%\VignetteIndexEntry{xtable List of Tables Gallery}
%\VignetteDepends{xtable, spdep, splm, sphet}
%\VignetteKeywords{LaTeX, HTML, table}
%\VignettePackage{xtable}
% !Rnw weave = knitr
% \VignetteEngine{knitr::knitr}
%**************************************************************************
\documentclass{article}
\usepackage[a4paper, height=24cm]{geometry} % geometry first
\usepackage{array}
\usepackage{booktabs}
\usepackage{longtable}
\usepackage{parskip}
\usepackage{rotating}
\usepackage{tabularx}
\usepackage{titlesec}
\usepackage{hyperref} % hyperref last
\titleformat\subsubsection{\bfseries\itshape}{}{0pt}{}
\newcommand\p{\vspace{2ex}}
\newcommand\code[1]{\texttt{#1}}
\newcommand\pkg[1]{\textbf{#1}}
\setcounter{tocdepth}{2}
\begin{document}

\title{\bfseries\Large The Other Packages Gallery}
\author{\bfseries David J. Scott}
\maketitle

\tableofcontents

\newpage

\section{Introduction}
This document represents a test of the functions in \pkg{xtable} which
deal with other packages.

<<set, include=FALSE>>=
library(knitr)
opts_chunk$set(fig.path = 'Figures/other', debug = TRUE, echo = TRUE)
opts_chunk$set(out.width = '0.9\\textwidth')
@

The first step is to load the package and set some options for this document.
<<package, results='asis'>>=
library(xtable)
options(xtable.floating = FALSE)
options(xtable.timestamp = "")
options(width = 60)
set.seed(1234)
@

\section{The packages \pkg{spdep}, \pkg{splm}, and \pkg{sphet}}

Code for supporting these packages and most of the examples used in
this section was originally provided by Martin Gubri
(\url{martin.gubri@framasoft.org}).

\subsection{The package \pkg{spdep}}
\label{sec:package-pkgspdep}

First load the package and create some objects.
<<dataspdep>>=
library(spdep)
data("oldcol", package = "spdep")
COL.lag.eig <- lagsarlm(CRIME ~ INC + HOVAL, data = COL.OLD[],
                        nb2listw(COL.nb))
class(COL.lag.eig)
COL.errW.GM <- GMerrorsar(CRIME ~ INC + HOVAL, data = COL.OLD,
                          nb2listw(COL.nb, style = "W"),
                          returnHcov = TRUE)
class(COL.errW.GM)
COL.lag.stsls <- stsls(CRIME ~ INC + HOVAL, data = COL.OLD,
                       nb2listw(COL.nb))
class(COL.lag.stsls)

p1 <- predict(COL.lag.eig, newdata = COL.OLD[45:49,],
              listw = nb2listw(COL.nb))
class(p1)
p2 <- predict(COL.lag.eig, newdata = COL.OLD[45:49,],
              pred.type = "trend", type = "trend")
#type option for retrocompatibility with spdep 0.5-92
class(p2)

imp.exact <- impacts(COL.lag.eig, listw = nb2listw(COL.nb))
class(imp.exact)
imp.sim <- impacts(COL.lag.eig, listw = nb2listw(COL.nb), R = 200)
class(imp.sim)
@ %def


\subsubsection{\code{sarlm} objects}
\label{sec:codesarlm-objects}

There is an \code{xtable} method for objects of this type.
<<xtablesarlm, results = 'asis'>>=
xtable(COL.lag.eig)
@ %def

The method for \code{xtable} actually uses the summary of the object,
and an identical result is obtained when using the summary of the
object, even if the summary contains more additional information.

<<xtablesarlmsumm, results = 'asis'>>=
xtable(summary(COL.lag.eig, correlation = TRUE))
@ %def

This same pattern applies to the other objects from this group of packages.

Note that additional prettying of the resulting table is possible, as
for any table produced using \code{xtable}. For example using the
\pkg{booktabs} package we get:

<<xtablesarlmbooktabs, results = 'asis'>>=
print(xtable(COL.lag.eig), booktabs = TRUE)
@ %def

\subsubsection{\code{gmsar} objects}
\label{sec:codegmsar-objects}


<<xtablegmsar, results = 'asis'>>=
xtable(COL.errW.GM)
@ %def

\subsubsection{\code{stsls} objects}
\label{sec:codestsls-objects}


<<xtablestsls, results = 'asis'>>=
xtable(COL.lag.stsls)
@ %def

\subsubsection{\code{sarlm.pred} objects}
\label{sec:codesarlmpred-objects}

\code{xtable} has a method for predictions of \code{sarlm} models.

<<xtablesarlmpred, results = 'asis'>>=
xtable(p1)
@ %def

This method transforms the \code{sarlm.pred} objects into data frames, allowing any number of attributes vectors which may vary according to predictor types.

