[r-cran-zelig] 74/102: Import Upstream version 3.4-8
Andreas Tille
tille at debian.org
Sun Jan 8 17:00:00 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository r-cran-zelig.
commit 5a8b50f11ec9ea5e3d9e36736f5f5a64cc5dcf65
Author: Andreas Tille <tille at debian.org>
Date: Sun Jan 8 09:40:22 2017 +0100
Import Upstream version 3.4-8
---
DESCRIPTION | 43 +-
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inst/doc/vigpics/quantile-DummyPlot.pdf | 26 +-
inst/doc/vigpics/quantile-ExamplesPlot.eps | 2 +
inst/doc/vigpics/quantile-ExamplesPlot.pdf | 26 +-
inst/doc/vigpics/quantile-MultiplePlot.eps | 2 +
inst/doc/vigpics/quantile-MultiplePlot.pdf | 28 +-
inst/doc/vigpics/relogit-Example1Plot.eps | 2 +
inst/doc/vigpics/relogit-Example1Plot.pdf | 26 +-
inst/doc/vigpics/relogit-Example3Plot.eps | 2 +
inst/doc/vigpics/relogit-Example3Plot.pdf | 26 +-
inst/doc/vigpics/rq-DummyPlot.eps | 2 +
inst/doc/vigpics/rq-DummyPlot.pdf | 26 +-
inst/doc/vigpics/rq-ExamplesPlot.eps | 2 +
inst/doc/vigpics/rq-ExamplesPlot.pdf | 26 +-
inst/doc/vigpics/rq-MultiplePlot.eps | 2 +
inst/doc/vigpics/rq-MultiplePlot.pdf | 28 +-
inst/doc/vigpics/threesls-Examplesthreesls.eps | 2 +
inst/doc/vigpics/threesls-Examplesthreesls.pdf | 26 +-
inst/doc/vigpics/twosls-Examplestwosls.eps | 2 +
inst/doc/vigpics/twosls-Examplestwosls.pdf | 26 +-
inst/doc/vigpics/weibull-ExamplePlot.eps | 2 +
inst/doc/vigpics/weibull-ExamplePlot.pdf | 26 +-
inst/doc/weibull.log | 695 +
inst/doc/weibull.pdf | Bin 135232 -> 135232 bytes
inst/doc/whatsnew.tex | 6 +-
inst/doc/zelig.log | 1604 +
inst/doc/zelig.pdf | Bin 2380484 -> 370675 bytes
inst/doc/zelig.tex | 2 +-
man/plot.ci.Rd | 4 +
man/zeligVDC.Rd | 2 +-
429 files changed, 101730 insertions(+), 57085 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index 197c932..06b1c02 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,28 +1,29 @@
Package: Zelig
-Version: 3.4-7
-Date: 2009-10-23
+Version: 3.4-8
+Date: 2010-01-20
Title: Everyone's Statistical Software
-Author: Kosuke Imai <kimai at Princeton.Edu>,
- Gary King <king at harvard.edu>,
- Olivia Lau <olivia.lau at post.harvard.edu>
+Author: Kosuke Imai <kimai at Princeton.Edu>, Gary King
+ <king at harvard.edu>, Olivia Lau <olivia.lau at post.harvard.edu>
Maintainer: Kosuke Imai <kimai at Princeton.Edu>
Depends: R (>= 2.6.0), MASS, boot
Description: Zelig is an easy-to-use program that can estimate, and
- help interpret the results of, an enormous range of
- statistical models. It literally is ``everyone's statistical
- software'' because Zelig's simple unified framework
- incorporates everyone else's (R) code. We also hope it will
- become ``everyone's statistical software'' for applications
- and teaching, and so have designed Zelig so that anyone can
- easily use it or add their programs to it. Zelig also comes
- with infrastructure that facilitates the use of any existing
- method, such as by allowing multiply imputed data for any
- model, and mimicking the program Clarify (for Stata) that
- takes the raw output of existing statistical procedures and
- translates them into quantities of direct interest.
-License: GPL (>=2)
+ help interpret the results of, an enormous range of statistical
+ models. It literally is ``everyone's statistical software''
+ because Zelig's simple unified framework incorporates everyone
+ else's (R) code. We also hope it will become ``everyone's
+ statistical software'' for applications and teaching, and so
+ have designed Zelig so that anyone can easily use it or add
+ their programs to it. Zelig also comes with infrastructure
+ that facilitates the use of any existing method, such as by
+ allowing multiply imputed data for any model, and mimicking the
+ program Clarify (for Stata) that takes the raw output of
+ existing statistical procedures and translates them into
+ quantities of direct interest.
+License: GPL (>= 2)
URL: http://gking.harvard.edu/zelig
Suggests: VGAM (>= 0.7-5), MCMCpack (>= 0.8-2), mvtnorm, survival,
- sandwich (>= 2.1-0), zoo (>= 1.5-0), coda, nnet, sna, gee,
- systemfit, mgcv, lme4, anchors (>= 2.0), survey
-Packaged: 2009-10-23 16:29:00 UTC; rbuild
+ sandwich (>= 2.1-0), zoo (>= 1.5-0), coda, nnet, sna, gee,
+ systemfit, mgcv, lme4, anchors (>= 2.0), survey, quantreg
+Packaged: 2010-01-21 01:48:21 UTC; rbuild
+Repository: CRAN
+Date/Publication: 2010-01-21 07:13:07
diff --git a/R/model.frame.multiple.R b/R/model.frame.multiple.R
index 48491fe..85f44d0 100644
--- a/R/model.frame.multiple.R
+++ b/R/model.frame.multiple.R
@@ -26,7 +26,7 @@ model.frame.multiple <- function (formula,data,eqn=NULL,...){
rhs<-as.formula(paste("~",rhs))
Xs[[eqns[[i]]]]<-model.matrix.default(rhs,data=data)
tlNew[[eqns[[i]]]]<-colnames(Xs[[eqns[[i]]]])
- tlNew[[eqns[[i]]]]<-gsub("as.factor\\(.*\\)","",tlNew[[eqns[[i]]]],extended=TRUE)
+ tlNew[[eqns[[i]]]]<-gsub("as.factor\\(.*\\)","",tlNew[[eqns[[i]]]])
colnames(Xs[[eqns[[i]]]])<-tlNew[[eqns[[i]]]]
}
}
@@ -41,7 +41,7 @@ model.frame.multiple <- function (formula,data,eqn=NULL,...){
lhs<-as.formula(paste("~",lhs))
Ys<-model.matrix.default(lhs,data=data)
dvNew<-colnames(Ys)
- dvNew<-gsub("as.factor\\(.*\\)","",dvNew,extended=TRUE)
+ dvNew<-gsub("as.factor\\(.*\\)","",dvNew)
colnames(Ys)<-dvNew
}
attr(terms,"term.labels")[names(tlNew)]<-tlNew
diff --git a/R/zvcClient.R b/R/zvcClient.R
index c22818d..0edc012 100644
--- a/R/zvcClient.R
+++ b/R/zvcClient.R
@@ -403,7 +403,7 @@ zelig.new.packages <- function(lib.loc=NULL,zmat=matrixDependencies(),matin=NULL
lrw <- unlist(suppressWarnings(sapply(lrw, FUN="trim.blanks")))
lrwuq <- unique.default(lrw)
dec <- 0
- if(length(grep("^R",lrwuq[length(lrwuq)], extended=TRUE)) > 0) dec <- 1
+ if(length(grep("^R",lrwuq[length(lrwuq)])) > 0) dec <- 1
### print(zrwuq)
ind <- sapply(lrwuq, match, zrwuq)
@@ -441,7 +441,7 @@ zelig.new.packages <- function(lib.loc=NULL,zmat=matrixDependencies(),matin=NULL
newpkgmat <- NULL
pkgmod <- sapply(pkgsnoinst,function(m) paste("^",m,"$",sep=""))
- ind <- unlist(sapply(pkgmod,grep,zrw,extended=TRUE))
+ ind <- unlist(sapply(pkgmod,grep,zrw))
if(length(ind) > 0){
ind <- unlist(ind)
@@ -612,7 +612,7 @@ selectLevels <- function(mat, depth){
nmcol <- colnames(mat)
ix <- unique.default(c(grep("depth", nmvec),grep("depth", nmcol)))
mat.depth <- mat[[ix]]
- if(length(grep("^1[z-Z]$",mat.depth,extended=TRUE))<=0){
+ if(length(grep("^1[z-Z]$",mat.depth))<=0){
bool1 <- as.numeric(mat.depth) <= depth
}else{
bool1 <- mat.depth <= "1z" || mat.depth <= "1Z"
diff --git a/inst/doc/Rplots.pdf b/inst/doc/Rplots.pdf
index 78db5c2..9ad7d26 100644
--- a/inst/doc/Rplots.pdf
+++ b/inst/doc/Rplots.pdf
@@ -2,10 +2,10 @@
%���ρ�\r
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-/ModDate (D:20091023121825)
+/CreationDate (D:20100120203731)
+/ModDate (D:20100120203731)
/Title (R Graphics Output)
-/Producer (R 2.9.2)
+/Producer (R 2.10.1)
/Creator (R)
>>
endobj
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+\setcounter{lsubsubsection}{0}
+\setcounter{lparagraph}{0}
+\setcounter{lsubparagraph}{0}
+\setcounter{lsubsubparagraph}{0}
+\setcounter{FancyVerbLine}{1}
+\setcounter{section at level}{3}
+}
diff --git a/inst/doc/commands/print.aux b/inst/doc/commands/print.aux
index b32dd97..d83a156 100644
--- a/inst/doc/commands/print.aux
+++ b/inst/doc/commands/print.aux
@@ -1,14 +1,14 @@
\relax
-\@writefile{toc}{\contentsline {section}{\numberline {10.4}{\tt print}: Printing Quantities of Interest}{93}{section.10.4}}
-\newlabel{ss:print}{{10.4}{93}{{\tt print}: Printing Quantities of Interest\relax }{section.10.4}{}}
-\@writefile{toc}{\contentsline {subsubsection}{Description}{93}{section*.52}}
-\@writefile{toc}{\contentsline {subsubsection}{Syntax}{93}{section*.53}}
-\@writefile{toc}{\contentsline {subsubsection}{Arguments}{93}{section*.54}}
-\@writefile{toc}{\contentsline {subsubsection}{Examples}{93}{section*.55}}
-\@writefile{toc}{\contentsline {subsubsection}{See Also}{93}{section*.56}}
-\@writefile{toc}{\contentsline {subsubsection}{Contributors}{93}{section*.57}}
+\@writefile{toc}{\contentsline {section}{\numberline {10.1}{\tt print}: Printing Quantities of Interest}{86}{section.10.1}}
+\newlabel{ss:print}{{10.1}{86}{{\tt print}: Printing Quantities of Interest\relax }{section.10.1}{}}
+\@writefile{toc}{\contentsline {subsubsection}{Description}{86}{section*.33}}
+\@writefile{toc}{\contentsline {subsubsection}{Syntax}{86}{section*.34}}
+\@writefile{toc}{\contentsline {subsubsection}{Arguments}{86}{section*.35}}
+\@writefile{toc}{\contentsline {subsubsection}{Examples}{86}{section*.36}}
+\@writefile{toc}{\contentsline {subsubsection}{See Also}{86}{section*.37}}
+\@writefile{toc}{\contentsline {subsubsection}{Contributors}{86}{section*.38}}
\@setckpt{commands/print}{
-\setcounter{page}{94}
+\setcounter{page}{87}
\setcounter{equation}{0}
\setcounter{enumi}{4}
\setcounter{enumii}{3}
@@ -18,7 +18,7 @@
\setcounter{mpfootnote}{0}
\setcounter{part}{3}
\setcounter{chapter}{10}
-\setcounter{section}{4}
+\setcounter{section}{1}
\setcounter{subsection}{0}
\setcounter{subsubsection}{0}
\setcounter{paragraph}{0}
@@ -27,7 +27,7 @@
\setcounter{table}{0}
\setcounter{LT at tables}{0}
\setcounter{LT at chunks}{0}
-\setcounter{NAT at ctr}{0}
+\setcounter{NAT at ctr}{52}
\setcounter{parentequation}{0}
\setcounter{Item}{216}
\setcounter{Hfootnote}{8}
diff --git a/inst/doc/commands/put.start.aux b/inst/doc/commands/put.start.aux
new file mode 100644
index 0000000..3705de6
--- /dev/null
+++ b/inst/doc/commands/put.start.aux
@@ -0,0 +1,36 @@
+\relax
+\@setckpt{commands/put.start}{
+\setcounter{page}{533}
+\setcounter{equation}{0}
+\setcounter{enumi}{2}
+\setcounter{enumii}{2}
+\setcounter{enumiii}{2}
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+\setcounter{parentequation}{0}
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diff --git a/inst/doc/commands/set.start.aux b/inst/doc/commands/set.start.aux
new file mode 100644
index 0000000..3120a80
--- /dev/null
+++ b/inst/doc/commands/set.start.aux
@@ -0,0 +1,36 @@
+\relax
+\@setckpt{commands/set.start}{
+\setcounter{page}{533}
+\setcounter{equation}{0}
+\setcounter{enumi}{2}
+\setcounter{enumii}{2}
+\setcounter{enumiii}{2}
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+\setcounter{LT at chunks}{0}
+\setcounter{NAT at ctr}{0}
+\setcounter{parentequation}{0}
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+\setcounter{section at level}{3}
+}
diff --git a/inst/doc/commands/tag.aux b/inst/doc/commands/tag.aux
new file mode 100644
index 0000000..e12497e
--- /dev/null
+++ b/inst/doc/commands/tag.aux
@@ -0,0 +1,45 @@
+\relax
+\@writefile{toc}{\contentsline {section}{\numberline {13.1}{\tt tag}: Constrain parameter effects across equations}{533}{section.13.1}}
+\newlabel{tag}{{13.1}{533}{{\tt tag}: Constrain parameter effects across equations\relax }{section.13.1}{}}
+\@writefile{toc}{\contentsline {subsubsection}{Description}{533}{section*.617}}
+\@writefile{toc}{\contentsline {subsubsection}{Syntax}{533}{section*.618}}
+\@writefile{toc}{\contentsline {subsubsection}{Arguments}{533}{section*.619}}
+\@writefile{toc}{\contentsline {subsubsection}{Output Values}{533}{section*.620}}
+\@writefile{toc}{\contentsline {subsubsection}{Examples}{533}{section*.621}}
+\@writefile{toc}{\contentsline {subsubsection}{See Also}{533}{section*.622}}
+\@writefile{toc}{\contentsline {subsubsection}{Contributors}{533}{section*.623}}
+\@setckpt{commands/tag}{
+\setcounter{page}{534}
+\setcounter{equation}{0}
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+\setcounter{FancyVerbLine}{1}
+\setcounter{section at level}{3}
+}
diff --git a/inst/doc/commandsRd/MatchIt.url.pdf b/inst/doc/commandsRd/MatchIt.url.pdf
deleted file mode 100644
index 43c27a6..0000000
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diff --git a/inst/doc/commandsRd/MatchIt.url.tex b/inst/doc/commandsRd/MatchIt.url.tex
deleted file mode 100644
index a7d93bd..0000000
--- a/inst/doc/commandsRd/MatchIt.url.tex
+++ /dev/null
@@ -1,7 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt MatchIt.url}: Table of links for Zelig}\label{ss:MatchIt.url}
-\keyword{datasets}{MatchIt.url}
-\begin{Description}\relax
-Table of linds for \code{help.zelig} for the companion MatchIt package.
-\end{Description}
-
-\end{document}
diff --git a/inst/doc/commandsRd/PErisk.pdf b/inst/doc/commandsRd/PErisk.pdf
deleted file mode 100644
index ac5826a..0000000
Binary files a/inst/doc/commandsRd/PErisk.pdf and /dev/null differ
diff --git a/inst/doc/commandsRd/PErisk.tex b/inst/doc/commandsRd/PErisk.tex
deleted file mode 100644
index c4e5521..0000000
--- a/inst/doc/commandsRd/PErisk.tex
+++ /dev/null
@@ -1,68 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt PErisk}: Political Economic Risk Data from 62 Countries in 1987}\label{ss:PErisk}
-\keyword{datasets}{PErisk}
-\begin{Description}\relax
-Political Economic Risk Data from 62 Countries in 1987.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}data(PErisk)\end{verbatim}
-\end{Usage}
-\begin{Format}\relax
-A data frame with 62 observations on the following 6 variables.
-All data points are from 1987. See Quinn (2004) for more
-details.
-
-country: a factor with levels 'Argentina' 'Australia' 'Austria'
-'Bangladesh' 'Belgium' 'Bolivia' 'Botswana' 'Brazil' 'Burma'
-'Cameroon' 'Canada' 'Chile' 'Colombia' 'Congo-Kinshasa'
-'Costa Rica' 'Cote d'Ivoire' 'Denmark' 'Dominican Republic'
-'Ecuador' 'Finland' 'Gambia, The' 'Ghana' 'Greece' 'Hungary'
-'India' 'Indonesia' 'Iran' 'Ireland' 'Israel' 'Italy' 'Japan'
-'Kenya' 'Korea, South' 'Malawi' 'Malaysia' 'Mexico' 'Morocco'
-'New Zealand' 'Nigeria' 'Norway' 'Papua New Guinea'
-'Paraguay' 'Philippines' 'Poland' 'Portugal' 'Sierra Leone'
-'Singapore' 'South Africa' 'Spain' 'Sri Lanka' 'Sweden'
-'Switzerland' 'Syria' 'Thailand' 'Togo' 'Tunisia' 'Turkey'
-'United Kingdom' 'Uruguay' 'Venezuela' 'Zambia' 'Zimbabwe'
-
-courts: an ordered factor with levels '0' \textless{} '1'.'courts' is an
-indicator of whether the country in question is judged to
-have an independent judiciary. From Henisz (2002).
-
-barb2: a numeric vector giving the natural log of the black market
-premium in each country. The black market premium is coded as
-the black market exchange rate (local currency per dollar)
-divided by the official exchange rate minus 1. From
-Marshall, Gurr, and Harff (2002).
-
-prsexp2: an ordered factor with levels '0' \textless{} '1' \textless{} '2' \textless{} '3' \textless{} '4'
-\textless{} '5', giving the lack of expropriation risk. From Marshall,
-Gurr, and Harff (2002).
-
-prscorr2: an ordered factor with levels '0' \textless{} '1' \textless{} '2' \textless{} '3' \textless{} '4'
-\textless{} '5', measuring the lack of corruption. From Marshall, Gurr,
-and Harff (2002).
-
-gdpw2: a numeric vector giving the natural log of real GDP per
-worker in 1985 international prices. From Alvarez et al.
-(1999).
-\end{Format}
-\begin{Source}\relax
-Mike Alvarez, Jose Antonio Cheibub, Fernando Limongi, and Adam
-Przeworski. 1999. ``ACLP Political and Economic Database.'' \textless{}URL:
-http://www.ssc.upenn.edu/\textasciitilde{}cheibub/data/\textgreater{}.
-
-Witold J. Henisz. 2002. ``The Political Constraint Index (POLCON)
-Dataset.'' \ \textless{}URL:
-http://www-management.wharton.upenn.edu/henisz/POLCON/ContactInfo.
-html\textgreater{}.
-
-Monty G. Marshall, Ted Robert Gurr, and Barbara Harff. 2002.
-``State Failure Task Force Problem Set.'' \textless{}URL:
-http://www.cidcm.umd.edu/inscr/stfail/index.htm\textgreater{}.
