org")
install.packages("plotrix",destdir=desktop,lib=desktop)
library(plotrix,lib=desktop)
install.packages("gplots",destdir=desktop,lib=desktop)
install.packages("gtools",destdir=desktop,lib=desktop)
install.packages("gdata",destdir=desktop,lib=desktop)
library(gtools,lib=desktop)
library(gdata,lib=desktop)
library(gplots,lib=desktop)
@ 
}
\item{\textbf{Dealing with times in \R\ (lab 2):}
use the \code{times()} function in
the \code{chron} library to convert character
vectors or factor to times.  e.g.:
<<eval=FALSE>>=
install.packages("chron")
@ 
<<>>=
library(chron)
timevec1 = c("11:00:00","11:25:30","15:30:20")
times1 = times(timevec1)
@ 
If you have times with no seconds component,
use something like
\code{timevec1=paste(timevec1,":00",sep="")}
to add seconds before you try to convert.
}
\item{
\textbf{More on reshaping data:}
<<>>=
set.seed(1001)
mydata = data.frame(indiv=rep(1:3,c(3,4,5)),
  sex=factor(c(rep("F",7),rep("M",5))),
  day=c(1:3,1:4,1:5),dist=runif(12))
@

Reshaping data (as Caro says) introduces \code{NA}
values:
<<>>=
r1 = reshape(mydata,direction="wide",idvar="indiv",timevar="day",
        v.names="dist"); r1
@ 
Tabulate number of individual females in this format:
<<>>=
table(r1$sex)
@

There may be a better way to do this but I haven't thought
of it yet \ldots

<<>>=
splitdata = split.data.frame(mydata,mydata$indiv)
firstlines = lapply(splitdata,function(x)x[1,])
recombined = do.call("rbind",firstlines)
@ 

}
\item{\textbf{setting default colors in \code{lattice} graphics:}
To set all colors to gray scale:
<<>>=
library(lattice)
trellis.par.set(canonical.theme(color=FALSE))
@ 

To set background color to white, leave foreground
colors alone:
<<>>=
trellis.par.set(col.whitebg())
@ 
\end{enumerate}

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