<<xtablesarlmpred2, results = 'asis'>>=
xtable(p2)
@ %def

\subsubsection{\code{lagImpact} objects}
\label{sec:codelagimpact-objects}

The \code{xtable} method returns the values of direct, indirect and total impacts for all the variables in the model. The class \code{lagImpact} have two different sets of attributes according to if simulations are used. But the \code{xtable} method always returns the three components of the non-simulation case.

<<xtablelagimpactexact, results = 'asis'>>=
xtable(imp.exact)
@ %def

\p
<<xtablelagimpactmcmc, results = 'asis'>>=
xtable(imp.sim)
@ %def


\subsubsection{\code{spautolm} objects}
\label{sec:codespautolm-objects}

The need for an \code{xtable} method for \code{spautolm} was expressed
by Guido Schulz (\url{schulzgu@student.hu-berlin.de}), who also
provided an example of an object of this type. The required code was
implemented by David Scott (\url{d.scott@auckland.ac.nz}).

First create an object of the required type.

<<minimalexample, results = 'hide'>>=
library(spdep)
example(NY_data)
spautolmOBJECT <- spautolm(Z ~ PEXPOSURE + PCTAGE65P,data = nydata,
                           listw = listw_NY, family = "SAR",
                           method = "eigen", verbose = TRUE)
summary(spautolmOBJECT, Nagelkerke = TRUE)
@ %def

\p
<<spautolmclass>>=
class(spautolmOBJECT)
@ %def


<<xtablespautolm, results = 'asis'>>=
xtable(spautolmOBJECT,
       display = c("s",rep("f", 3), "e"), digits = 4)
@ %def



\subsection{The package \pkg{splm}}
\label{sec:package-pkgsplm}

First load the package and create some objects.
<<datasplm>>=
library(splm)
data("Produc", package = "plm")
data("usaww",  package = "splm")
fm <- log(gsp) ~ log(pcap) + log(pc) + log(emp) + unemp
respatlag <- spml(fm, data = Produc, listw = mat2listw(usaww),
                   model="random", spatial.error="none", lag=TRUE)
class(respatlag)
GM <- spgm(log(gsp) ~ log(pcap) + log(pc) + log(emp) + unemp, data = Produc,
           listw = usaww, moments = "fullweights", spatial.error = TRUE)
class(GM)

imp.spml <- impacts(respatlag, listw = mat2listw(usaww, style = "W"), time = 17)
class(imp.spml)
@ %def


\subsubsection{\code{splm} objects}
\label{sec:codesplm-objects}

<<xtablesplm, results = 'asis'>>=
xtable(respatlag)
@ %def


\p
<<xtablesplm1, results = 'asis'>>=
xtable(GM)
@ %def

The \code{xtable} method works the same on impacts of \code{splm} models.

<<xtablesplmimpacts, results = 'asis'>>=
xtable(imp.spml)
@ %def

\subsection{The package \pkg{sphet}}
\label{sec:package-pkgsphet}

First load the package and create some objects.
<<datasphet>>=
library(sphet)
data("columbus", package = "spdep")
listw <- nb2listw(col.gal.nb)
data("coldis", package = "sphet")
res.stsls <- stslshac(CRIME ~ HOVAL + INC, data = columbus, listw = listw,
                      distance = coldis, type = 'Triangular')
class(res.stsls)

res.gstsls <- gstslshet(CRIME ~ HOVAL + INC, data = columbus, listw = listw)
class(res.gstsls)

imp.gstsls <- impacts(res.gstsls, listw = listw)
class(imp.gstsls)
@ %def


\subsubsection{\code{sphet} objects}
\label{sec:codesphet-objects}

<<xtablesphet, results = 'asis'>>=
xtable(res.stsls)
@ %def

\p
<<xtablesphet1, results = 'asis'>>=
xtable(res.gstsls)
@ %def

\code{sphet} also provides a method for computing impacts.

<<xtablesphetimpacts, results = 'asis'>>=
xtable(imp.gstsls)
@ %def

\section{The \pkg{zoo} package}
\label{sec:pkgzoo-package}

 
<<zoo, results = 'asis'>>=
library(zoo)
xDate <- as.Date("2003-02-01") + c(1, 3, 7, 9, 14) - 1
as.ts(xDate)
x <- zoo(rnorm(5), xDate)
xtable(x)
@ %def 


\p

<<zoots, results = 'asis'>>=
tempTs <- ts(cumsum(1 + round(rnorm(100), 0)),
              start = c(1954, 7), frequency = 12)
tempTable <- xtable(tempTs, digits = 0)
tempTable
tempZoo <- as.zoo(tempTs)
xtable(tempZoo, digits = 0)
@ %def 


\section{The \pkg{survival} package}
\label{sec:pkgsurvival-package}

 
<<survival, results = 'asis'>>=
library(survival)
test1 <- list(time=c(4,3,1,1,2,2,3), 
              status=c(1,1,1,0,1,1,0), 
              x=c(0,2,1,1,1,0,0), 
              sex=c(0,0,0,0,1,1,1)) 
coxFit <- coxph(Surv(time, status) ~ x + strata(sex), test1) 
xtable(coxFit)
@ %def 

\end{document}