-\end{Source}
-\begin{References}\relax
-Kevin M. Quinn. 2004. ``Bayesian Factor Analysis for Mixed Ordinal
-and Continuous Response.'' \emph{Political Analyis}. Vol. 12, pp.338--353.
-\end{References}
-
-\end{document}
diff --git a/inst/doc/commandsRd/SupremeCourt.pdf b/inst/doc/commandsRd/SupremeCourt.pdf
deleted file mode 100644
index ec1fa81..0000000
Binary files a/inst/doc/commandsRd/SupremeCourt.pdf and /dev/null differ
diff --git a/inst/doc/commandsRd/SupremeCourt.tex b/inst/doc/commandsRd/SupremeCourt.tex
deleted file mode 100644
index 317d752..0000000
--- a/inst/doc/commandsRd/SupremeCourt.tex
+++ /dev/null
@@ -1,27 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt SupremeCourt}: U.S. Supreme Court Vote Matrix}\label{ss:SupremeCourt}
-\keyword{datasets}{SupremeCourt}
-\begin{Description}\relax
-This dataframe contains a matrix votes cast by U.S. Supreme Court
-justices in all cases in the 2000 term.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}data(SupremeCourt)\end{verbatim}
-\end{Usage}
-\begin{Format}\relax
-The dataframe has contains data for justices Rehnquist, Stevens,
-O'Connor, Scalia, Kennedy, Souter, Thomas, Ginsburg, and Breyer
-for the 2000 term of the U.S. Supreme Court. It contains data
-from 43 non-unanimous cases. The votes are coded liberal (1) and
-conservative (0) using the protocol of Spaeth (2003). The unit
-of analysis is the case citation (ANALU=0). We are concerned with
-formally decided cases issued with written opinions, after full
-oral argument and cases decided by an equally divided vote
-(DECTYPE=1,5,6,7).
-\end{Format}
-\begin{Source}\relax
-Harold J. Spaeth (2005). ``Original United States Supreme Court
-Database: 1953-2004 Terms.''
-\textless{}URL:http://www.as.uky.edu/polisci/ulmerproject/sctdata.htm\textgreater{}.
-\end{Source}
-
-\end{document}
diff --git a/inst/doc/commandsRd/Weimar.pdf b/inst/doc/commandsRd/Weimar.pdf
deleted file mode 100644
index 8d86b3c..0000000
Binary files a/inst/doc/commandsRd/Weimar.pdf and /dev/null differ
diff --git a/inst/doc/commandsRd/Weimar.tex b/inst/doc/commandsRd/Weimar.tex
deleted file mode 100644
index 2c3fffd..0000000
--- a/inst/doc/commandsRd/Weimar.tex
+++ /dev/null
@@ -1,28 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt Weimar}: 1932 Weimar election data}\label{ss:Weimar}
-\keyword{datasets}{Weimar}
-\begin{Description}\relax
-This data set contains election results for 10 kreise (equivalent to precincts) from the 1932 Weimar (German) election.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}data(Weimar)\end{verbatim}
-\end{Usage}
-\begin{Format}\relax
-A table containing 11 variables and 10 observations. The variables are
-\describe{
-\item[Nazi] Number of votes for the Nazi party
-\item[Government] Number of votes for the Government
-\item[Communists] Number of votes for the Communist party
-\item[FarRight] Number of votes for far right parties
-\item[Other] Number of votes for other parties, and non-voters
-\item[shareunemployed] Proportion unemployed
-\item[shareblue] Proportion working class
-\item[sharewhite] Proportion white-collar workers
-\item[sharedomestic] Proportion domestic servants
-\item[shareprotestants] Proportion Protestant
-}
-\end{Format}
-\begin{Source}\relax
-ICPSR
-\end{Source}
-
-\end{document}
diff --git a/inst/doc/commandsRd/Zelig-package.pdf b/inst/doc/commandsRd/Zelig-package.pdf
deleted file mode 100644
index 44c2139..0000000
Binary files a/inst/doc/commandsRd/Zelig-package.pdf and /dev/null differ
diff --git a/inst/doc/commandsRd/Zelig-package.tex b/inst/doc/commandsRd/Zelig-package.tex
deleted file mode 100644
index 378da16..0000000
--- a/inst/doc/commandsRd/Zelig-package.tex
+++ /dev/null
@@ -1,157 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt Zelig-package}: Zelig: Everyone's Statistical Software}\label{ss:Zelig.Rdash.package}
-\aliasA{Zelig}{Zelig-package}{Zelig}
-\keyword{package}{Zelig-package}
-\begin{Description}\relax
-Zelig is an easy-to-use program that can estimate, and
-help interpret the results of, an enormous range of statistical
-models. It literally is ``everyone's statistical software''
-because Zelig's simple unified framework incorporates everyone
-else's (R) code. We also hope it will become ``everyone's
-statistical software'' for applications and teaching, and so
-have designed Zelig so that anyone can easily use it or add
-their programs to it. Zelig also comes with infrastructure
-that facilitates the use of any existing method, such as by
-allowing multiply imputed data for any model, and mimicking the
-program Clarify (for Stata) that takes the raw output of
-existing statistical procedures and translates them into
-quantities of direct interest.
-\end{Description}
-\begin{Details}\relax
-\Tabular{ll}{
-Package: & Zelig\\
-Version: & 2.8-5\\
-Date: & 2007-06-12\\
-Depends: & R (\textgreater{}= 2.4.0), MASS, boot\\
-Suggests: & VGAM (\textgreater{}= 0.7-1), MCMCpack (\textgreater{}= 0.7-4), mvtnorm, survival,
-sandwich (\textgreater{}= 2.0-0), zoo (\textgreater{}= 1.2-1), coda, nnet, sna, gee,
-systemfit, mgcv\\
-License: & GPL version 2 or newer\\
-URL: & http://gking.harvard.edu/zelig\\
-}
-
-Index:
-\begin{alltt}
-approval U.S. Presidential Approval Data
-coalition Coalition Dissolution in Parliamentary
- Democracies
-current.packages Find all packages in a dependency chain
-dims Return Dimensions of Vectors, Arrays, and Data
- Frames
-eidat Simulation Data for Ecological Inference
-friendship Simulated Example of Schoolchildren Friendship
- Network
-gsource Read Data As a Space-Delimited Table
-help.zelig HTML Help for Zelig Commands and Models
-hoff Social Security Expenditure Data
-immigration Individual Preferences Over Immigration Policy
-macro Macroeconomic Data
-match.data Output matched data sets
-MatchIt.url Table of links for Zelig
-mexico Voting Data from the 1988 Mexican Presidental
- Election
-mi Bundle multiply imputed data sets as a list
-mid Militarized Interstate Disputes
-model.end Cleaning up after optimization
-model.frame.multiple Extracting the "environment" of a model formula
-model.matrix.multiple Design matrix for multivariate models
-network Format matricies into a data frame for social
- network analysis
-newpainters The Discretized Painter's Data of de Piles
-parse.formula Parsing user-input formulas into multiple
- syntax
-parse.par Select and reshape parameter vectors
-PErisk Political Economic Risk Data from 62 Countries
- in 1987
-plot.ci Plotting Vertical confidence Intervals
-plot.zelig Graphing Quantities of Interest
-put.start Set specific starting values for certain
- parameters
-repl Replicating Analyses
-rocplot Receiver Operator Characteristic Plots
-sanction Multilateral Economic Sanctions
-set.start Set starting values for all parameters
-setx Setting Explanatory Variable Values
-sim Simulating Quantities of Interest
-sna.ex Simulated Example of Social Network Data
-summary.zelig Summary of Simulated Quantities of Interest
-SupremeCourt U.S. Supreme Court Vote Matrix
-swiss Swiss Fertility and Socioeconomic Indicators
- (1888) Data
-ternaryplot Ternary diagram
-ternarypoints Adding Points to Ternary Diagrams
-tobin Tobin's Tobit Data
-turnout Turnout Data Set from the National Election
- Survey
-user.prompt Pause in demo files
-Weimar 1932 Weimar election data
-zelig Estimating a Statistical Model
-zeligDepStatus Zelig Dependencies Packages Client Status
-zeligDepUpdate Download Zelig Dependencies Packages
-zeligDescribeModelXML Zelig interface functions
-Zelig-package Everyone's Statistical Software
-Zelig.url Table of links for Zelig
-zideal Zelig Matrix of Dependencies
-\end{alltt}
-
-Further information is available in the following vignettes:
-
-\Tabular{ll}{
-\code{arima} & ARIMA Models for Time Series Data (source)\\
-\code{blogit} & Bivariate Logistic Regression for Two Dichotomous Dependent Variables (source)\\
-\code{bprobit} & Bivariate Probit Regression for Dichotomous Dependent Variables (source)\\
-\code{ei.RxC} & Hierarchical Multinomial-Dirichlet Ecological Inference Model (source)\\
-\code{ei.dynamic} & Quinn's Dynamic Ecological Inference (source)\\
-\code{ei.hier} & Hierarchical Ecological Inference Model (source)\\
-\code{exp} & Exponential Regression for Duration Dependent Variables (source)\\
-\code{factor.bayes} & Bayesian Factor Analysis (source)\\
-\code{factor.mix} & Mixed Data Factor Analysis (source)\\
-\code{factor.ord} & Ordinal Data Factor Analysis (source)\\
-\code{gam.logit} & gam.logit: Generalized Additive Model for Dichotomous Dependent Variables (source)\\
-\code{gam.normal} & Generalized Additive Model for Continuous Dependent Variables (source)\\
-\code{gam.poisson} & Generalized Additive Model for Count Dependent Variables (source)\\
-\code{gam.probit} & Generalized Additive Model for Dichotomous Dependent Variables (source)\\
-\code{gamma} & Gamma Regression for Continuous, Positive Dependent Variables (source)\\
-\code{irt1d} & One Dimensional Item Response Mode (source)\\
-\code{irtkd} & K-Dimensional Item Response Model (source)\\
-\code{logit} & Logistic Regression for Dichotomous Dependent Variables (source)\\
-\code{logit.bayes} & Bayesian Logistic Regression for Dichotomous Dependent Variables (source)\\
-\code{logit.gee} & Generalized Estimating Equation for Logistic Regression (source)\\
-\code{lognorm} & Log-Normal Regression for Duration Dependent Variables (source)\\
-\code{ls} & Least Squares Regression for Continuous Dependent Variables (source)\\
-\code{mlogit} & Multinomial Logistic Regression for Dependent Variables with Unordered Categorical Values (source)\\
-\code{mlogit.bayes} & Bayesian Multinomial Logistic Regression for Dependent Variables with Unordered Categorical Values (source)\\
-\code{mloglm} & Multinomial Log-Linear Regression for Contingency Table Models (source)\\
-\code{negbin} & Negative Binomial Regression for Event Count Dependent Variables (source)\\
-\code{netcloglog} & Least Squares Regression for Continuous Dependent Variables (source)\\
-\code{netgamma} & Least Squares Regression for Continuous Dependent Variables (source)\\
-\code{netlogit} & Least Squares Regression for Continuous Dependent Variables (source)\\
-\code{netls} & Network Least Squares Regression for Continuous Proximity Matrix Dependent Variables (source)\\
-\code{netnormal} & Least Squares Regression for Continuous Dependent Variables (source)\\
-\code{netpoisson} & Least Squares Regression for Continuous Dependent Variables (source)\\
-\code{netprobit} & Least Squares Regression for Continuous Dependent Variables (source)\\
-\code{normal} & Normal Regression for Continuous Dependent Variables (source)\\
-\code{normal.bayes} & Bayesian Normal Linear Regression (source)\\
-\code{ologit} & Ordinal Logistic Regression for Ordered Categorical Dependent Variables (source)\\
-\code{oprobit} & Ordinal Probit Regression for Ordered Categorical Dependent Variables (source)\\
-\code{oprobit.bayes} & Bayesian Ordered Probit Regression (source)\\
-\code{poisson} & Poisson Regression for Event Count Dependent Variables (source)\\
-\code{poisson.bayes} & Bayesian Poisson Regression (source)\\
-\code{probit} & Probit Regression for Dichotomous Dependent Variables (source)\\
-\code{probit.bayes} & Bayesian Probit Regression for Dichotomous Dependent Variable (source)\\
-\code{relogit} & Rare Events Logistic Regression for Dichotomous Dependent Variables (source)\\
-\code{sur} & Seemingly Unrelated Regression (source)\\
-\code{threesls} & Three Stage Least Squares (source)\\
-\code{tobit} & Linear regression for Left-Censored Dependet Variable (source)\\
-\code{tobit.bayes} & Bayesian Linear Regression for a Censored Dependent Variable (source)\\
-\code{twosls} & Two Stage Least Squares (source)\\
-\code{weibull} & Weibull Regression for Duration Dependent Variables (source)\\
-}
-\end{Details}
-\begin{Author}\relax
-Kosuke Imai \textless{}kimai at Princeton.Edu\textgreater{}, Gary King
-\textless{}king at harvard.edu\textgreater{}, Olivia Lau \textless{}olau at fas.harvard.edu\textgreater{}
-
-Maintainer: Kosuke Imai \textless{}kimai at Princeton.Edu\textgreater{}
-\end{Author}
-
-\end{document}
diff --git a/inst/doc/commandsRd/Zelig.pdf b/inst/doc/commandsRd/Zelig.pdf
deleted file mode 100644
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diff --git a/inst/doc/commandsRd/Zelig.tex b/inst/doc/commandsRd/Zelig.tex
deleted file mode 100644
index 637d95b..0000000
--- a/inst/doc/commandsRd/Zelig.tex
+++ /dev/null
@@ -1,67 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt zelig}: Estimating a Statistical Model}\label{ss:zelig}
-\keyword{file}{zelig}
-\begin{Description}\relax
-The \code{zelig} command estimates a variety of statistical
-models. Use \code{zelig} output with \code{setx} and \code{sim} to compute
-quantities of interest, such as predicted probabilities, expected values, and
-first differences, along with the associated measures of uncertainty
-(standard errors and confidence intervals).
-\end{Description}
-\begin{Usage}
-\begin{verbatim}
-z.out <- zelig(formula, model, data, by, save.data, cite, ...)
-\end{verbatim}
-\end{Usage}
-\begin{Arguments}
-\begin{ldescription}
-\item[\code{formula}] a symbolic representation of the model to be
-estimated, in the form \code{y \textasciitilde{}\bsl{}, x1 + x2}, where \code{y} is the
-dependent variable and \code{x1} and \code{x2} are the explanatory
-variables, and \code{y}, \code{x1}, and \code{x2} are contained in the
-same dataset. (You may include more than two explanatory variables,
-of course.) The \code{+} symbol means ``inclusion'' not
-``addition.'' You may also include interaction terms and main
-effects in the form \code{x1*x2} without computing them in prior
-steps; \code{I(x1*x2)} to include only the interaction term and
-exclude the main effects; and quadratic terms in the form
-\code{I(x1\textasciicircum{}2)}.
-\item[\code{model}] the name of a statistical model, enclosed in \code{""}.
-Type \code{help.zelig("models")} to see a list of currently supported
-models.
-\item[\code{data}] the name of a data frame containing the variables
-referenced in the formula, or a list of multiply imputed data frames
-each having the same variable names and row numbers (created by
-\code{mi}).
-\item[\code{save.data}] If is set to "TRUE", the input dataframe will be saved
-as an attribute ("zelig.data") of the zelig output object.
-\item[\code{cite}] If is set to "TRUE" (default), the model citation will be
-will be printed out when this function is called.
-\item[\code{by}] a factor variable contained in \code{data}. Zelig will subset
-the data frame based on the levels in the \code{by} variable, and
-estimate a model for each subset. This a particularly powerful option
-which will allow you to save a considerable amount of effort. For
-example, to run the same model on all fifty states, you could type:
-\code{z.out <- zelig(y \textasciitilde{} x1 + x2, data = mydata, model = "ls", by = "state")}
-You may also use \code{by} to run models using MatchIt subclass.
-\item[\code{...}] additional arguments passed to \code{zelig},
-depending on the model to be estimated.
-\end{ldescription}
-\end{Arguments}
-\begin{Value}
-Depending on the class of model selected, \code{zelig} will return
-an object with elements including \code{coefficients}, \code{residuals},
-and \code{formula} which may be summarized using
-\code{summary(z.out)} or individually extracted using, for example,
-\code{z.out\$coefficients}. See the specific models listed above
-for additional output values, or simply type \code{names(z.out)}.
-\end{Value}
-\begin{Author}\relax
-Kosuke Imai \textless{}\email{kimai at princeton.edu}\textgreater{}; Gary King
-\textless{}\email{king at harvard.edu}\textgreater{}; Olivia Lau \textless{}\email{olau at fas.harvard.edu}\textgreater{}
-\end{Author}
-\begin{SeeAlso}\relax
-The full Zelig manual is available at
-\url{http://gking.harvard.edu/zelig}.
-\end{SeeAlso}
-
-\end{document}
diff --git a/inst/doc/commandsRd/Zelig.url.pdf b/inst/doc/commandsRd/Zelig.url.pdf
deleted file mode 100644
index 86c0be6..0000000
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diff --git a/inst/doc/commandsRd/Zelig.url.tex b/inst/doc/commandsRd/Zelig.url.tex
deleted file mode 100644
index b8fb7f4..0000000
--- a/inst/doc/commandsRd/Zelig.url.tex
+++ /dev/null
@@ -1,7 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt Zelig.url}: Table of links for Zelig}\label{ss:Zelig.url}
-\keyword{datasets}{Zelig.url}
-\begin{Description}\relax
-Table of linds for \code{help.zelig} for the core Zelig package.
-\end{Description}
-
-\end{document}
diff --git a/inst/doc/commandsRd/approval.pdf b/inst/doc/commandsRd/approval.pdf
deleted file mode 100644
index dfbae6e..0000000
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diff --git a/inst/doc/commandsRd/approval.tex b/inst/doc/commandsRd/approval.tex
deleted file mode 100644
index f0e12df..0000000
--- a/inst/doc/commandsRd/approval.tex
+++ /dev/null
@@ -1,21 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt approval}: U.S. Presidential Approval Data}\label{ss:approval}
-\keyword{datasets}{approval}
-\begin{Description}\relax
-Monthy public opinion data for 2001-2006.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}data(approval)\end{verbatim}
-\end{Usage}
-\begin{Format}\relax
-A table containing 8 variables ("month", "year", "approve",
-"disapprove", "unsure", "sept.oct.2001", "iraq.war", and "avg.price")
-and 65 observations.
-\end{Format}
-\begin{Source}\relax
-ICPSR
-\end{Source}
-\begin{References}\relax
-Stuff here
-\end{References}
-
-\end{document}
diff --git a/inst/doc/commandsRd/bivariate.pdf b/inst/doc/commandsRd/bivariate.pdf
deleted file mode 100644
index d486bd7..0000000
Binary files a/inst/doc/commandsRd/bivariate.pdf and /dev/null differ
diff --git a/inst/doc/commandsRd/bivariate.tex b/inst/doc/commandsRd/bivariate.tex
deleted file mode 100644
index a5b0180..0000000
--- a/inst/doc/commandsRd/bivariate.tex
+++ /dev/null
@@ -1,22 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt bivariate}: Sample data for bivariate probit regression}\label{ss:bivariate}
-\keyword{datasets}{bivariate}
-\begin{Description}\relax
-Sample data for the bivariate probit regression.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}data(bivariate)\end{verbatim}
-\end{Usage}
-\begin{Format}\relax
-A table containing 6 variables ("y1", "y2", "x1",
-"x2", "x3", and "x4") and 78 observations.
-\end{Format}
-\begin{Source}\relax
-This is a cleaned and relabelled version of the sanction data
-set, available in Zelig.
