\chapter{Functions, Packages, and Data}
\label{app:functionspackagesdatasets}
\SweaveOpts{keep.source=TRUE, pdf=TRUE}
<<options and clear workspace, echo=FALSE, eval=TRUE>>=
options(digits=3, show.signif.stars=FALSE, width=53)
options(width=50)
rm(list=ls())
@

Here we provide tables of the functions, packages, and data sets used in this book.

\section{Functions}

Here we list the R functions used in this book.  Some of the functions are used ``behind the scenes'' and are available on the book's website.

<<read functions file, echo=FALSE, eval=TRUE, results=tex>>=
require(xtable)
tmp = read.fwf("functionsUsed.txt", widths=c(33, 35, 31),
  stringsAsFactors=FALSE, colClasses="character")
colnames(tmp) = c("Function {Package}", "Application", "Chapters")
tbl = xtable(tmp[, 1:3], 
  caption="R functions used in this book.")
print(tbl, tabular.environment="longtable", 
  floating=FALSE, size="small", include.rownames=FALSE,
  caption.placement="top")
@

\section{Packages}

We use a variety of R packages available on CRAN.  Here we list the packages by chapter and the version used to create the book.  Before you begin copying the code, make sure the packages are installed on your computer.  Many of the packages depend on other packages that are not listed but are automatically installed.
\begin{itemize}
\item Chapter 1: None
\item Chapter 2: UsingR(0.1-17)
\item Chapter 3: ellipse(0.3-5), xtable(1.6-0)
\item Chapter 4: rjags(3-5), R2WinBUGS(2.1-18), lattice(0.20-0), LearnBayes(2.12)
\item Chapter 5: lubridate(0.2.6), maps(2.2-5), classInt(0.1-17), maptools(0.8-14), rgdal(0.7-8), mapdata(2.2-1), ggplot2(0.9.0), ggmap(1.2)
\item Chapter 6: lubridate(0.2.6), maps(2.2-5), survival(2.36-10), ncdf(1.6.6)
\item Chapter 7: pscl(1.04.1), xtable(1.6-0), plotmo(1.3-1), earth(3.2-1)
\item Chapter 8: quantreg(4.76), xtable(1.6-0), ismev(1.37), gamlss(4.1-1), gamlss.cens(4.0.4)
\item Chapter 9: gstat(1.0-10), maptools(0.8-14), sp(0.9-94), rgdal(0.7-8), maps(2.2-5), colorRamps(2.3), spdep(0.5-43), spgwr(0.6-13)
\item Chapter 10: gamlss(4.1-1), xtable(1.6-0), chron(2.3-42), ggplot2(0.8.9), network(1.7), sna(2.2-0), igraph(0.5.5-4)
\item Chapter 11: maps(2.2-5), spatstat(1.25-3), sp(0.9-94), rgdal(0.7-8), maptools(0.8-14), cluster(1.14.1), xtable(1.6-0)
\item Chapter 12: rjags(3-5), fields(6.6.3), BMA(3.15), sp(0.9-94), rgdal(0.7-8), maps(2.2-5), maptools(0.8-14), colorRamps(2.3), spdep(0.5-43), coda(0.14-6), bootstrap(1.0-22), xtable(1.6-0)
\item Chapter 13: maps(2.2-5), ggplot2(0.9.0), oce(0.8-4), sp(0.9-94), quantreg(4.76)
\end{itemize}

\section{Data Sets}

We also use a variety of data sets.  Most of the data sets are explained in Chapter~\ref{chap:datasets}.  Here we list the data used in each chapter.  The data are available by chapter on the book's website.
\begin{itemize}
\item Chapter 1: None
\item Chapter 2: {\it US.txt}, {\it NAO.txt}
\item Chapter 3: {\it H.txt}, {\it NAO.txt}, {\it SST.txt}
\item Chapter 4: {\it ATL.txt}, {\it H.txt}, {\it hurart.txt}, {\it modelc}, {\it modelupdates.RData}
\item Chapter 5: {\it SOI.txt}, {\it NAO.txt}, {\it SST.txt}, {\it ATL.txt}, {\it H.txt}, {\it Ivan.txt}, {\it LMI.txt}, {\it FLPop.txt}, {\it JulySST2005.txt}
\item Chapter 6: {\it BTflat.csv}, {\it gridboxes.txt}, {\it HS.csv}, {\it landGrid.RData}, {\it best.RData}, {\it best.use.RData}, {\it sstna.nc}
\item Chapter 7: {\it US.txt}, {\it annual.RData}, {\it bi.csv}
\item Chapter 8: {\it LMI.txt}, {\it SST.txt}, {\it SOI.txt}, {\it catwinds.RData}, {\it catcounts.RData}
\item Chapter 9: {\it best.use.RData}, {\it sstJuly2005.txt}, {\it FayRain.txt}
\item Chapter 10: {\it annual.RData}, {\it best.use.RData}, {\it SST.txt}
\item Chapter 11: {\it gridboxes.txt}, {\it bi.csv}, {\it annual.RData}, {\it best.use.RData}
\item Chapter 12: {\it US.txt}, {\it annual.RData}, {\it best.use.RData}, {\it ncdataframe.RData}, {\it Chain1.txt}, {\it Chain2.txt}, {\it Index.txt}, {\it SSTChain.txt}, {\it SSTIndex.txt}, {\it SOIChain.txt}, {\it SOIIndex.txt}
\item Chapter 13: {\it Losses.txt}, {\it best.use.RData}, {\it ncdataframe.RData}
\end{itemize}