-\end{Source}
-\begin{References}\relax
-Martin, Lisa (1992). \emph{Coercive Cooperation: Explaining Multilateral
-Economic Sanctions}, Princeton: Princeton University Press.
-\end{References}
-
-\end{document}
diff --git a/inst/doc/commandsRd/coalition.pdf b/inst/doc/commandsRd/coalition.pdf
deleted file mode 100644
index 2a12562..0000000
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diff --git a/inst/doc/commandsRd/coalition.tex b/inst/doc/commandsRd/coalition.tex
deleted file mode 100644
index c33b60a..0000000
--- a/inst/doc/commandsRd/coalition.tex
+++ /dev/null
@@ -1,32 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt coalition}: Coalition Dissolution in Parliamentary Democracies}\label{ss:coalition}
-\keyword{datasets}{coalition}
-\begin{Description}\relax
-This data set contains survival data on government coalitions in
-parliamentary democracies (Belgium, Canada, Denmark, Finland, France,
-Iceland, Ireland, Israel, Italy, Netherlands, Norway, Portugal, Spain,
-Sweden, and the United Kingdom) for the period 1945-1987. For
-parsimony, country indicator variables are omitted in the sample data.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}data(coalition)\end{verbatim}
-\end{Usage}
-\begin{Format}\relax
-A table containing 7 variables ("duration", "ciep12", "invest",
-"fract", "polar", "numst2", "crisis") and 314 observations. For
-variable descriptions, please refer to King, Alt, Burns and Laver
-(1990).
-\end{Format}
-\begin{Source}\relax
-ICPSR
-\end{Source}
-\begin{References}\relax
-King, Gary, James E. Alt, Nancy Elizabeth Burns and Michael Laver (1990).
-``A Unified Model of Cabinet Dissolution in Parliamentary
-Democracies,'' \emph{American Journal of Political Science}, vol. 34,
-no. 3, pp. 846-870.
-
-Gary King, James E. Alt, Nancy Burns, and Michael Laver. ICPSR
-Publication Related Archive, 1115.
-\end{References}
-
-\end{document}
diff --git a/inst/doc/commandsRd/coalition2.pdf b/inst/doc/commandsRd/coalition2.pdf
deleted file mode 100644
index 69d1e07..0000000
Binary files a/inst/doc/commandsRd/coalition2.pdf and /dev/null differ
diff --git a/inst/doc/commandsRd/coalition2.tex b/inst/doc/commandsRd/coalition2.tex
deleted file mode 100644
index b3d208d..0000000
--- a/inst/doc/commandsRd/coalition2.tex
+++ /dev/null
@@ -1,31 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt coalition2}: Coalition Dissolution in Parliamentary Democracies, Modified Version}\label{ss:coalition2}
-\keyword{datasets}{coalition2}
-\begin{Description}\relax
-This data set contains survival data on government coalitions in
-parliamentary democracies (Belgium, Canada, Denmark, Finland, France,
-Iceland, Ireland, Israel, Italy, Netherlands, Norway, Portugal, Spain,
-Sweden, and the United Kingdom) for the period 1945-1987. Country indicator variables are included in the sample data.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}data(coalition2)\end{verbatim}
-\end{Usage}
-\begin{Format}\relax
-A data frame containing 8 variables ("duration", "ciep12", "invest",
-"fract", "polar", "numst2", "crisis", "country") and 314 observations. For
-variable descriptions, please refer to King, Alt, Burns and Laver
-(1990).
-\end{Format}
-\begin{Source}\relax
-ICPSR
-\end{Source}
-\begin{References}\relax
-King, Gary, James E. Alt, Nancy Elizabeth Burns and Michael Laver (1990).
-``A Unified Model of Cabinet Dissolution in Parliamentary
-Democracies,'' \emph{American Journal of Political Science}, vol. 34,
-no. 3, pp. 846-870.
-
-Gary King, James E. Alt, Nancy Burns, and Michael Laver. ICPSR
-Publication Related Archive, 1115.
-\end{References}
-
-\end{document}
diff --git a/inst/doc/commandsRd/current.packages.pdf b/inst/doc/commandsRd/current.packages.pdf
deleted file mode 100644
index eecfdb6..0000000
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diff --git a/inst/doc/commandsRd/current.packages.tex b/inst/doc/commandsRd/current.packages.tex
deleted file mode 100644
index ccdd775..0000000
--- a/inst/doc/commandsRd/current.packages.tex
+++ /dev/null
@@ -1,36 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt current.packages}: Find all packages in a dependency chain}\label{ss:current.packages}
-\keyword{file}{current.packages}
-\begin{Description}\relax
-Use \code{current.packages} to find all the packages suggested or
-required by a given package, and the currently installed version number
-for each.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}
-current.packages(package)
-\end{verbatim}
-\end{Usage}
-\begin{Arguments}
-\begin{ldescription}
-\item[\code{package}] a character string corresponding to the name of an
-installed package
-\end{ldescription}
-\end{Arguments}
-\begin{Value}
-A matrix containing the current version number of the packages
-suggested or required by \code{package}.
-\end{Value}
-\begin{Author}\relax
-Olivia Lau \textless{}\email{olau at fas.harvard.edu}\textgreater{}
-\end{Author}
-\begin{SeeAlso}\relax
-\code{packageDescription}
-\end{SeeAlso}
-\begin{Examples}
-\begin{ExampleCode}
-## Not run:
-current.packages("Zelig")
-## End(Not run)\end{ExampleCode}
-\end{Examples}
-
-\end{document}
diff --git a/inst/doc/commandsRd/dims.pdf b/inst/doc/commandsRd/dims.pdf
deleted file mode 100644
index fd5b8a1..0000000
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diff --git a/inst/doc/commandsRd/dims.tex b/inst/doc/commandsRd/dims.tex
deleted file mode 100644
index b79addb..0000000
--- a/inst/doc/commandsRd/dims.tex
+++ /dev/null
@@ -1,38 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt dims}: Return Dimensions of Vectors, Arrays, and Data Frames}\label{ss:dims}
-\keyword{file}{dims}
-\begin{Description}\relax
-Retrieve the dimensions of a vector, array, or data frame.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}
-dims(x)
-\end{verbatim}
-\end{Usage}
-\begin{Arguments}
-\begin{ldescription}
-\item[\code{x}] An R object. For example, a vector, matrix, array, or data
-frame.
-\end{ldescription}
-\end{Arguments}
-\begin{Value}
-The function \code{dims} performs exactly the same as \code{dim}, and
-additionally returns the \code{length} of vectors (treating them as
-one-dimensional arrays).
-\end{Value}
-\begin{Author}\relax
-Olivia Lau \textless{}\email{olau at fas.harvard.edu}\textgreater{}
-\end{Author}
-\begin{SeeAlso}\relax
-\code{dim}, \code{length}
-\end{SeeAlso}
-\begin{Examples}
-\begin{ExampleCode}
-a <- 1:12
-dims(a)
-
-a <- matrix(1, nrow = 4, ncol = 9)
-dims(a)
-\end{ExampleCode}
-\end{Examples}
-
-\end{document}
diff --git a/inst/doc/commandsRd/eidat.pdf b/inst/doc/commandsRd/eidat.pdf
deleted file mode 100644
index af8cd2a..0000000
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diff --git a/inst/doc/commandsRd/eidat.tex b/inst/doc/commandsRd/eidat.tex
deleted file mode 100644
index 0499e3c..0000000
--- a/inst/doc/commandsRd/eidat.tex
+++ /dev/null
@@ -1,15 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt eidat}: Simulation Data for Ecological Inference}\label{ss:eidat}
-\keyword{datasets}{eidat}
-\begin{Description}\relax
-This dataframe contains a simulated data set to illustrate the models
-for ecological inference.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}data(eidat)\end{verbatim}
-\end{Usage}
-\begin{Format}\relax
-A table containing 4 variables ("t0", "t1", "x0", "x1") and 10
-observations.
-\end{Format}
-
-\end{document}
diff --git a/inst/doc/commandsRd/free1.pdf b/inst/doc/commandsRd/free1.pdf
deleted file mode 100644
index a5c0616..0000000
Binary files a/inst/doc/commandsRd/free1.pdf and /dev/null differ
diff --git a/inst/doc/commandsRd/free1.tex b/inst/doc/commandsRd/free1.tex
deleted file mode 100644
index df55e16..0000000
--- a/inst/doc/commandsRd/free1.tex
+++ /dev/null
@@ -1,96 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt free1}: Freedom of Speech Data}\label{ss:free1}
-\keyword{datasets}{free1}
-\begin{Description}\relax
-Selection of individual-level survey data for freedom of speech.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}data(free1)\end{verbatim}
-\end{Usage}
-\begin{Details}\relax
-A table with 150 observations and 12 variables. \Itemize{
-\item[sex] 1 for men and 0 for women
-\item[age] Age of respondent in years
-\item[educ] Levels of education, coded as a numeric variable with
-\Itemize{
-\item[1] No formal education
-\item[2] Less than primary school education
-\item[3] Completed primary school
-\item[4] Completed secondary school
-\item[5] Completed high school
-\item[6] Completed college
-\item[7] Completed post-graduate degree
-}
-
-\item[country] Character strings consisting of "Oceana",
-"Eurasia", and "Eastasia", after Orwell's \emph{1984}.
-\item[y] Self assessment (see below).
-\item[v1-v6] Response to vignettes (see below).
-}
-Survey respondents were asked in almost the same language for a
-self-assessment and for an assessment of several hypothetical persons
-described by written vignettes. The self assessment (\code{self}, in
-the data set), "How free do you think [name/you] [is/are] to express
-[him-her/your]self without fear of government reprisal?" was first
-asked of the survey respondent with respect to him or herself, and
-then after each of vignette. The possible response categories are: \Itemize{
-\item[1] Completely free
-\item[2] Very free
-\item[3] Moderately free
-\item[4] Slightly free
-\item[5] Not free at all
-}
-The vignettes, ordered from most free to least free, are:
-\Itemize{
-\item[vign1] [Kay] does not like many of the government's
-policies. She frequently publishes her opinion in newspapers,
-criticizing decisions by officials and calling for change. She sees
-little reason these actions could lead to government reprisal.
-
-\item[vign2] [Michael] disagrees with many of the government's
-policies. Though he knows criticism is frowned upon, he doesn't
-believe the government would punish someone for expressing critical
-views. He makes his opinion known on most issues without regard to
-who is listening.
-
-\item[vign3] [Bob] has political views at odds with the
-government. He has heard of people occasionally being arrested for
-speaking out against the government, and government leaders
-sometimes make political speeches condemning those who criticize. He
-sometimes writes letters to newspapers about politics, but he is
-careful not to use his real name.
-
-\item[vign4] [Connie] does not like the government's stance on many
-issues. She has a friend who was arrested for being too openly
-critical of governmental leaders, and so she avoids voicing her
-opinions in public places.
-
-\item[vign5] [Vito] disagrees with many of the government's
-policies, and is very careful about whom he says this to, reserving
-his real opinions for family and close friends only. He knows
-several men who have been taken away by government officials for
-saying negative things in public.
-
-\item[vign6] [Sonny] lives in fear of being harassed for his
-political views. Everyone he knows who has spoken out against the
-government has been arrested or taken away. He never says a word
-about anything the government does, not even when he is at home
-alone with his family.
-}
-\end{Details}
-\begin{References}\relax
-\emph{WHO's World Health Survey}
-by Lydia Bendib, Somnath Chatterji, Alena Petrakova, Ritu Sadana,
-Joshua A. Salomon, Margie Schneider, Bedirhan Ustun, Maria
-Villanueva
-
-Jonathan Wand, Gary King and Olivia Lau. (2007) ``Anchors: Software for
-Anchoring Vignettes''. \emph{Journal of Statistical Software}. Forthcoming.
-copy at http://wand.stanford.edu/research/anchors-jss.pdf
-
-Gary King and Jonathan Wand. "Comparing Incomparable Survey
-Responses: New Tools for Anchoring Vignettes," Political Analysis, 15,
-1 (Winter, 2007): Pp. 46-66,
-copy at http://gking.harvard.edu/files/abs/c-abs.shtml.
-\end{References}
-
-\end{document}
diff --git a/inst/doc/commandsRd/free2.pdf b/inst/doc/commandsRd/free2.pdf
deleted file mode 100644
index 416770d..0000000
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diff --git a/inst/doc/commandsRd/free2.tex b/inst/doc/commandsRd/free2.tex
deleted file mode 100644
index 78ab75b..0000000
--- a/inst/doc/commandsRd/free2.tex
+++ /dev/null
@@ -1,96 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt free2}: Freedom of Speech Data}\label{ss:free2}
-\keyword{datasets}{free2}
-\begin{Description}\relax
-Selection of individual-level survey data for freedom of speech.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}data(free2)\end{verbatim}
-\end{Usage}
-\begin{Details}\relax
-A table with 150 observations and 12 variables. \Itemize{
-\item[sex] 1 for men and 0 for women
-\item[age] Age of respondent in years
-\item[educ] Levels of education, coded as a numeric variable with
-\Itemize{
-\item[1] No formal education
-\item[2] Less than primary school education
-\item[3] Completed primary school
-\item[4] Completed secondary school
-\item[5] Completed high school
-\item[6] Completed college
-\item[7] Completed post-graduate degree
-}
-
-\item[country] Character strings consisting of "Oceana",
-"Eurasia", and "Eastasia", after Orwell's \emph{1984}.
-\item[y] Self assessment (see below).
-\item[v1-v6] Response to vignettes (see below).
-}
-Survey respondents were asked in almost the same language for a
-self-assessment and for an assessment of several hypothetical persons
-described by written vignettes. The self assessment (\code{self}, in
-the data set), "How free do you think [name/you] [is/are] to express
-[him-her/your]self without fear of government reprisal?" was first
-asked of the survey respondent with respect to him or herself, and
-then after each of vignette. The possible response categories are: \Itemize{
-\item[1] Completely free
-\item[2] Very free
-\item[3] Moderately free
-\item[4] Slightly free
-\item[5] Not free at all
-}
-The vignettes, ordered from most free to least free, are:
-\Itemize{
-\item[vign1] [Kay] does not like many of the government's
-policies. She frequently publishes her opinion in newspapers,
-criticizing decisions by officials and calling for change. She sees
-little reason these actions could lead to government reprisal.
-
-\item[vign2] [Michael] disagrees with many of the government's
-policies. Though he knows criticism is frowned upon, he doesn't
-believe the government would punish someone for expressing critical
-views. He makes his opinion known on most issues without regard to
-who is listening.
-
-\item[vign3] [Bob] has political views at odds with the
-government. He has heard of people occasionally being arrested for
-speaking out against the government, and government leaders
-sometimes make political speeches condemning those who criticize. He
-sometimes writes letters to newspapers about politics, but he is
-careful not to use his real name.
-
-\item[vign4] [Connie] does not like the government's stance on many
-issues. She has a friend who was arrested for being too openly
-critical of governmental leaders, and so she avoids voicing her
-opinions in public places.
-
-\item[vign5] [Vito] disagrees with many of the government's
-policies, and is very careful about whom he says this to, reserving
-his real opinions for family and close friends only. He knows
-several men who have been taken away by government officials for
-saying negative things in public.
-
-\item[vign6] [Sonny] lives in fear of being harassed for his
-political views. Everyone he knows who has spoken out against the
-government has been arrested or taken away. He never says a word
-about anything the government does, not even when he is at home
-alone with his family.
-}
-\end{Details}
-\begin{References}\relax
-\emph{WHO's World Health Survey}
-by Lydia Bendib, Somnath Chatterji, Alena Petrakova, Ritu Sadana,
-Joshua A. Salomon, Margie Schneider, Bedirhan Ustun, Maria
-Villanueva
-
-Jonathan Wand, Gary King and Olivia Lau. (2007) ``Anchors: Software for
-Anchoring Vignettes''. \emph{Journal of Statistical Software}. Forthcoming.
-copy at http://wand.stanford.edu/research/anchors-jss.pdf
-
-Gary King and Jonathan Wand. "Comparing Incomparable Survey
-Responses: New Tools for Anchoring Vignettes," Political Analysis, 15,
-1 (Winter, 2007): Pp. 46-66,
-copy at http://gking.harvard.edu/files/abs/c-abs.shtml.
-\end{References}
-
-\end{document}
diff --git a/inst/doc/commandsRd/friendship.pdf b/inst/doc/commandsRd/friendship.pdf
deleted file mode 100644
index 1d05214..0000000
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diff --git a/inst/doc/commandsRd/friendship.tex b/inst/doc/commandsRd/friendship.tex
deleted file mode 100644
index a593eee..0000000
--- a/inst/doc/commandsRd/friendship.tex
+++ /dev/null
@@ -1,25 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt friendship}: Simulated Example of Schoolchildren Friendship Network}\label{ss:friendship}
-\keyword{datasets}{friendship}
-\begin{Description}\relax
-This data set contains six sociomatrices of simulated data on friendship ties among schoolchildren.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}data(friendship)\end{verbatim}
-\end{Usage}
-\begin{Format}\relax
-Each variable in the dataset is a 15 by 15 matrix representing some form of social network tie held by the fictitious children. The matrices are labeled "friends", "advice", "prestige", "authority", "perpower" and "per".
-
-The sociomatrices were combined into the friendship dataset using the format.network.data function from the netglm package by Skyler Cranmer as shown in the example.
-\end{Format}
-\begin{Source}\relax
-fictitious
-\end{Source}
-\begin{Examples}
-\begin{ExampleCode}
- ## Not run:
- friendship <- format.network.data(friends, advice, prestige, authority, perpower, per)
-
-## End(Not run)\end{ExampleCode}
-\end{Examples}
-
-\end{document}
diff --git a/inst/doc/commandsRd/grunfeld.pdf b/inst/doc/commandsRd/grunfeld.pdf
deleted file mode 100644
index 24a3edc..0000000
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diff --git a/inst/doc/commandsRd/grunfeld.tex b/inst/doc/commandsRd/grunfeld.tex
deleted file mode 100644
index bbc9687..0000000
--- a/inst/doc/commandsRd/grunfeld.tex
+++ /dev/null
@@ -1,19 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt grunfeld}: Simulation Data for model Seemingly Unrelated Regression (sur) that corresponds to method SUR of systemfit}\label{ss:grunfeld}
-\keyword{datasets}{grunfeld}
-\begin{Description}\relax
-Dataframe contains 20 annual observations from 1935 to
-1954 of 7 variables for two firms General Electric and Westinghouse.
-Columns are Year; Ige and Iw = Gross investment for GE and
-W,respectively; Fge and Fw=Market value of Firm as of
-begin of the year; Cge and Cw= Capital stock measure as of begin of
-the year.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}data(grunfeld)\end{verbatim}
-\end{Usage}
-\begin{Format}\relax
-A table containing 7 variables ("Year", "Ige", "Fge", "Cge","Iw", "Fw","Cw")
-and 20 observations.
-\end{Format}
-
-\end{document}
diff --git a/inst/doc/commandsRd/gsource.pdf b/inst/doc/commandsRd/gsource.pdf
deleted file mode 100644
index a9e5bd8..0000000
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diff --git a/inst/doc/commandsRd/gsource.tex b/inst/doc/commandsRd/gsource.tex
deleted file mode 100644
index c6a9118..0000000
--- a/inst/doc/commandsRd/gsource.tex
+++ /dev/null
@@ -1,50 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt gsource}: Read Data As a Space-Delimited Table}\label{ss:gsource}
-\keyword{file}{gsource}
-\begin{Description}\relax
-The \code{gsource} function allows you to read a space delimited table
-as a data frame. Unlike \code{scan}, you may use \code{gsource} in a
-\code{source}ed file, and unlike \code{read.table}, you may use
-\code{gsource} to include a small (or large) data set in a file that
-also contains other commands.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}
-gsource(var.names = NULL, variables)
-\end{verbatim}
-\end{Usage}
-\begin{Arguments}
-\begin{ldescription}
-\item[\code{var.names}] An optional vector of character strings representing
-the column names. By default, \code{var.names = NULL}.
-\item[\code{variables}] A single character string representing the data.
-\end{ldescription}
-\end{Arguments}
-\begin{Value}
-The output from \code{gsource} is a data frame, which you may save to
-an object in your workspace.
-\end{Value}
-\begin{Author}\relax
-Olivia Lau \textless{}\email{olau at fas.harvard.edu}\textgreater{}
-\end{Author}
-\begin{SeeAlso}\relax
-\code{read.table}, \code{scan}
-\end{SeeAlso}
-\begin{Examples}
-\begin{ExampleCode}
-## Not run:
-data <- gsource(variables = "
- 1 2 3 4 5
- 6 7 8 9 10
- 3 4 5 1 3
- 6 7 8 1 9 ")
-
-data <- gsource(var.names = "Vote Age Party", variables = "
- 0 23 Democrat
- 0 27 Democrat
- 1 45 Republican
- 1 65 Democrat ")
-## End(Not run)
-\end{ExampleCode}
-\end{Examples}
-
-\end{document}
diff --git a/inst/doc/commandsRd/help.zelig.pdf b/inst/doc/commandsRd/help.zelig.pdf
deleted file mode 100644
index 594ce6d..0000000
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diff --git a/inst/doc/commandsRd/help.zelig.tex b/inst/doc/commandsRd/help.zelig.tex
deleted file mode 100644
index fc09e8c..0000000
--- a/inst/doc/commandsRd/help.zelig.tex
+++ /dev/null
@@ -1,30 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt help.zelig}: HTML Help for Zelig Commands and Models}\label{ss:help.zelig}
-\keyword{documentation}{help.zelig}
-\begin{Description}\relax
-The \code{help.zelig} command launches html help for Zelig commands
-and supported models. The full manual is available online at
-\url{http://gking.harvard.edu/zelig}.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}
-help.zelig(...)
-\end{verbatim}
-\end{Usage}
-\begin{Arguments}
-\begin{ldescription}
-\item[\code{...}] a Zelig command or model.
-\code{help.zelig(command)} will take you to an index of Zelig
-commands and \code{help.zelig(model)} will take you to a list of
-models.
-\end{ldescription}
-\end{Arguments}
-\begin{Author}\relax
-Kosuke Imai \textless{}\email{kimai at princeton.edu}\textgreater{}; Gary King
-\textless{}\email{king at harvard.edu}\textgreater{}; Olivia Lau\textless{}\email{olau at fas.harvard.edu}\textgreater{}
-\end{Author}
-\begin{SeeAlso}\relax
-The complete document is available online at
-\url{http://gking.harvard.edu/zelig}.
-\end{SeeAlso}
-
-\end{document}
diff --git a/inst/doc/commandsRd/hoff.pdf b/inst/doc/commandsRd/hoff.pdf
deleted file mode 100644
index 5642add..0000000
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diff --git a/inst/doc/commandsRd/hoff.tex b/inst/doc/commandsRd/hoff.tex
deleted file mode 100644
index fb4f861..0000000
--- a/inst/doc/commandsRd/hoff.tex
+++ /dev/null
@@ -1,25 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt hoff}: Social Security Expenditure Data}\label{ss:hoff}
-\keyword{datasets}{hoff}
-\begin{Description}\relax
-This data set contains annual social security expenditure (as percent
-of budget lagged by two years), the
-relative frequency of mentions social justice received in the party's
-platform in each year, and whether the president is Republican or
-Democrat.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}data(hoff)\end{verbatim}
-\end{Usage}
-\begin{Format}\relax
-A table containing 5 variables ("year", "L2SocSec", "Just503D", "Just503R", "RGovDumy") and 36 observations.
-\end{Format}
-\begin{Source}\relax
-ICPSR (replication dataset s1109)
-\end{Source}
-\begin{References}\relax
-Gary King and Michael Laver. ``On Party Platforms, Mandates, and
-Government Spending,'' \emph{American Political Science Review},
-Vol. 87, No. 3 (September, 1993): pp. 744-750.
-\end{References}
-
-\end{document}
diff --git a/inst/doc/commandsRd/homerun.pdf b/inst/doc/commandsRd/homerun.pdf
deleted file mode 100644
index 62cbb8b..0000000
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diff --git a/inst/doc/commandsRd/homerun.tex b/inst/doc/commandsRd/homerun.tex
deleted file mode 100644
index 5969cdc..0000000
--- a/inst/doc/commandsRd/homerun.tex
+++ /dev/null
@@ -1,26 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt homerun}: Sample Data on Home Runs Hit By Mark McGwire and Sammy Sosa in 1998.}\label{ss:homerun}
-\keyword{datasets}{homerun}
-\begin{Description}\relax
-Game-by-game information for the 1998 season for Mark McGwire and Sammy Sosa. Data are a subset of the dataset provided in Simonoff (1998).
-\end{Description}
-\begin{Usage}
-\begin{verbatim}data(homerun)\end{verbatim}
-\end{Usage}
-\begin{Format}\relax
-A data frame containing 5 variables ("gameno", "month", "homeruns", "playerstatus", "player") and 326 observations.
-\describe{
-\item[\code{gameno}] an integer variable denoting the game number
-\item[\code{month}] a factor variable taking with levels "March" through "September" denoting the month of the game
-\item[\code{homeruns}] an integer vector denoting the number of homeruns hit in that game for that player
-\item[\code{playerstatus}] an integer vector equal to "0" if the player played in the game, and "1" if they did not.
-\item[\code{player}] an integer vector equal to "0" (McGwire) or "1" (Sosa)
-}
-\end{Format}
-\begin{Source}\relax
-\url{http://www.amstat.org}
-\end{Source}
-\begin{References}\relax
-Simonoff, Jeffrey S. 1998. ``Move Over, Roger Maris: Breaking Baseball's Most Famous Record.'' \emph{Journal of Statistics Education} 6(3). Data used are a subset of the data in the article.
-\end{References}
-
-\end{document}
diff --git a/inst/doc/commandsRd/immigration.pdf b/inst/doc/commandsRd/immigration.pdf
deleted file mode 100644
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diff --git a/inst/doc/commandsRd/immigration.tex b/inst/doc/commandsRd/immigration.tex
deleted file mode 100644
index f36eced..0000000
--- a/inst/doc/commandsRd/immigration.tex
+++ /dev/null
@@ -1,29 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt immigration}: Individual Preferences Over Immigration Policy}\label{ss:immigration}
-\aliasA{immi1}{immigration}{immi1}
-\aliasA{immi2}{immigration}{immi2}
-\aliasA{immi3}{immigration}{immi3}
-\aliasA{immi4}{immigration}{immi4}
-\aliasA{immi5}{immigration}{immi5}
-\keyword{datasets}{immigration}
-\begin{Description}\relax
-These five datasets are part of a larger set of 10 multiply
-imputed data sets describing individual preferences toward immigration
-policy. Imputation was performed via Amelia.
-\end{Description}
-\begin{Format}\relax
-Each multiply-inputed data set consists of a table with 7 variables
-("ipip", "wage1992", "prtyid",
-"ideol", "gender") and 2,485 observations. For variable descriptions,
-please refer to Scheve and
-Slaugher, 2001.
-\end{Format}
-\begin{Source}\relax
-National Election Survey
-\end{Source}
-\begin{References}\relax
-Scheve, Kenneth and Matthew Slaughter (2001). ``Labor Market Competition
-and Individual Preferences Over Immigration Policy,'' \emph{The Review of
-Economics and Statistics}, vol. 83, no. 1, pp. 133-145.
-\end{References}
-
-\end{document}
diff --git a/inst/doc/commandsRd/klein.pdf b/inst/doc/commandsRd/klein.pdf
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diff --git a/inst/doc/commandsRd/klein.tex b/inst/doc/commandsRd/klein.tex
deleted file mode 100644
index b11b298..0000000
--- a/inst/doc/commandsRd/klein.tex
+++ /dev/null
@@ -1,22 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt klein}: Simulation Data for model Two-Stage Least Square (twosls) that corresponds to method 2SLS of systemfit}\label{ss:klein}
-\keyword{datasets}{klein}
-\begin{Description}\relax
-Dataframe contains annual observations of US economy from 1920 to
-1940. The columns are, Year, C=Consumption, P=Corporate profits,
-P1=Previous year corporate profit,Wtot=Total wage, Wp=Private wage
-bill, Wg=Government wage bill,I=Investment,
-K1=Previous year capital stock,X=GNP,G=Government spending, T=Taxes,
-X1=Previous year GNP, Tm=Year-1931.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}data(klein)\end{verbatim}
-\end{Usage}
-\begin{Format}\relax
-A table containing 14 variables ("year", "C", "P", "P1","Wtot", "Wp",
-"Wg", "I", "K1","X", "G", "T", "X1", "Tm") and 21 observations.
-\end{Format}
-\begin{Source}\relax
-http://pages.stern.nyu.edu/\textasciitilde{}wgreene/Text/econometricanalysis.htm
-\end{Source}
-
-\end{document}
diff --git a/inst/doc/commandsRd/kmenta.pdf b/inst/doc/commandsRd/kmenta.pdf
deleted file mode 100644
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diff --git a/inst/doc/commandsRd/kmenta.tex b/inst/doc/commandsRd/kmenta.tex
deleted file mode 100644
index dd1c891..0000000
--- a/inst/doc/commandsRd/kmenta.tex
+++ /dev/null
@@ -1,19 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt kmenta}: Simulation Data for model Three-Stage Least Square (threesls) that corresponds to method 3SLS of systemfit}\label{ss:kmenta}
-\keyword{datasets}{kmenta}
-\begin{Description}\relax
-Dataframe contains 20 annual observations of a supply/demand model
-with 5 variables. Columns are q=Food consumption per capita,
-p=Ratio of food price to general consumer prices,
-d=Disposable income in contstant dollars,
-f=Ratio of preceding year's prices received by farmers to general consumer prices,
-a=Time index.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}data(kmenta)\end{verbatim}
-\end{Usage}
-\begin{Format}\relax
-A table containing 5 variables ("q", "p", "d", "f","a")
-and 20 observations.
-\end{Format}
-
-\end{document}
diff --git a/inst/doc/commandsRd/macro.pdf b/inst/doc/commandsRd/macro.pdf
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diff --git a/inst/doc/commandsRd/macro.tex b/inst/doc/commandsRd/macro.tex
deleted file mode 100644
index 4cedd4b..0000000
--- a/inst/doc/commandsRd/macro.tex
+++ /dev/null
@@ -1,29 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt macro}: Macroeconomic Data}\label{ss:macro}
-\keyword{datasets}{macro}
-\begin{Description}\relax
-Selected macroeconomic indicators for Austria, Belgium, Canada,
-Denmark, Finland, France, Italy, Japan, the Netherlands, Norway,
-Sweden, the United Kingdom, the United States, and West Germany for
-the period 1966-1990.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}data(macro)\end{verbatim}
-\end{Usage}
-\begin{Format}\relax
-A table containing 6 variables ("country", "year", "gdp",
-"unem", "capmob", and "trade") and 350 observations.
-\end{Format}
-\begin{Source}\relax
-ICPSR
-\end{Source}
-\begin{References}\relax
-King, Gary, Michael Tomz and Jason Wittenberg. ICPSR Publication
-Related Archive, 1225.
-
-King, Gary, Michael Tomz and Jason Wittenberg (2000).
-``Making the Most of Statistical Analyses: Improving Interpretation and
-Presentation,'' \emph{American Journal of Political Science}, vol. 44,
-pp. 341-355.
-\end{References}
-
-\end{document}
diff --git a/inst/doc/commandsRd/match.data.pdf b/inst/doc/commandsRd/match.data.pdf
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diff --git a/inst/doc/commandsRd/match.data.tex b/inst/doc/commandsRd/match.data.tex
deleted file mode 100644
index a212dca..0000000
--- a/inst/doc/commandsRd/match.data.tex
+++ /dev/null
@@ -1,44 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt match.data}: Output matched data sets}\label{ss:match.data}
-\keyword{methods}{match.data}
-\begin{Description}\relax
-The code \code{match.data} creates output data sets from the \code{matchit}
-matching algorithm.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}
-match.data <- match.data(object, group = "all")
-\end{verbatim}
-\end{Usage}
-\begin{Arguments}
-\begin{ldescription}
-\item[\code{object}] Stored output from \code{matchit}.
-\item[\code{group}] Which units to output. Selecting "all" (default) gives all
-matched units (treated and control), "treat" gives just the matched
-treated units, and "control" gives just the matched control units.
-\end{ldescription}
-\end{Arguments}
-\begin{Value}
-The \code{match.data} command generates a matched data set from
-the output of the \code{matchit} function, according to the options
-selected in the \code{group} argument. The matched data set contains
-the additional variables:
-\begin{ldescription}
-\item[\code{pscore}] The propensity score for each unit.
-\item[\code{psclass}] The subclass index for each unit (if applicable).
-\item[\code{psweights}] The weight for each unit (generated from the matching
-procedure).
-\end{ldescription}
-
-See the \code{matchit} documentation for more details on these items.
-\end{Value}
-\begin{Author}\relax
-Daniel Ho \textless{}\email{deho at fas.harvard.edu}\textgreater{}; Kosuke Imai
-\textless{}\email{kimai at princeton.edu}\textgreater{}; Gary King
-\textless{}\email{king at harvard.edu}\textgreater{}; Elizabeth Stuart\textless{}\email{stuart at stat.harvard.edu}\textgreater{}
-\end{Author}
-\begin{SeeAlso}\relax
-The complete documentation for \code{matchit} is available online at
-\url{http://gking.harvard.edu/matchit}.
-\end{SeeAlso}
-
-\end{document}
diff --git a/inst/doc/commandsRd/mexico.pdf b/inst/doc/commandsRd/mexico.pdf
deleted file mode 100644
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diff --git a/inst/doc/commandsRd/mexico.tex b/inst/doc/commandsRd/mexico.tex
deleted file mode 100644
index 3b750db..0000000
--- a/inst/doc/commandsRd/mexico.tex
+++ /dev/null
@@ -1,25 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt mexico}: Voting Data from the 1988 Mexican Presidental Election}\label{ss:mexico}
-\keyword{datasets}{mexico}
-\begin{Description}\relax
-This dataset contains voting data for the 1988 Mexican presidential
-election.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}data(mexico)\end{verbatim}
-\end{Usage}
-\begin{Format}\relax
-A table containing 33 variables and 1,359 observations.
-\end{Format}
-\begin{Source}\relax
-ICPSR
-\end{Source}
-\begin{References}\relax
-King, Gary, Michael Tomz and Jason Wittenberg (2000).
-``Making the Most of Statistical Analyses: Improving Interpretation and
-Presentation,'' \emph{American Journal of Political Science}, vol. 44,
-pp. 341-355.
-
-King, Tomz and Wittenberg. ICPSR Publication Related Archive, 1255.
-\end{References}
-
-\end{document}
diff --git a/inst/doc/commandsRd/mi.pdf b/inst/doc/commandsRd/mi.pdf
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diff --git a/inst/doc/commandsRd/mi.tex b/inst/doc/commandsRd/mi.tex
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index b31d752..0000000
--- a/inst/doc/commandsRd/mi.tex
+++ /dev/null
@@ -1,40 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt mi}: Bundle multiply imputed data sets as a list}\label{ss:mi}
-\keyword{methods}{mi}
-\begin{Description}\relax
-The code \code{mi} bundles multiply imputed data sets as a
-list for further analysis.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}
- mi(...)
-\end{verbatim}
-\end{Usage}
-\begin{Arguments}
-\begin{ldescription}
-\item[\code{...}] multiply imputed data sets, separated by commas. The
-arguments can be tagged by \code{name=data} where \code{name} is the
-element named used for the data set \code{data}.
-\end{ldescription}
-\end{Arguments}
-\begin{Value}
-The list containing each multiply imputed data set as an
-element. The class name is \code{mi}. The list can be inputted into
-\code{zelig} for statistical analysis with multiply imputed data
-sets. See \code{zelig} for details.
-\end{Value}
-\begin{Author}\relax
-Kosuke Imai \textless{}\email{kimai at princeton.edu}\textgreater{}; Gary King
-\textless{}\email{king at harvard.edu}\textgreater{}; Olivia Lau \textless{}\email{olau at fas.harvard.edu}\textgreater{}
-\end{Author}
-\begin{SeeAlso}\relax
-The full Zelig manual is available at
-\url{http://gking.harvard.edu/zelig}.
-\end{SeeAlso}
-\begin{Examples}
-\begin{ExampleCode}
- data(immi1, immi2, immi3, immi4, immi5)
- mi(immi1, immi2, immi3, immi4, immi5)
-\end{ExampleCode}
-\end{Examples}
-
-\end{document}
diff --git a/inst/doc/commandsRd/mid.pdf b/inst/doc/commandsRd/mid.pdf
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diff --git a/inst/doc/commandsRd/mid.tex b/inst/doc/commandsRd/mid.tex
deleted file mode 100644
index c73de77..0000000
--- a/inst/doc/commandsRd/mid.tex
+++ /dev/null
@@ -1,29 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt mid}: Militarized Interstate Disputes}\label{ss:mid}
-\keyword{datasets}{mid}
-\begin{Description}\relax
-A small sample from the militarized interstate disputes database,
-available at \url{http://pss.la.psu.edu/MID_DATA.HTM}.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}data(mid)\end{verbatim}
-\end{Usage}
-\begin{Format}\relax
-A table containing 6 variables ("conflict", "major", "contig",
-"power", "maxdem", "mindem", and "years") and 3,126 observations. For
-full variable descriptions, please see King and Zeng, 2001.
-\end{Format}
-\begin{Source}\relax
-Militarized Interstate Disputes database
-\end{Source}
-\begin{References}\relax
-King, Gary, and Lanche Zeng (2001). ``Explaining Rare Events in
-International Relations,'' \emph{International Organization}, vol. 55,
-no. 3, pp. 693-715.
-
-Jones, Daniel M., Stuart A. Bremer and David Singer (1996). ``Militarized
-Interstate Disputes, 1816-1992: Rationale, Coding Rules, and Empirical
-Patterns,'' \emph{Conflict Management and Peace Science}, vol. 15,
-no. 2, pp. 163-213.
-\end{References}
-
-\end{document}
diff --git a/inst/doc/commandsRd/model.end.pdf b/inst/doc/commandsRd/model.end.pdf
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diff --git a/inst/doc/commandsRd/model.end.tex b/inst/doc/commandsRd/model.end.tex
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index ba36ddb..0000000
--- a/inst/doc/commandsRd/model.end.tex
+++ /dev/null
@@ -1,43 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt model.end}: Cleaning up after optimization}\label{ss:model.end}
-\keyword{utilities}{model.end}
-\begin{Description}\relax
-The \code{model.end} function creates a list of regression output from \code{\LinkA{optim}{optim}}
-output. The list includes coefficients (from the \code{\LinkA{optim}{optim}} \code{par} output), a
-variance-covariance matrix (from the \code{\LinkA{optim}{optim}} Hessian output), and any terms, contrasts, or
-xlevels (from the model frame). Use \code{model.end} after calling \code{\LinkA{optim}{optim}}, but before
-assigning a
-class to the regression output.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}
-model.end(res, mf)
-\end{verbatim}
-\end{Usage}
-\begin{Arguments}
-\begin{ldescription}
-\item[\code{res}] the output from \code{\LinkA{optim}{optim}} or another fitting-algorithm
-\item[\code{mf}] the model frame output by \code{\LinkA{model.frame}{model.frame}}
-\end{ldescription}
-\end{Arguments}
-\begin{Value}
-A list of regression output, including:
-\begin{ldescription}
-\item[\code{coefficients}] the optimized parameters
-\item[\code{variance}] the variance-covariance matrix (the negative
-inverse of the Hessian matrix returned from the optimization
-procedure)
-\item[\code{terms}] the terms object. See \code{\LinkA{terms.object}{terms.object}}
-for more information
-\item[\code{...}] additional elements passed from \code{res}
-\end{ldescription}
-\end{Value}
-\begin{Author}\relax
-Kosuke Imai \textless{}\email{kimai at princeton.edu}\textgreater{}; Gary King
-\textless{}\email{king at harvard.edu}\textgreater{}; Olivia Lau \textless{}\email{olau at fas.harvard.edu}\textgreater{}; Ferdinand Alimadhi
-\textless{}\email{falimadhi at iq.harvard.edu}\textgreater{}
-\end{Author}
-\begin{SeeAlso}\relax
-The full Zelig manual at \url{http://gking.harvard.edu/zelig} for examples.
-\end{SeeAlso}
-
-\end{document}
diff --git a/inst/doc/commandsRd/model.frame.multiple.pdf b/inst/doc/commandsRd/model.frame.multiple.pdf
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diff --git a/inst/doc/commandsRd/model.frame.multiple.tex b/inst/doc/commandsRd/model.frame.multiple.tex
deleted file mode 100644
index 24bf3b7..0000000
--- a/inst/doc/commandsRd/model.frame.multiple.tex
+++ /dev/null
@@ -1,57 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt model.frame.multiple}: Extracting the ``environment'' of a model formula}\label{ss:model.frame.multiple}
-\keyword{utilities}{model.frame.multiple}
-\begin{Description}\relax
-Use \code{model.frame.multiple} after \code{\LinkA{parse.par}{parse.par}} to create a
-data frame of the unique variables identified in the formula (or list
-of formulas).
-\end{Description}
-\begin{Usage}
-\begin{verbatim}
-model.frame.multiple(formula, data, eqn = NULL, ...)
-\end{verbatim}
-\end{Usage}
-\begin{Arguments}
-\begin{ldescription}
-\item[\code{formula}] a list of formulas of class \code{"multiple"}, returned from \code{\LinkA{parse.par}{parse.par}}
-\item[\code{data}] a data frame containing all the variables used in \code{formula}
-\item[\code{eqn}] an optional character string or vector of character strings specifying
-the equations (specified in \code{describe.mymodel}) for which you would like to
-pull out the relevant variables.
-\item[\code{...}] additional arguments passed to
-\code{\LinkA{model.frame.default}{model.frame.default}}
-\end{ldescription}
-\end{Arguments}
-\begin{Value}
-The output is a data frame (with a terms attribute) containing all the
-unique explanatory and response variables identified in the list of
-formulas. By default, missing (\code{NA}) values are listwise deleted.
-
-If \code{as.factor} appears on the left-hand side, the response
-variables will be returned as an indicator (0/1) matrix with columns
-corresponding to the unique levels in the factor variable.
-
-If any formula contains more than one \code{tag} statement, \code{model.frame.multiple}
-will return the original variable in the data frame and use the \code{tag} information in the terms
-attribute only.
-\end{Value}
-\begin{Author}\relax
-Kosuke Imai \textless{}\email{kimai at princeton.edu}\textgreater{}; Gary King
-\textless{}\email{king at harvard.edu}\textgreater{}; Olivia Lau \textless{}\email{olau at fas.harvard.edu}\textgreater{}; Ferdinand Alimadhi
-\textless{}\email{falimadhi at iq.harvard.edu}\textgreater{}
-\end{Author}
-\begin{SeeAlso}\relax
-\code{\LinkA{model.matrix.default}{model.matrix.default}}, \code{\LinkA{parse.formula}{parse.formula}} and the full Zelig manual at
-\url{http://gking.harvard.edu/zelig}
-\end{SeeAlso}
-\begin{Examples}
-\begin{ExampleCode}
-## Not run:
-data(sanction)
-formulae <- list(import ~ coop + cost + target,
- export ~ coop + cost + target)
-fml <- parse.formula(formulae, model = "bivariate.logit")
-D <- model.frame(fml, data = sanction)
-## End(Not run)\end{ExampleCode}
-\end{Examples}
-
-\end{document}
diff --git a/inst/doc/commandsRd/model.matrix.multiple.pdf b/inst/doc/commandsRd/model.matrix.multiple.pdf
deleted file mode 100644
index 3528355..0000000
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diff --git a/inst/doc/commandsRd/model.matrix.multiple.tex b/inst/doc/commandsRd/model.matrix.multiple.tex
deleted file mode 100644
index 427bf67..0000000
--- a/inst/doc/commandsRd/model.matrix.multiple.tex
+++ /dev/null
@@ -1,84 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt model.matrix.multiple}: Design matrix for multivariate models}\label{ss:model.matrix.multiple}
-\keyword{utilities}{model.matrix.multiple}
-\begin{Description}\relax
-Use \code{model.matrix.multiple} after \code{\LinkA{parse.formula}{parse.formula}} to
-create a design matrix for multiple-equation models.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}
-model.matrix.multiple(object, data, shape = "compact", eqn = NULL, ...)
-\end{verbatim}
-\end{Usage}
-\begin{Arguments}
-\begin{ldescription}
-\item[\code{object}] the list of formulas output from \code{\LinkA{parse.formula}{parse.formula}}
-\item[\code{data}] a data frame created with \code{\LinkA{model.frame.multiple}{model.frame.multiple}}
-\item[\code{shape}] a character string specifying the shape of the outputed matrix. Available options are
-\Itemize{
-\item["compact"] (default) the output matrix will be an \eqn{n \times v}{},
-where \eqn{v}{} is the number of unique variables in all of the equations
-(including the intercept term)
-\item["array"] the output is an \eqn{n \times K \times J}{} array where \eqn{J}{} is the
-total number of equations and \eqn{K}{} is the total number of parameters
-across all the equations. If a variable is not in a certain equation,
-it is observed as a vector of 0s.
-\item["stacked"] the output will be a \eqn{2n \times K}{} matrix where \eqn{K}{} is the total number of
-parameters across all the equations.
-}
-\item[\code{eqn}] a character string or a vector of character strings identifying the equations from which to
-construct the design matrix. The defaults to \code{NULL}, which only uses the systematic
-parameters (for which \code{DepVar = TRUE} in the appropriate \code{describe.model} function)
-\item[\code{...}] additional arguments passed to \code{model.matrix.default}
-\end{ldescription}
-\end{Arguments}
-\begin{Value}
-A design matrix or array, depending on the options chosen in \code{shape}, with appropriate terms
-attributes.
-\end{Value}
-\begin{Author}\relax
-Kosuke Imai \textless{}\email{kimai at princeton.edu}\textgreater{}; Gary King
-\textless{}\email{king at harvard.edu}\textgreater{}; Olivia Lau \textless{}\email{olau at fas.harvard.edu}\textgreater{}; Ferdinand Alimadhi
-\textless{}\email{falimadhi at iq.harvard.edu}\textgreater{}
-\end{Author}
-\begin{SeeAlso}\relax
-\code{\LinkA{parse.par}{parse.par}}, \code{\LinkA{parse.formula}{parse.formula}} and the full Zelig manual at
-\url{http://gking.harvard.edu/zelig}
-\end{SeeAlso}
-\begin{Examples}
-\begin{ExampleCode}
-
-# Let's say that the name of the model is "bivariate.probit", and
-# the corresponding describe function is describe.bivariate.probit(),
-# which identifies mu1 and mu2 as systematic components, and an
-# ancillary parameter rho, which may be parameterized, but is estimated
-# as a scalar by default. Let par be the parameter vector (including
-# parameters for rho), formulae a user-specified formula, and mydata
-# the user specified data frame.
-
-# Acceptable combinations of parse.par() and model.matrix() are as follows:
-## Setting up
-## Not run:
-data(sanction)
-formulae <- cbind(import, export) ~ coop + cost + target
-fml <- parse.formula(formulae, model = "bivariate.probit")
-D <- model.frame(fml, data = sanction)
-terms <- attr(D, "terms")
-
-## Intuitive option
-Beta <- parse.par(par, terms, shape = "vector", eqn = c("mu1", "mu2"))
-X <- model.matrix(fml, data = D, shape = "stacked", eqn = c("mu1", "mu2")
-eta <- X
-
-## Memory-efficient (compact) option (default)
-Beta <- parse.par(par, terms, eqn = c("mu1", "mu2"))
-X <- model.matrix(fml, data = D, eqn = c("mu1", "mu2"))
-eta <- X
-
-## Computationally-efficient (array) option
-Beta <- parse.par(par, terms, shape = "vector", eqn = c("mu1", "mu2"))
-X <- model.matrix(fml, data = D, shape = "array", eqn = c("mu1", "mu2"))
-eta <- apply(X, 3, '
-## End(Not run)\end{ExampleCode}
-\end{Examples}
-
-\end{document}
diff --git a/inst/doc/commandsRd/network.pdf b/inst/doc/commandsRd/network.pdf
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diff --git a/inst/doc/commandsRd/network.tex b/inst/doc/commandsRd/network.tex
deleted file mode 100644
index 8970ebb..0000000
--- a/inst/doc/commandsRd/network.tex
+++ /dev/null
@@ -1,43 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt network}: Format matricies into a data frame for social network analysis}\label{ss:network}
-\keyword{methods}{network}
-\begin{Description}\relax
-This function accepts individual matricies as its inputs,
-combining the input matricies into a single data frame which can then be
-used in the \code{data} argument for social network analysis (models
-\code{"netlm"} and \code{"netlogit"}) in Zelig.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}
-network(...)
-\end{verbatim}
-\end{Usage}
-\begin{Arguments}
-\begin{ldescription}
-\item[\code{...}] matricies representing variables, with rows and columns corresponding to
-individuals. These can be given as named arguments and should be
-given in the order the in which the user wishes them to appear in
-the output data frame.
-\end{ldescription}
-\end{Arguments}
-\begin{Value}
-The \code{network} function creates a data frame which
-contains matricies instead of vectors as its variables. Inputs to the
-function should all be square matricies and can be given as named
-arguments.
-\end{Value}
-\begin{Author}\relax
-Skyler J. Cranmer
-\end{Author}
-\begin{SeeAlso}\relax
-The full Zelig manual is available at
-\url{http://gking.harvard.edu/zelig}.
-\end{SeeAlso}
-\begin{Examples}
-\begin{ExampleCode}## Not run:
-## Let Var1, Var2, Var3, Var4, and Var5 be matrices
-friendship <- network(Var1, Var2, Var3, Var4, Var5)
-## End(Not run)
-\end{ExampleCode}
-\end{Examples}
-
-\end{document}
diff --git a/inst/doc/commandsRd/newpainters.pdf b/inst/doc/commandsRd/newpainters.pdf
deleted file mode 100644
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diff --git a/inst/doc/commandsRd/newpainters.tex b/inst/doc/commandsRd/newpainters.tex
deleted file mode 100644
index 99c46e1..0000000
--- a/inst/doc/commandsRd/newpainters.tex
+++ /dev/null
@@ -1,33 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt newpainters}: The Discretized Painter's Data of de Piles}\label{ss:newpainters}
-\keyword{datasets}{newpainters}
-\begin{Description}\relax
-The original painters data contain the subjective assessment,
-on a 0 to 20 integer scale, of 54 classical painters. The
-newpainters data discretizes the subjective assessment by
-quartiles with thresholds 25\%, 50\%, 75\%. The painters were
-assessed on four characteristics: composition, drawing,
-colour and expression. The data is due to the Eighteenth century
-art critic, de Piles.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}data(newpainters)\end{verbatim}
-\end{Usage}
-\begin{Format}\relax
-A table containing 5 variables ("Composition", "Drawing", "Colour",
-"Expression", and "School") and 54 observations.
-\end{Format}
-\begin{Source}\relax
-A. J. Weekes (1986).``A Genstat Primer''. Edward Arnold.
-
-M. Davenport and G. Studdert-Kennedy (1972). ``The statistical
-analysis of aesthetic judgement: an exploration.'' \emph{Applied
-Statistics}, vol. 21, pp. 324--333.
-
-I. T. Jolliffe (1986) ``Principal Component Analysis.'' Springer.
-\end{Source}
-\begin{References}\relax
-Venables, W. N. and Ripley, B. D. (2002) ``Modern Applied
-Statistics with S,'' Fourth edition. Springer.
-\end{References}
-
-\end{document}
diff --git a/inst/doc/commandsRd/parse.formula.pdf b/inst/doc/commandsRd/parse.formula.pdf
deleted file mode 100644
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diff --git a/inst/doc/commandsRd/parse.formula.tex b/inst/doc/commandsRd/parse.formula.tex
deleted file mode 100644
index b6f48d1..0000000
--- a/inst/doc/commandsRd/parse.formula.tex
+++ /dev/null
@@ -1,78 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt parse.formula}: Parsing user-input formulas into multiple syntax}\label{ss:parse.formula}
-\keyword{utilities}{parse.formula}
-\begin{Description}\relax
-Parse the input formula (or list of formulas) into the
-standard format described below. Since labels for this format will vary
-by model, \code{parse.formula} will evaluate a function \code{describe.model},
-where \code{model} is given as an input to \code{parse.formula}.
-
-If the \code{describe.model} function has more than one parameter for
-which \code{ExpVar = TRUE} and \code{DepVar = TRUE}, then the
-user-specified equations must have labels to match those parameters,
-else \code{parse.formula} should return an error. In addition, if the
-formula entries are not unambiguous, then \code{parse.formula} returns an error.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}
-parse.formula(formula, model, data = NULL)
-\end{verbatim}
-\end{Usage}
-\begin{Arguments}
-\begin{ldescription}
-\item[\code{formula}] either a single formula or a list of \code{formula} objects
-\item[\code{model}] a character string specifying the name of the model
-\item[\code{data}] an optional data frame for models that require a factor response variable
-\end{ldescription}
-\end{Arguments}
-\begin{Details}\relax
-Acceptable user inputs are as follows:
-
-\Tabular{lll}{
-& User Input & Output from \code{parse.formula}\\
-& & \\
-Same covariates, & cbind(y1, y2) \textasciitilde{} x1 + x2 * x3 & list(mu1 = y1 \textasciitilde{} x1 + x2 * x3,\\
-separate effects & & mu2 = y2 \textasciitilde{} x1 + x2 * x3,\\
-& & rho = \textasciitilde{} 1)\\
-& & \\
-With \code{rho} as a & list(cbind(y1, y2) \textasciitilde{} x1 + x2, & list(mu1 = y1 \textasciitilde{} x1 + x2,\\
-systematic equation & rho = \textasciitilde{} x4 + x5) & mu2 = y2 \textasciitilde{} x1 + x2,\\
-& & rho = \textasciitilde{} x4 + x5)\\
-& & \\
-With constraints & list(mu1 = y1 \textasciitilde{} x1 + tag(x2, "x2"), & list(mu1 = y1 \textasciitilde{} x1 + tag(x2, "x2"),\\
-(same variable) & mu2 = y2 \textasciitilde{} x3 + tag(x2, "x2")) & mu2 = y2 \textasciitilde{} x3 + tag(x2, "x2"),\\
-& & rho = \textasciitilde{} 1)\\
-& & \\
-With constraints & list(mu1 = y1 \textasciitilde{} x1 + tag(x2, "z1"), & list(mu1 = y1 \textasciitilde{} x1 + tag(x2, "z1"),\\
-(different variables) & mu2 = y2 \textasciitilde{} x3 + tag(x4, "z1")) & mu2 = y2 \textasciitilde{} x3 + tag(x4, "z1"),\\
-& & rho = \textasciitilde{} 1)\\
-}
-\end{Details}
-\begin{Value}
-The output is a list of formula objects with class
-\code{c("multiple", "list")}. Let's say that the name of the model is
-\code{"bivariate.probit"}, and the corresponding describe function is
-\code{describe.bivariate.probit}, which identifies \code{mu1} and
-\code{mu2} as systematic components, and an ancillary parameter \code{rho}, which
-may be parameterized, but is estimated as a scalar by default.
-\end{Value}
-\begin{Author}\relax
-Kosuke Imai \textless{}\email{kimai at princeton.edu}\textgreater{}; Gary King
-\textless{}\email{king at harvard.edu}\textgreater{}; Olivia Lau \textless{}\email{olau at fas.harvard.edu}\textgreater{}; Ferdinand Alimadhi
-\textless{}\email{falimadhi at iq.harvard.edu}\textgreater{}
-\end{Author}
-\begin{SeeAlso}\relax
-\code{\LinkA{parse.par}{parse.par}}, \code{\LinkA{model.frame.multiple}{model.frame.multiple}},
-\code{\LinkA{model.matrix.multiple}{model.matrix.multiple}}, and the full Zelig manual at
-\url{http://gking.harvard.edu/zelig}.
-\end{SeeAlso}
-\begin{Examples}
-\begin{ExampleCode}
-## Not run:
-data(sanction)
-formulae <- list(cbind(import, export) ~ coop + cost + target)
-fml <- parse.formula(formulae, model = "bivariate.probit")
-D <- model.frame(fml, data = sanction)
-## End(Not run)\end{ExampleCode}
-\end{Examples}
-
-\end{document}
diff --git a/inst/doc/commandsRd/parse.par.pdf b/inst/doc/commandsRd/parse.par.pdf
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diff --git a/inst/doc/commandsRd/parse.par.tex b/inst/doc/commandsRd/parse.par.tex
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--- a/inst/doc/commandsRd/parse.par.tex
+++ /dev/null
@@ -1,83 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt parse.par}: Select and reshape parameter vectors}\label{ss:parse.par}
-\keyword{utilities}{parse.par}
-\begin{Description}\relax
-The \code{parse.par} function reshapes parameter vectors for
-comfortability with the output matrix from \code{\LinkA{model.matrix.multiple}{model.matrix.multiple}}.
-Use \code{parse.par} to identify sets of parameters; for example, within
-optimization functions that require vector input, or within \code{qi}
-functions that take matrix input of all parameters as a lump.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}
-parse.par(par, terms, shape = "matrix", eqn = NULL)
-\end{verbatim}
-\end{Usage}
-\begin{Arguments}
-\begin{ldescription}
-\item[\code{par}] the vector (or matrix) of parameters
-\item[\code{terms}] the terms from either \code{\LinkA{model.frame.multiple}{model.frame.multiple}} or
-\code{\LinkA{model.matrix.multiple}{model.matrix.multiple}}
-\item[\code{shape}] a character string (either \code{"matrix"} or \code{"vector"})
-that identifies the type of output structure
-\item[\code{eqn}] a character string (or strings) that identify the
-parameters that you would like to subset from the larger \code{par}
-structure
-\end{ldescription}
-\end{Arguments}
-\begin{Value}
-A matrix or vector of the sub-setted (and reshaped) parameters for the specified
-parameters given in \code{"eqn"}. By default, \code{eqn = NULL}, such that all systematic
-components are selected. (Systematic components have \code{ExpVar = TRUE} in the appropriate
-\code{describe.model} function.)
-
-If an ancillary parameter (for which \code{ExpVar = FALSE} in
-\code{describe.model}) is specified in \code{eqn}, it is
-always returned as a vector (ignoring \code{shape}). (Ancillary
-parameters are all parameters that have intercept only formulas.)
-\end{Value}
-\begin{Author}\relax
-Kosuke Imai \textless{}\email{kimai at princeton.edu}\textgreater{}; Gary King
-\textless{}\email{king at harvard.edu}\textgreater{}; Olivia Lau \textless{}\email{olau at fas.harvard.edu}\textgreater{}; Ferdinand Alimadhi
-\textless{}\email{falimadhi at iq.harvard.edu}\textgreater{}
-\end{Author}
-\begin{SeeAlso}\relax
-\code{\LinkA{model.matrix.multiple}{model.matrix.multiple}}, \code{\LinkA{parse.formula}{parse.formula}} and the full Zelig manual at
-\url{http://gking.harvard.edu/zelig}
-\end{SeeAlso}
-\begin{Examples}
-\begin{ExampleCode}
-# Let's say that the name of the model is "bivariate.probit", and
-# the corresponding describe function is describe.bivariate.probit(),
-# which identifies mu1 and mu2 as systematic components, and an
-# ancillary parameter rho, which may be parameterized, but is estimated
-# as a scalar by default. Let par be the parameter vector (including
-# parameters for rho), formulae a user-specified formula, and mydata
-# the user specified data frame.
-
-# Acceptable combinations of parse.par() and model.matrix() are as follows:
-## Setting up
-## Not run:
-data(sanction)
-formulae <- cbind(import, export) ~ coop + cost + target
-fml <- parse.formula(formulae, model = "bivariate.probit")
-D <- model.frame(fml, data = sanction)
-terms <- attr(D, "terms")
-
-## Intuitive option
-Beta <- parse.par(par, terms, shape = "vector", eqn = c("mu1", "mu2"))
-X <- model.matrix(fml, data = D, shape = "stacked", eqn = c("mu1", "mu2")
-eta <- X
-
-## Memory-efficient (compact) option (default)
-Beta <- parse.par(par, terms, eqn = c("mu1", "mu2"))
-X <- model.matrix(fml, data = D, eqn = c("mu1", "mu2"))
-eta <- X
-
-## Computationally-efficient (array) option
-Beta <- parse.par(par, terms, shape = "vector", eqn = c("mu1", "mu2"))
-X <- model.matrix(fml, data = D, shape = "array", eqn = c("mu1", "mu2"))
-eta <- apply(X, 3, '
-## End(Not run)\end{ExampleCode}
-\end{Examples}
-
-\end{document}
diff --git a/inst/doc/commandsRd/plot.ci.pdf b/inst/doc/commandsRd/plot.ci.pdf
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diff --git a/inst/doc/commandsRd/plot.ci.tex b/inst/doc/commandsRd/plot.ci.tex
deleted file mode 100644
index 899b823..0000000
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+++ /dev/null
@@ -1,69 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt plot.ci}: Plotting Vertical confidence Intervals}\label{ss:plot.ci}
-\keyword{hplot}{plot.ci}
-\begin{Description}\relax
-The \code{plot.ci} command generates vertical
-confidence intervals for linear or generalized linear univariate
-response models.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}
-plot.ci(x, CI = 95, qi = "ev", main = "", ylab = NULL, xlab = NULL,
- xlim = NULL, ylim = NULL, col = c("red", "blue"), ...)
-\end{verbatim}
-\end{Usage}
-\begin{Arguments}
-\begin{ldescription}
-\item[\code{x}] stored output from \code{sim}. The \code{x\$x} and optional
-\code{x\$x1} values used to generate the \code{sim} output object must
-have more than one observation.
-\item[\code{CI}] the selected confidence interval. Defaults to 95
-percent.
-\item[\code{qi}] the selected quantity of interest. Defaults to
-expected values.
-\item[\code{main}] a title for the plot.
-\item[\code{ylab}] label for the y-axis.
-\item[\code{xlab}] label for the x-axis.
-\item[\code{xlim}] limits on the x-axis.
-\item[\code{ylim}] limits on the y-axis.
-\item[\code{col}] a vector of at most two colors for plotting the
-expected value given by \code{x} and the alternative set of expected
-values given by \code{x1} in \code{sim}. If the quantity of
-interest selected is not the expected value, or \code{x1 = NULL},
-only the first color will be used.
-\item[\code{...}] Additional parameters passed to \code{plot}.
-\end{ldescription}
-\end{Arguments}
-\begin{Value}
-For all univariate response models, \code{plot.ci()} returns vertical
-confidence intervals over a specified range of one explanatory
-variable. You may save this plot using the commands described in the
-Zelig manual (\url{http://gking.harvard.edu/zelig}).
-\end{Value}
-\begin{Author}\relax
-Kosuke Imai \textless{}\email{kimai at princeton.edu}\textgreater{}; Gary King
-\textless{}\email{king at harvard.edu}\textgreater{}; Olivia Lau \textless{}\email{olau at fas.harvard.edu}\textgreater{}
-\end{Author}
-\begin{SeeAlso}\relax
-The full Zelig manual is available at
-\url{http://gking.harvard.edu/zelig}, and users may also wish to see
-\code{plot}, \code{lines}.
-\end{SeeAlso}
-\begin{Examples}
-\begin{ExampleCode}
-data(turnout)
-z.out <- zelig(vote ~ race + educate + age + I(age^2) + income,
- model = "logit", data = turnout)
-age.range <- 18:95
-x.low <- setx(z.out, educate = 12, age = age.range)
-x.high <- setx(z.out, educate = 16, age = age.range)
-s.out <- sim(z.out, x = x.low, x1 = x.high)
-plot.ci(s.out, xlab = "Age in Years",
- ylab = "Predicted Probability of Voting",
- main = "Effect of Education and Age on Voting Behavior")
-legend(45, 0.52, legend = c("College Education (16 years)",
- "High School Education (12 years)"), col = c("blue","red"),
- lty = c("solid"))
-\end{ExampleCode}
-\end{Examples}
-
-\end{document}
diff --git a/inst/doc/commandsRd/plot.surv.pdf b/inst/doc/commandsRd/plot.surv.pdf
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diff --git a/inst/doc/commandsRd/plot.surv.tex b/inst/doc/commandsRd/plot.surv.tex
deleted file mode 100644
index e8c7b82..0000000
--- a/inst/doc/commandsRd/plot.surv.tex
+++ /dev/null
@@ -1,58 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt plot.surv}: Plotting Confidence Intervals for Survival Curves}\label{ss:plot.surv}
-\keyword{hplot}{plot.surv}
-\begin{Description}\relax
-The \code{plot.surv} command generates confidence intervals for Kaplan-Meier survival curves
-\end{Description}
-\begin{Usage}
-\begin{verbatim}
- plot.surv(x, duration, censor, type = "line", plotcensor=TRUE,
- plottimes = FALSE, int = c(0.025,0.975), ...)
-\end{verbatim}
-\end{Usage}
-\begin{Arguments}
-\begin{ldescription}
-\item[\code{x}] output from \code{sim} stored as a list. Each element of the list is the \code{sim} output for a particular survival curve.
-\item[\code{duration}] the duration variable (e.g. lifetime, survival, etc.).
-\item[\code{censor}] the censored data
-\item[\code{type}] the type of confidence interval. Defaults to \code{"line"}, which draws vertical confidence intervals at observed event times. \code{"poly"} draws confidence regions using polygons.
-\item[\code{plotcensor}] default is \code{TRUE}. Plots censoring times as a \code{rug} object.
-\item[\code{plottimes}] default is \code{FALSE}. Plots step function with indicators at observed event times.
-\item[\code{int}] vector of quantile limits for the confidence interval. Default is 95\% interval.
-\item[\code{...}] Additional parameters passed to \code{plot}.
-\end{ldescription}
-\end{Arguments}
-\begin{Value}
-For survival models, \code{plot.surv()} returns vertical
-confidence intervals or polygon survival regions for Kaplan-Meier survival curves. You may save this plot using the commands described in the
-Zelig manual (\url{http://gking.harvard.edu/zelig}).
-\end{Value}
-\begin{Author}\relax
-John A. Graves \textless{}\email{graveja0 at gmail.com}\textgreater{}
-\end{Author}
-\begin{SeeAlso}\relax
-The full Zelig manual is available at
-\url{http://gking.harvard.edu/zelig}, and users may also wish to see
-\code{plot}, \code{lines}.
-\end{SeeAlso}
-\begin{Examples}
-\begin{ExampleCode}## Not run:
-data(coalition)
-z.out1 <- zelig(Surv(duration,ciep12)~invest+numst2+crisis,
-robust=TRUE,cluster="polar",model="coxph",data=coalition)
-low <- setx(z.out1,numst2=0)
-high <- setx(z.out1,numst2=1
-# Simulate Survival Curves for Each Group
-s.out1 <- sim(z.out1,x=low)
-s.out2 <- sim(z.out1,x=high)
-
-# Organize simulated output as a list
-out <- list(s.out1,s.out2)
-
-plot.surv(x = out, duration = coalition$duration, censor=coalition$ciep12,
- type="line", plottimes=FALSE, plotcensor=FALSE,
- main="Survival", xlab="Time", ylab="Survival")
-## End(Not run)
-\end{ExampleCode}
-\end{Examples}
-
-\end{document}
diff --git a/inst/doc/commandsRd/plot.zelig.pdf b/inst/doc/commandsRd/plot.zelig.pdf
deleted file mode 100644
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diff --git a/inst/doc/commandsRd/plot.zelig.tex b/inst/doc/commandsRd/plot.zelig.tex
deleted file mode 100644
index 31e9c7e..0000000
--- a/inst/doc/commandsRd/plot.zelig.tex
+++ /dev/null
@@ -1,49 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt plot.zelig}: Graphing Quantities of Interest}\label{ss:plot.zelig}
-\aliasA{plot}{plot.zelig}{plot}
-\keyword{hplot}{plot.zelig}
-\begin{Description}\relax
-The \code{zelig} method for the generic \code{plot}
-command generates default plots for \code{\LinkA{sim}{sim}} output with
-one-observation values in \code{x} and \code{x1}.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}
-## S3 method for class 'zelig':
-plot(x, xlab = "", user.par = FALSE, ...)
-\end{verbatim}
-\end{Usage}
-\begin{Arguments}
-\begin{ldescription}
-\item[\code{x}] stored output from \code{\LinkA{sim}{sim}}. If the \code{x\$x} or
-\code{x\$x1} values stored in the object contain more than one
-observation, \code{plot.zelig} will return an error. For linear or
-generalized linear models with more than one observation in \code{x\$x}
-and optionally \code{x\$x1}, you may use \code{\LinkA{plot.ci}{plot.ci}}.
-\item[\code{xlab}] a character string for the x-axis label for all graphs.
-\item[\code{user.par}] a logical value indicating whether to use the default
-Zelig plotting parameters (\code{user.par = FALSE}) or
-user-defined parameters (\code{user.par = TRUE}), set using the
-\code{par} function prior to plotting.
-\item[\code{...}] Additional parameters passed to \code{plot.default}.
-Because \code{plot.zelig} primarily produces diagnostic plots, many
-of these parameters are hard-coded for convenience and
-presentation.
-\end{ldescription}
-\end{Arguments}
-\begin{Value}
-Depending on the class of model selected, \code{plot.zelig} will
-return an on-screen window with graphs of the various quantities of
-interest. You may save these plots using the commands described in
-the Zelig manual (available at \url{http://gking.harvard.edu/zelig}).
-\end{Value}
-\begin{Author}\relax
-Kosuke Imai \textless{}\email{kimai at princeton.edu}\textgreater{}; Gary King
-\textless{}\email{king at harvard.edu}\textgreater{}; Olivia Lau \textless{}\email{olau at fas.harvard.edu}\textgreater{}
-\end{Author}
-\begin{SeeAlso}\relax
-The full Zelig manual at
-\url{http://gking.harvard.edu/zelig} and \code{plot}, \code{lines},
-and \code{par}.
-\end{SeeAlso}
-
-\end{document}
diff --git a/inst/doc/commandsRd/put.start.pdf b/inst/doc/commandsRd/put.start.pdf
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diff --git a/inst/doc/commandsRd/put.start.tex b/inst/doc/commandsRd/put.start.tex
deleted file mode 100644
index 21a7a23..0000000
--- a/inst/doc/commandsRd/put.start.tex
+++ /dev/null
@@ -1,34 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt put.start}: Set specific starting values for certain parameters}\label{ss:put.start}
-\keyword{utilities}{put.start}
-\begin{Description}\relax
-After calling \code{\LinkA{set.start}{set.start}} to create default starting values, use \code{put.start}
-to change starting values for specific parameters or parameter sets.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}
-put.start(start.val, value, terms, eqn)
-\end{verbatim}
-\end{Usage}
-\begin{Arguments}
-\begin{ldescription}
-\item[\code{start.val}] the vector of starting values created by \code{\LinkA{set.start}{set.start}}
-\item[\code{value}] the scalar or vector of replacement starting values
-\item[\code{terms}] the terms output from \code{\LinkA{model.frame.multiple}{model.frame.multiple}}
-\item[\code{eqn}] character vector of the parameters for which you would like to replace
-the default values with \code{value}
-\end{ldescription}
-\end{Arguments}
-\begin{Value}
-A vector of starting values (of the same length as \code{start.val})
-\end{Value}
-\begin{Author}\relax
-Kosuke Imai \textless{}\email{kimai at princeton.edu}\textgreater{}; Gary King
-\textless{}\email{king at harvard.edu}\textgreater{}; Olivia Lau \textless{}\email{olau at fas.harvard.edu}\textgreater{}; Ferdinand Alimadhi
-\textless{}\email{falimadhi at iq.harvard.edu}\textgreater{}
-\end{Author}
-\begin{SeeAlso}\relax
-\code{\LinkA{set.start}{set.start}}, and the full Zelig manual at
-\url{http://gking.harvard.edu/zelig}.
-\end{SeeAlso}
-
-\end{document}
diff --git a/inst/doc/commandsRd/repl.pdf b/inst/doc/commandsRd/repl.pdf
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diff --git a/inst/doc/commandsRd/repl.tex b/inst/doc/commandsRd/repl.tex
deleted file mode 100644
index 0284a5a..0000000
--- a/inst/doc/commandsRd/repl.tex
+++ /dev/null
@@ -1,90 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt repl}: Replicating Analyses}\label{ss:repl}
-\methaliasA{repl.default}{repl}{repl.default}
-\methaliasA{repl.zelig}{repl}{repl.zelig}
-\keyword{file}{repl}
-\begin{Description}\relax
-The generic function \code{repl} command takes
-\code{\LinkA{zelig}{zelig}} or
-\code{\LinkA{sim}{sim}} output objects and replicates (literally, re-runs)
-the entire analysis. The results should be an output
-object
-identical to the original input object in the case of
-\code{\LinkA{zelig}{zelig}} output. In the case of \code{\LinkA{sim}{sim}}
-output, the replicated analyses may differ slightly due to
-stochastic randomness in the simulation procedure.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}
-repl(object, data, ...)
-## Default S3 method:
-repl(object, data = NULL, ...)
-## S3 method for class 'zelig':
-repl(object, data = NULL, prev = NULL, x = NULL, x1 = NULL,
- bootfn = NULL, ...)
-\end{verbatim}
-\end{Usage}
-\begin{Arguments}
-\begin{ldescription}
-\item[\code{object}] Stored output from either \code{\LinkA{zelig}{zelig}} or
-\code{\LinkA{sim}{sim}}.
-\item[\code{data}] You may manually input the data frame name rather
-than allowing \code{repl} to draw the data frame name from the object
-to be replicated.
-\item[\code{prev}] When replicating \code{\LinkA{sim}{sim}} output, you may
-optionally use the previously simulated parameters to calculate the
-quantities of interest rather than simulating a new set of
-parameters. For all models, this should produce identical
-quantities of interest. In addition, for if the parameters were
-bootstrapped in the original analysis, this will save a considerable
-amount of time.
-\item[\code{x}] When replicating \code{\LinkA{sim}{sim}} output, you may
-optionally use an alternative \code{\LinkA{setx}{setx}} value for the \code{x}
-input.
-\item[\code{x1}] When replicating \code{\LinkA{sim}{sim}} output, you may
-optionally use an alternative \code{\LinkA{setx}{setx}} object for the \code{x1}
-input to replicating the \code{\LinkA{sim}{sim}} object.
-\item[\code{bootfn}] When replicating \code{\LinkA{sim}{sim}} output with
-bootstrapped parameters, you should manually specify the
-\code{bootfn} if a non-default option was used.
-\item[\code{...}] Additional arguments passed to either \code{\LinkA{zelig}{zelig}} or
-\code{\LinkA{sim}{sim}}.
-\end{ldescription}
-\end{Arguments}
-\begin{Value}
-For \code{\LinkA{zelig}{zelig}} output, \code{repl} will create output that is in
-every way identical to the original input. You may check to see
-whether they are identical by using the \code{identical} command.
-
-For \code{\LinkA{sim}{sim}} output, \code{repl} output will be will be
-identical to the original object if you choose not to simulate new
-parameters, and instead choose to calculate quantities of interest
-using the previously simulated parameters (using the \code{prev}
-option. If you choose to simulate new parameters, the summary
-statistics for each quantity of interest should be identical, up to a
-random approximation error. As the number of simulations increases,
-this error decreases.
-\end{Value}
-\begin{Author}\relax
-Kosuke Imai \textless{}\email{kimai at princeton.edu}\textgreater{}; Gary King
-\textless{}\email{king at harvard.edu}\textgreater{}; Olivia Lau \textless{}\email{olau at fas.harvard.edu}\textgreater{}
-\end{Author}
-\begin{SeeAlso}\relax
-\code{\LinkA{zelig}{zelig}}, \code{\LinkA{setx}{setx}}, and
-\code{\LinkA{sim}{sim}}. In addition, the full Zelig manual may be
-accessed online at \url{http://gking.harvard.edu/zelig}.
-\end{SeeAlso}
-\begin{Examples}
-\begin{ExampleCode}
-data(turnout)
-z.out <- zelig(vote ~ race + educate, model = "logit", data = turnout[1:1000,])
-x.out <- setx(z.out)
-s.out <- sim(z.out, x = x.out)
-z.rep <- repl(z.out)
-identical(z.out$coef, z.rep$coef)
-z.alt <- repl(z.out, data = turnout[1001:2000,])
-s.rep <- repl(s.out, prev = s.out$par)
-identical(s.out$ev, s.rep$ev)
-\end{ExampleCode}
-\end{Examples}
-
-\end{document}
diff --git a/inst/doc/commandsRd/rocplot.pdf b/inst/doc/commandsRd/rocplot.pdf
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--- a/inst/doc/commandsRd/rocplot.tex
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@@ -1,86 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt rocplot}: Receiver Operator Characteristic Plots}\label{ss:rocplot}
-\aliasA{ROC}{rocplot}{ROC}
-\aliasA{roc}{rocplot}{roc}
-\aliasA{ROCplot}{rocplot}{ROCplot}
-\keyword{file}{rocplot}
-\begin{Description}\relax
-The \code{rocplot} command generates a receiver operator
-characteristic plot to compare the in-sample (default) or out-of-sample
-fit for two logit or probit regressions.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}
-rocplot(y1, y2, fitted1, fitted2, cutoff = seq(from=0, to=1, length=100),
- lty1 = "solid", lty2 = "dashed", lwd1 = par("lwd"), lwd2 = par("lwd"),
- col1 = par("col"), col2 = par("col"), main, xlab, ylab,
- plot = TRUE, ...)
-\end{verbatim}
-\end{Usage}
-\begin{Arguments}
-\begin{ldescription}
-\item[\code{y1}] Response variable for the first model.
-\item[\code{y2}] Response variable for the second model.
-\item[\code{fitted1}] Fitted values for the first model. These values
-may represent either the in-sample or out-of-sample fitted values.
-\item[\code{fitted2}] Fitted values for the second model.
-\item[\code{cutoff}] A vector of cut-off values between 0 and 1, at
-which to evaluate the proportion of 0s and 1s correctly predicted by
-the first and second model. By default, this is 100 increments
-between 0 and 1, inclusive.
-\item[\code{lty1, lty2}] The line type for the first model (\code{lty1}) and
-the second model (\code{lty2}), defaulting to solid and dashed,
-respectively.
-\item[\code{lwd1, lwd2}] The width of the line for the first model
-(\code{lwd1}) and the second model (\code{lwd2}), defaulting to 1 for both.
-\item[\code{col1, col2}] The colors of the line for the first
-model (\code{col1}) and the second model (\code{col2}), defaulting to
-black for both.
-\item[\code{main}] a title for the plot. Defaults to \samp{ROC Curve}.
-\item[\code{xlab}] a label for the x-axis. Defaults to \samp{Proportion of 1's
-Correctly Predicted}.
-\item[\code{ylab}] a label for the y-axis. Defaults to \samp{Proportion of 0's
-Correctly Predicted}.
-\item[\code{plot}] defaults to \code{TRUE}, which generates a plot to the
-selected device. If \code{FALSE}, returns a list of
-items (see below).
-\item[\code{...}] Additional parameters passed to plot, including
-\code{xlab}, \code{ylab}, and \code{main}.
-\end{ldescription}
-\end{Arguments}
-\begin{Value}
-If \code{plot = TRUE}, \code{rocplot} generates an ROC plot for
-two logit or probit models. If \code{plot = FALSE}, \code{rocplot}
-returns a list with the following elements:
-\begin{ldescription}
-\item[\code{roc1}] a matrix containing a vector of x-coordinates and
-y-coordinates corresponding to the number of ones and zeros correctly
-predicted for the first model.
-\item[\code{roc2}] a matrix containing a vector of x-coordinates and
-y-coordinates corresponding to the number of ones and zeros correctly
-predicted for the second model.
-\item[\code{area1}] the area under the first ROC curve, calculated using
-Reimann sums.
-\item[\code{area2}] the area under the second ROC curve, calculated using
-Reimann sums.
-\end{ldescription}
-\end{Value}
-\begin{Author}\relax
-Kosuke Imai \textless{}\email{kimai at princeton.edu}\textgreater{}; Gary King
-\textless{}\email{king at harvard.edu}\textgreater{}; Olivia Lau \textless{}\email{olau at fas.harvard.edu}\textgreater{}
-\end{Author}
-\begin{SeeAlso}\relax
-The full Zelig manual (available at
-\url{http://gking.harvard.edu/zelig}), \code{plot}, \code{lines}.
-\end{SeeAlso}
-\begin{Examples}
-\begin{ExampleCode}
-data(turnout)
-z.out1 <- zelig(vote ~ race + educate + age, model = "logit",
- data = turnout)
-z.out2 <- zelig(vote ~ race + educate, model = "logit",
- data = turnout)
-rocplot(z.out1$y, z.out2$y, fitted(z.out1), fitted(z.out2))
-\end{ExampleCode}
-\end{Examples}
-
-\end{document}
diff --git a/inst/doc/commandsRd/sanction.pdf b/inst/doc/commandsRd/sanction.pdf
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diff --git a/inst/doc/commandsRd/sanction.tex b/inst/doc/commandsRd/sanction.tex
deleted file mode 100644
index c2a6a7c..0000000
--- a/inst/doc/commandsRd/sanction.tex
+++ /dev/null
@@ -1,25 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt sanction}: Multilateral Economic Sanctions}\label{ss:sanction}
-\keyword{datasets}{sanction}
-\begin{Description}\relax
-Data on bilateral sanctions behavior for selected years during the
-general period 1939-1983. This data contains errors that have since
-been corrected. Please contact Lisa Martin before using this data for
-publication.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}data(sanction)\end{verbatim}
-\end{Usage}
-\begin{Format}\relax
-A table containing 8 variables ("mil", "coop", "target",
-"import", "export", "cost", "num", and "ncost") and 78 observations.
-For full variable description, see Martin, 1992.
-\end{Format}
-\begin{Source}\relax
-Martin, 1992
-\end{Source}
-\begin{References}\relax
-Martin, Lisa (1992). \emph{Coercive Cooperation: Explaining Multilateral
-Economic Sanctions}, Princeton: Princeton University Press.
-\end{References}
-
-\end{document}
diff --git a/inst/doc/commandsRd/set.start.pdf b/inst/doc/commandsRd/set.start.pdf
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-\include{zinput} \begin{document}\section{{\tt set.start}: Set starting values for all parameters}\label{ss:set.start}
-\keyword{utilities}{set.start}
-\begin{Description}\relax
-After using \code{\LinkA{parse.par}{parse.par}} and \code{\LinkA{model.matrix.multiple}{model.matrix.multiple}}, use
-\code{set.start} to set starting values for all parameters. By default, starting values are set to 0. If
-you wish to select alternative starting values for certain parameters, use \code{\LinkA{put.start}{put.start}} after
-\code{set.start}.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}
-set.start(start.val = NULL, terms)
-\end{verbatim}
-\end{Usage}
-\begin{Arguments}
-\begin{ldescription}
-\item[\code{start.val}] user-specified starting values. If \code{NULL} (default), the default
-starting values for all parameters are set to 0.
-\item[\code{terms}] the terms output from \code{\LinkA{model.frame.multiple}{model.frame.multiple}}
-\end{ldescription}
-\end{Arguments}
-\begin{Value}
-A named vector of starting values for all parameters specified in \code{terms}, defaulting to 0.
-\end{Value}
-\begin{Author}\relax
-Kosuke Imai \textless{}\email{kimai at princeton.edu}\textgreater{}; Gary King
-\textless{}\email{king at harvard.edu}\textgreater{}; Olivia Lau \textless{}\email{olau at fas.harvard.edu}\textgreater{}; Ferdinand Alimadhi
-\textless{}\email{falimadhi at iq.harvard.edu}\textgreater{}
-\end{Author}
-\begin{SeeAlso}\relax
-\code{\LinkA{put.start}{put.start}}, \code{\LinkA{parse.par}{parse.par}}, \code{\LinkA{model.frame.multiple}{model.frame.multiple}}, and the
-full Zelig manual at \url{http://gking.harvard.edu/zelig}.
-\end{SeeAlso}
-\begin{Examples}
-\begin{ExampleCode}
-## Not run:
-fml <- parse.formula(formula, model = "bivariate.probit")
-D <- model.frame(fml, data = data)
-terms <- attr(D, "terms")
-start.val <- set.start(start.val = NULL, terms)
-## End(Not run)\end{ExampleCode}
-\end{Examples}
-
-\end{document}
diff --git a/inst/doc/commandsRd/setx.pdf b/inst/doc/commandsRd/setx.pdf
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diff --git a/inst/doc/commandsRd/setx.tex b/inst/doc/commandsRd/setx.tex
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+++ /dev/null
@@ -1,116 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt setx}: Setting Explanatory Variable Values}\label{ss:setx}
-\keyword{file}{setx}
-\begin{Description}\relax
-The \code{setx} command uses the variables identified in
-the \code{formula} generated by \code{zelig} and sets the values of
-the explanatory variables to the selected values. Use \code{setx}
-after \code{zelig} and before \code{sim} to simulate quantities of
-interest.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}
-x.out <- setx(object, fn = list(numeric = mean, ordered = median,
- others = mode),
- data = NULL, cond = FALSE, ...)
-\end{verbatim}
-\end{Usage}
-\begin{Arguments}
-\begin{ldescription}
-\item[\code{object}] the saved output from \code{\LinkA{zelig}{zelig}}.
-\item[\code{fn}] a list of functions to apply to three types of variables:
-\Itemize{
-\item[numeric] \code{numeric} variables are set to their mean by
-default, but you may select any mathematical function to apply to
-numeric variables.
-\item[ordered] \code{ordered} factors are set to their meidan by
-default, and most mathematical operations will work on them. If
-you select \code{ordered = mean}, however, \code{setx} will
-default to median with a warning.
-\item[other] variables may consist of unordered factors, character
-strings, or logical variables. The \code{other} variables may
-only be set to their mode. If you wish to set one of the other
-variables to a specific value, you may do so using \code{...}
-below.
-}
-In the special case \code{fn = NULL}, \code{setx} will return all
-of the observations without applying any function to the data.
-\item[\code{data}] a new data frame used to set the values of
-explanatory variables. If \code{data = NULL} (the default), the
-data frame called in \code{zelig} is used.
-\item[\code{cond}] a logical value indicating whether unconditional
-(default) or conditional (choose \code{cond = TRUE}) prediction
-should be performed. If you choose \code{cond = TRUE}, \code{setx}
-will coerce \code{fn = NULL} and ignore the additional arguments in
-\code{...}. If \code{cond = TRUE} and \code{data = NULL},
-\code{setx} will prompt you for a data frame.
-\item[\code{...}] user-defined values of specific variables
-overwriting the default values set by the function \code{fn}. For
-example, adding \code{var1 = mean(data\$var1)} or \code{x1 = 12}
-explicitly sets the value of \code{x1} to 12. In addition, you may
-specify one explanatory variable as a range of values, creating one
-observation for every unique value in the range of values.
-\end{ldescription}
-\end{Arguments}
-\begin{Value}
-For unconditional prediction, \code{x.out} is a model matrix based
-on the specified values for the explanatory variables. For multiple
-analyses (i.e., when choosing the \code{by} option in \code{\LinkA{zelig}{zelig}},
-\code{setx} returns the selected values calculated over the entire
-data frame. If you wish to calculate values over just one subset of
-the data frame, the 5th subset for example, you may use:
-\code{x.out <- setx(z.out[[5]])}
-
-For conditional prediction, \code{x.out} includes the model matrix
-and the dependent variables. For multiple analyses (when choosing
-the \code{by} option in \code{zelig}), \code{setx} returns the
-observed explanatory variables in each subset.
-\end{Value}
-\begin{Author}\relax
-Kosuke Imai \textless{}\email{kimai at princeton.edu}\textgreater{}; Gary King
-\textless{}\email{king at harvard.edu}\textgreater{}; Olivia Lau \textless{}\email{olau at fas.harvard.edu}\textgreater{}
-\end{Author}
-\begin{SeeAlso}\relax
-The full Zelig manual may be accessed online at
-\url{http://gking.harvard.edu/zelig}.
-\end{SeeAlso}
-\begin{Examples}
-\begin{ExampleCode}
-# Unconditional prediction:
-data(turnout)
-z.out <- zelig(vote ~ race + educate, model = "logit", data = turnout)
-x.out <- setx(z.out)
-s.out <- sim(z.out, x = x.out)
-
-# Unconditional prediction with all observations:
-x.out <- setx(z.out, fn = NULL)
-s.out <- sim(z.out, x = x.out)
-
-# Unconditional prediction with out of sample data:
-z.out <- zelig(vote ~ race + educate, model = "logit",
- data = turnout[1:1000,])
-x.out <- setx(z.out, data = turnout[1001:2000,])
-s.out <- sim(z.out, x = x.out)
-
-# Using a user-defined function in fn:
-## Not run:
-quants <- function(x)
- quantile(x, 0.25)
-x.out <- setx(z.out, fn = list(numeric = quants))
-## End(Not run)
-
-# Conditional prediction:
-## Not run:
-library(MatchIt)
-data(lalonde)
-match.out <- matchit(treat ~ age + educ + black + hispan + married +
- nodegree + re74 + re75, data = lalonde)
-z.out <- zelig(re78 ~ distance, data = match.data(match.out, "control"),
- model = "ls")
-x.out <- setx(z.out, fn = NULL, data = match.data(match.out, "treat"),
- cond = TRUE)
-s.out <- sim(z.out, x = x.out)
-## End(Not run)
-\end{ExampleCode}
-\end{Examples}
-
-\end{document}
diff --git a/inst/doc/commandsRd/sim.pdf b/inst/doc/commandsRd/sim.pdf
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diff --git a/inst/doc/commandsRd/sim.tex b/inst/doc/commandsRd/sim.tex
deleted file mode 100644
index e406e3c..0000000
--- a/inst/doc/commandsRd/sim.tex
+++ /dev/null
@@ -1,133 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt sim}: Simulating Quantities of Interest}\label{ss:sim}
-\keyword{file}{sim}
-\begin{Description}\relax
-Simulate quantities of interest from the estimated model
-output from \code{zelig()} given specified values of explanatory
-variables established in \code{setx()}. For classical \emph{maximum
-likelihood} models, \code{sim()} uses asymptotic normal
-approximation to the log-likelihood. For \emph{Bayesian models},
-Zelig simulates quantities of interest from the posterior density,
-whenever possible. For \emph{robust Bayesian models}, simulations
-are drawn from the identified class of Bayesian posteriors.
-Alternatively, you may generate quantities of interest using
-bootstrapped parameters.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}
-s.out <- sim(object, x, x1 = NULL, num = c(1000, 100), prev = NULL,
- bootstrap = FALSE, bootfn = NULL, ...)
-\end{verbatim}
-\end{Usage}
-\begin{Arguments}
-\begin{ldescription}
-\item[\code{object}] the output object from \code{\LinkA{zelig}{zelig}}.
-\item[\code{x}] values of explanatory variables used for simulation,
-generated by \code{\LinkA{setx}{setx}}.
-\item[\code{x1}] optional values of explanatory variables (generated by a
-second call of \code{\LinkA{setx}{setx}}), used to simulate first
-differences and risk ratios. (Not available for conditional
-prediction.)
-\item[\code{num}] the number of simulations, i.e., posterior draws. If the
-\code{num} argument is omitted, \code{sim} draws 1,000
-simulations by if \code{bootstrap = FALSE} (the default), or 100
-simulations if \code{bootstrap = TRUE}. You may increase this
-value to improve accuracy. (Not available for conditional
-prediction.)
-\item[\code{bootstrap}] a logical value indicating if parameters
-should be generated by re-fitting the model for bootstrapped
-data, rather than from the likelihood or posterior. (Not
-available for conditional prediction.)
-\item[\code{bootfn}] a function which governs how the data is
-sampled, re-fits the model, and returns the bootstrapped model
-parameters. If \code{bootstrap = TRUE} and \code{bootfn = NULL},
-\code{\LinkA{sim}{sim}} will sample observations from the original data
-(with
-replacement) until it creates a sampled dataset with the same
-number of observations as the original data. Alternative
-bootstrap methods include sampling the residuals rather than the
-observations, weighted sampling, and parametric bootstrapping.
-(Not available for conditional prediction.)
-\item[\code{...}] additional optional arguments passed to
-\code{boot}.
-\end{ldescription}
-\end{Arguments}
-\begin{Value}
-The output stored in \code{s.out} varies by model. Use the
-\code{names} command to view the output stored in \code{s.out}.
-Common elements include:
-\begin{ldescription}
-\item[\code{x}] the \code{\LinkA{setx}{setx}} values for the explanatory variables,
-used to calculate the quantities of interest (expected values,
-predicted values, etc.).
-\item[\code{x1}] the optional \code{\LinkA{setx}{setx}} object used to simulate
-first differences, and other model-specific quantities of
-interest, such as risk-ratios.
-\item[\code{call}] the options selected for \code{\LinkA{sim}{sim}}, used to
-replicate quantities of interest.
-\item[\code{zelig.call}] the original command and options for
-\code{\LinkA{zelig}{zelig}}, used to replicate analyses.
-\item[\code{num}] the number of simulations requested.
-\item[\code{par}] the parameters (coefficients, and additional
-model-specific parameters). You may wish to use the same set of
-simulated parameters to calculate quantities of interest rather
-than simulating another set.
-\item[\code{qi\$ev}] simulations of the expected values given the
-model and \code{x}.
-\item[\code{qi\$pr}] simulations of the predicted values given by the
-fitted values.
-\item[\code{qi\$fd}] simulations of the first differences (or risk
-difference for binary models) for the given \code{x} and \code{x1}.
-The difference is calculated by subtracting the expected values
-given \code{x} from the expected values given \code{x1}. (If do not
-specify \code{x1}, you will not get first differences or risk
-ratios.)
-\item[\code{qi\$rr}] simulations of the risk ratios for binary and
-multinomial models. See specific models for details.
-\item[\code{qi\$ate.ev}] simulations of the average expected
-treatment effect for the treatment group, using conditional
-prediction. Let \eqn{t_i}{} be a binary explanatory variable defining
-the treatment (\eqn{t_i=1}{}) and control (\eqn{t_i=0}{}) groups. Then the
-average expected treatment effect for the treatment group is
-\deqn{ \frac{1}{n}\sum_{i=1}^n [ \, Y_i(t_i=1) -
-E[Y_i(t_i=0)] \mid t_i=1 \,],}{}
-where \eqn{Y_i(t_i=1)}{} is the value of the dependent variable for
-observation \eqn{i}{} in the treatment group. Variation in the
-simulations are due to uncertainty in simulating \eqn{E[Y_i(t_i=0)]}{},
-the counterfactual expected value of \eqn{Y_i}{} for observations in the
-treatment group, under the assumption that everything stays the
-same except that the treatment indicator is switched to \eqn{t_i=0}{}.
-\item[\code{qi\$ate.pr}] simulations of the average predicted
-treatment effect for the treatment group, using conditional
-prediction. Let \eqn{t_i}{} be a binary explanatory variable defining
-the treatment (\eqn{t_i=1}{}) and control (\eqn{t_i=0}{}) groups. Then the
-average predicted treatment effect for the treatment group is
-\deqn{ \frac{1}{n}\sum_{i=1}^n [ \, Y_i(t_i=1) -
-\widehat{Y_i(t_i=0)} \mid t_i=1 \,],}{}
-where \eqn{Y_i(t_i=1)}{} is the value of the dependent variable for
-observation \eqn{i}{} in the treatment group. Variation in the
-simulations are due to uncertainty in simulating
-\eqn{\widehat{Y_i(t_i=0)}}{}, the counterfactual predicted value of
-\eqn{Y_i}{} for observations in the treatment group, under the
-assumption that everything stays the same except that the
-treatment indicator is switched to \eqn{t_i=0}{}.
-
-\end{ldescription}
-
-
-In the case of censored $Y$ in the exponential, Weibull, and lognormal
-models, \code{sim} first imputes the uncensored values for $Y$ before
-calculating the ATE.
-
-You may use the \code{\$} operator to extract any of the
-above from \code{s.out}. For example, \code{s.out\$qi\$ev} extracts the
-simulated expected values.
-\end{Value}
-\begin{Author}\relax
-Kosuke Imai \textless{}\email{kimai at princeton.edu}\textgreater{}; Gary King
-\textless{}\email{king at harvard.edu}\textgreater{}; Olivia Lau \textless{}\email{olau at fas.harvard.edu}\textgreater{}
-\end{Author}
-\begin{SeeAlso}\relax
-The full Zelig at \url{http://gking.harvard.edu/zelig}, and \code{boot}.
-\end{SeeAlso}
-
-\end{document}
diff --git a/inst/doc/commandsRd/sna.ex.pdf b/inst/doc/commandsRd/sna.ex.pdf
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diff --git a/inst/doc/commandsRd/sna.ex.tex b/inst/doc/commandsRd/sna.ex.tex
deleted file mode 100644
index 2c48efe..0000000
--- a/inst/doc/commandsRd/sna.ex.tex
+++ /dev/null
@@ -1,16 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt sna.ex}: Simulated Example of Social Network Data}\label{ss:sna.ex}
-\keyword{datasets}{sna.ex}
-\begin{Description}\relax
-This data set contains five sociomatrices of simulated data social network data.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}data(sna.ex)\end{verbatim}
-\end{Usage}
-\begin{Format}\relax
-Each variable in the dataset is a 25 by 25 matrix of simulated social network data. The matrices are labeled "Var1", "Var2", "Var3", "Var4", and "Var5".
-\end{Format}
-\begin{Source}\relax
-fictitious
-\end{Source}
-
-\end{document}
diff --git a/inst/doc/commandsRd/summary.zelig.pdf b/inst/doc/commandsRd/summary.zelig.pdf
deleted file mode 100644
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diff --git a/inst/doc/commandsRd/summary.zelig.tex b/inst/doc/commandsRd/summary.zelig.tex
deleted file mode 100644
index fd2ef56..0000000
--- a/inst/doc/commandsRd/summary.zelig.tex
+++ /dev/null
@@ -1,54 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt summary.zelig}: Summary of Simulated Quantities of Interest}\label{ss:summary.zelig}
-\aliasA{summary}{summary.zelig}{summary}
-\keyword{file}{summary.zelig}
-\begin{Description}\relax
-Summarizes the object of class \code{\LinkA{zelig}{zelig}} (output
-from \code{\LinkA{sim}{sim}}) which contains simulated quantities of
-interst.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}
-## S3 method for class 'zelig':
-summary(object, subset = NULL, CI = 95, stats = c("mean", "sd"), ...)
-\end{verbatim}
-\end{Usage}
-\begin{Arguments}
-\begin{ldescription}
-\item[\code{object}] output object from \code{\LinkA{sim}{sim}} (of class
-\code{"zelig"}).
-\item[\code{subset}] takes one of three values:
-\Itemize{
-\item[NULL] (default) for more than one observation, summarizes all the
-observations at once for each quantity of interest.
-\item[a numeric vector] indicates which observations to summarize,
-and summarizes each one independently.
-\item[all] summarizes all the observations independently.
-}
-
-\item[\code{stats}] summary statistics to be calculated.
-\item[\code{CI}] a confidence interval to be calculated.
-\item[\code{...}] further arguments passed to or from other methods.
-\end{ldescription}
-\end{Arguments}
-\begin{Value}
-\begin{ldescription}
-\item[\code{sim}] number of simulations, i.e., posterior draws.
-\item[\code{x}] values of explanatory variables used for simulation.
-\item[\code{x1}] values of explanatory variables used for simulation of first
-differences etc.
-\item[\code{qi.stats}] summary of quantities of interst. Use
-\code{\LinkA{names}{names}} to view the model-specific items available in
-\code{qi.stats}.
-\end{ldescription}
-\end{Value}
-\begin{Author}\relax
-Kosuke Imai \textless{}\email{kimai at princeton.edu}\textgreater{}; Gary King
-\textless{}\email{king at harvard.edu}\textgreater{}; Olivia Lau \textless{}\email{olau at fas.harvard.edu}\textgreater{}
-\end{Author}
-\begin{SeeAlso}\relax
-\code{\LinkA{zelig}{zelig}}, \code{\LinkA{setx}{setx}}, \code{\LinkA{sim}{sim}},
-and \code{\LinkA{names}{names}}, and the full Zelig manual at
-\url{http://gking.harvard.edu/zelig}.
-\end{SeeAlso}
-
-\end{document}
diff --git a/inst/doc/commandsRd/swiss.pdf b/inst/doc/commandsRd/swiss.pdf
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diff --git a/inst/doc/commandsRd/swiss.tex b/inst/doc/commandsRd/swiss.tex
deleted file mode 100644
index b2251e7..0000000
--- a/inst/doc/commandsRd/swiss.tex
+++ /dev/null
@@ -1,41 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt swiss}: Swiss Fertility and Socioeconomic Indicators (1888) Data}\label{ss:swiss}
-\keyword{datasets}{swiss}
-\begin{Description}\relax
-Standardized fertility measure and socio-economic indicators for
-each of 47 French-speaking provinces of Switzerland at about 1888.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}data(swiss)\end{verbatim}
-\end{Usage}
-\begin{Format}\relax
-A data frame with 47 observations on 6 variables, each of which
-is in percent, i.e., in [0,100].
-
-[,1] Fertility Ig, "common standardized fertility measure"
-[,2] Agriculture
-[,3] Examination
-nation
-[,4] Education
-[,5] Catholic
-[,6] Infant.Mortality live births who live less than 1 year.
-
-All variables but 'Fert' give proportions of the population.
-\end{Format}
-\begin{Source}\relax
-Project "16P5", pages 549-551 in
-
-Mosteller, F. and Tukey, J. W. (1977) ``Data Analysis and
-Regression: A Second Course in Statistics''. Addison-Wesley,
-Reading Mass.
-
-indicating their source as "Data used by permission of Franice van
-de Walle. Office of Population Research, Princeton University,
-1976. Unpublished data assembled under NICHD contract number No
-1-HD-O-2077."
-\end{Source}
-\begin{References}\relax
-Becker, R. A., Chambers, J. M. and Wilks, A. R. (1988) ``The New S
-Language''. Wadsworth \& Brooks/Cole.
-\end{References}
-
-\end{document}
diff --git a/inst/doc/commandsRd/ternaryplot.pdf b/inst/doc/commandsRd/ternaryplot.pdf
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deleted file mode 100644
index 02e126e..0000000
--- a/inst/doc/commandsRd/ternaryplot.tex
+++ /dev/null
@@ -1,78 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt ternaryplot}: Ternary diagram}\label{ss:ternaryplot}
-\keyword{hplot}{ternaryplot}
-\begin{Description}\relax
-Visualizes compositional, 3-dimensional data in an equilateral triangle
-(from the vcd library, Version 0.1-3.3, Date 2004-04-21), using plot graphics.
-Differs from implementation in vcd (0.9-7), which uses grid graphics.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}
-ternaryplot(x, scale = 1, dimnames = NULL, dimnames.position = c("corner","edge","none"),
- dimnames.color = "black", id = NULL, id.color = "black", coordinates = FALSE,
- grid = TRUE, grid.color = "gray", labels = c("inside", "outside", "none"),
- labels.color = "darkgray", border = "black", bg = "white", pch = 19, cex = 1,
- prop.size = FALSE, col = "red", main = "ternary plot", ...)
-\end{verbatim}
-\end{Usage}
-\begin{Arguments}
-\begin{ldescription}
-\item[\code{x}] a matrix with three columns.
-\item[\code{scale}] row sums scale to be used.
-\item[\code{dimnames}] dimension labels (defaults to the column names of
-\code{x}).
-\item[\code{dimnames.position, dimnames.color}] position and color of dimension labels.
-\item[\code{id}] optional labels to be plotted below the plot
-symbols. \code{coordinates} and \code{id} are mutual exclusive.
-\item[\code{id.color}] color of these labels.
-\item[\code{coordinates}] if \code{TRUE}, the coordinates of the points are
-plotted below them. \code{coordinates} and \code{id} are mutual exclusive.
-\item[\code{grid}] if \code{TRUE}, a grid is plotted. May optionally
-be a string indicating the line type (default: \code{"dotted"}).
-\item[\code{grid.color}] grid color.
-\item[\code{labels, labels.color}] position and color of the grid labels.
-\item[\code{border}] color of the triangle border.
-\item[\code{bg}] triangle background.
-\item[\code{pch}] plotting character. Defaults to filled dots.
-\item[\code{cex}] a numerical value giving the amount by which plotting text
-and symbols should be scaled relative to the default. Ignored for
-the symbol size if \code{prop.size} is not \code{FALSE}.
-\item[\code{prop.size}] if \code{TRUE}, the symbol size is plotted
-proportional to the row sum of the three variables, i.e. represents
-the weight of the observation.
-\item[\code{col}] plotting color.
-\item[\code{main}] main title.
-\item[\code{...}] additional graphics parameters (see \code{par})
-\end{ldescription}
-\end{Arguments}
-\begin{Details}\relax
-A points' coordinates are found by computing the gravity center
-of mass points using the data entries as weights. Thus, the coordinates
-of a point P(a,b,c), \eqn{a + b + c = 1}{}, are: P(b + c/2, c * sqrt(3)/2).
-\end{Details}
-\begin{Author}\relax
-David Meyer\\
-\email{david.meyer at ci.tuwien.ac.at}
-\end{Author}
-\begin{References}\relax
-M. Friendly (2000),
-\emph{Visualizing Categorical Data}. SAS Institute, Cary, NC.
-\end{References}
-\begin{SeeAlso}\relax
-\code{\LinkA{ternarypoints}{ternarypoints}}
-\end{SeeAlso}
-\begin{Examples}
-\begin{ExampleCode}
-data(mexico)
-if (require(VGAM)) {
-z.out <- zelig(as.factor(vote88) ~ pristr + othcok + othsocok,
- model = "mlogit", data = mexico)
-x.out <- setx(z.out)
-s.out <- sim(z.out, x = x.out)
-
-ternaryplot(s.out$qi$ev, pch = ".", col = "blue",
- main = "1988 Mexican Presidential Election")
-}
-\end{ExampleCode}
-\end{Examples}
-
-\end{document}
diff --git a/inst/doc/commandsRd/ternarypoints.pdf b/inst/doc/commandsRd/ternarypoints.pdf
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diff --git a/inst/doc/commandsRd/ternarypoints.tex b/inst/doc/commandsRd/ternarypoints.tex
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--- a/inst/doc/commandsRd/ternarypoints.tex
+++ /dev/null
@@ -1,40 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt ternarypoints}: Adding Points to Ternary Diagrams}\label{ss:ternarypoints}
-\keyword{aplot}{ternarypoints}
-\begin{Description}\relax
-Use \code{ternarypoints} to add points to a ternary diagram generated
-using the \code{ternaryplot} function in the vcd library. Use
-ternary diagrams to plot expected values for multinomial choice models
-with three categories in the dependent variable.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}
-ternarypoints(object, pch = 19, col = "blue", ...)
-\end{verbatim}
-\end{Usage}
-\begin{Arguments}
-\begin{ldescription}
-\item[\code{object}] The input object must be a matrix with three
-columns.
-\item[\code{pch}] The selected type of point. By default, \code{pch =
- 19}, solid disks.
-\item[\code{col}] The color of the points. By default, \code{col =
- "blue"}.
-\item[\code{...}] Additional parameters passed to \code{points}.
-\end{ldescription}
-\end{Arguments}
-\begin{Value}
-The \code{ternarypoints} command adds points to a previously existing
-ternary diagram. Use \code{ternaryplot} in the \code{vcd} library to
-generate the main ternary diagram.
-\end{Value}
-\begin{Author}\relax
-Kosuke Imai \textless{}\email{kimai at princeton.edu}\textgreater{}; Gary King
-\textless{}\email{king at harvard.edu}\textgreater{}; Olivia Lau \textless{}\email{olau at fas.harvard.edu}\textgreater{}
-\end{Author}
-\begin{SeeAlso}\relax
-The full Zelig manual at
-\url{http://gking.harvard.edu/zelig}, \code{points}, and
-\code{\LinkA{ternaryplot}{ternaryplot}}.
-\end{SeeAlso}
-
-\end{document}
diff --git a/inst/doc/commandsRd/tobin.pdf b/inst/doc/commandsRd/tobin.pdf
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diff --git a/inst/doc/commandsRd/tobin.tex b/inst/doc/commandsRd/tobin.tex
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index 6179d38..0000000
--- a/inst/doc/commandsRd/tobin.tex
+++ /dev/null
@@ -1,24 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt tobin}: Tobin's Tobit Data}\label{ss:tobin}
-\keyword{datasets}{tobin}
-\begin{Description}\relax
-Economists fit a parametric censored data model called the
-`tobit'. These data are from Tobin's original paper.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}data(tobin)\end{verbatim}
-\end{Usage}
-\begin{Format}\relax
-A data frame with 20 observations on the following 3 variables.
-
-durable: Durable goods purchase
-
-age: Age in years
-
-quant: Liquidity ratio (x 1000)
-\end{Format}
-\begin{Source}\relax
-J. Tobin, Estimation of relationships for limited dependent
-variables, Econometrica, v26, 24-36, 1958.
-\end{Source}
-
-\end{document}
diff --git a/inst/doc/commandsRd/turnout.pdf b/inst/doc/commandsRd/turnout.pdf
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diff --git a/inst/doc/commandsRd/turnout.tex b/inst/doc/commandsRd/turnout.tex
deleted file mode 100644
index c8a6582..0000000
--- a/inst/doc/commandsRd/turnout.tex
+++ /dev/null
@@ -1,26 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt turnout}: Turnout Data Set from the National Election Survey}\label{ss:turnout}
-\keyword{datasets}{turnout}
-\begin{Description}\relax
-This data set contains individual-level turnout data. It pools several
-American National Election Surveys conducted during the 1992 presidential
-election year. Only the first 2,000 observations (from a total of 15,837
-observations) are included in the sample data.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}data(turnout)\end{verbatim}
-\end{Usage}
-\begin{Format}\relax
-A table containing 5 variables ("race", "age", "educate",
-"income", and "vote") and 2,000 observations.
-\end{Format}
-\begin{Source}\relax
-National Election Survey
-\end{Source}
-\begin{References}\relax
-King, Gary, Michael Tomz, Jason Wittenberg (2000).
-``Making the Most of Statistical Analyses: Improving Interpretation and
-Presentation,'' \emph{American Journal of Political Science}, vol. 44,
-pp.341--355.
-\end{References}
-
-\end{document}
diff --git a/inst/doc/commandsRd/user.prompt.pdf b/inst/doc/commandsRd/user.prompt.pdf
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+++ /dev/null
@@ -1,26 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt user.prompt}: Pause in demo files}\label{ss:user.prompt}
-\keyword{file}{user.prompt}
-\begin{Description}\relax
-Use \code{user.prompt} while writing demo files to force users to hit
-return before continuing.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}
-user.prompt()
-\end{verbatim}
-\end{Usage}
-\begin{Author}\relax
-Olivia Lau \textless{}\email{olau at fas.harvard.edu}\textgreater{}
-\end{Author}
-\begin{SeeAlso}\relax
-\code{readline}
-\end{SeeAlso}
-\begin{Examples}
-\begin{ExampleCode}
-## Not run:
-user.prompt()
-## End(Not run)
-\end{ExampleCode}
-\end{Examples}
-
-\end{document}
diff --git a/inst/doc/commandsRd/voteincome.pdf b/inst/doc/commandsRd/voteincome.pdf
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diff --git a/inst/doc/commandsRd/voteincome.tex b/inst/doc/commandsRd/voteincome.tex
deleted file mode 100644
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--- a/inst/doc/commandsRd/voteincome.tex
+++ /dev/null
@@ -1,28 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt voteincome}: Sample Turnout and Demographic Data from the 2000 Current Population Survey}\label{ss:voteincome}
-\keyword{datasets}{voteincome}
-\begin{Description}\relax
-This data set contains turnout and demographic data from a sample of respondents to the 2000 Current Population Survey (CPS). The states represented are South Carolina and Arkansas. The data represent only a sample and results from this example should not be used in publication.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}data(voteincome)\end{verbatim}
-\end{Usage}
-\begin{Format}\relax
-A data frame containing 7 variables ("state", "year", "vote", "income", "education", "age", "female") and 1500 observations.
-\describe{
-\item[\code{state}] a factor variable with levels equal to "AR" (Arkansas) and "SC" (South Carolina)
-\item[\code{year}] an integer vector
-\item[\code{vote}] an integer vector taking on values "1" (Voted) and "0" (Did Not Vote)
-\item[\code{income}] an integer vector ranging from "4" (Less than \$5000) to "17" (Greater than \$75000) denoting family income. See the CPS codebook for more information on variable coding
-\item[\code{education}] an integer vector ranging from "1" (Less than High School Education) to "4" (More than a College Education). See the CPS codebook for more information on variable coding
-\item[\code{age}] an integer vector ranging from "18" to "85"
-\item[\code{female}] an integer vector taking on values "1" (Female) and "0" (Male)
-}
-\end{Format}
-\begin{Source}\relax
-Census Bureau Current Population Survey
-\end{Source}
-\begin{References}\relax
-\url{http://www.census.gov/cps}
-\end{References}
-
-\end{document}
diff --git a/inst/doc/commandsRd/zeligDepStatus.pdf b/inst/doc/commandsRd/zeligDepStatus.pdf
deleted file mode 100644
index ba60379..0000000
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diff --git a/inst/doc/commandsRd/zeligDepStatus.tex b/inst/doc/commandsRd/zeligDepStatus.tex
deleted file mode 100644
index a6ca1d7..0000000
--- a/inst/doc/commandsRd/zeligDepStatus.tex
+++ /dev/null
@@ -1,64 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt zeligDepStatus}: Zelig Dependencies Packages Client Status}\label{ss:zeligDepStatus}
-\keyword{documentation}{zeligDepStatus}
-\begin{Description}\relax
-Compares Zelig-matrix of dependencies to the locally installed
-packages. Finds those packages that \pkg{Zelig} depends on and are not
-installed in local environment. Also finds those packages that are
-locally installed but with lower versions than those required in the
-dependencies matrix.
-The Zelig-matrix includes any of dependency fields in the
-\sQuote{DESCRIPTION} files, i.e. depends, imports and suggests,
-for any packages directly derived from \pkg{Zelig} and for any of the models that \pkg{Zelig} supports.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}
-zeligDepStatus(lib.loc = NULL)
-\end{verbatim}
-\end{Usage}
-\begin{Arguments}
-\begin{ldescription}
-\item[\code{lib.loc}] a character vector of directory names
-of \code{R} libraries, or NULL.
-The default value NULL corresponds to all libraries currently known. If the default is used, the loaded packages are searched before the libraries.
-\end{ldescription}
-\end{Arguments}
-\begin{Value}
-Returns a matrix of packages that are either installed locally
-with lower versions, or packages not installed but listed in the
-Zelig-matrix of dependencies. The matrix rows correspond to the packages and
-the columns contain the following fields
-\begin{ldescription}
-\item[\code{Package}] names of packages.
-\item[\code{Version}] versions locally installed
-\item[\code{Zideal}] versions required in Zelig-matrix of dependencies.
-\end{ldescription}
-\end{Value}
-\begin{Note}\relax
-If the R version in the local environment is different from the R
-version that \pkg{Zelig}
-depends on, then, it is reported with a message and no futher action is taken.
-If the installed packages have versions higher than the corresponding
-values in the Zelig-matrix, it is reported with a message.
-\end{Note}
-\begin{Author}\relax
-Ferdinand Alimadhi and Elena Villalon
-\end{Author}
-\begin{References}\relax
-King, Gary. Zelig: Everyones Statistical Software.
-\url{http://gking.harvard.edu/zelig}.
-\end{References}
-\begin{SeeAlso}\relax
-\code{\LinkA{installed.packages}{installed.packages}}
-\code{\LinkA{packageDescription}{packageDescription}}
-\code{\LinkA{zeligDepUpdate}{zeligDepUpdate}}
-\end{SeeAlso}
-\begin{Examples}
-\begin{ExampleCode}
-## find packages in all libraries currently installed
-## Not run: zstatus <- zeligDepStatus()
-## find packages only in lib.loc
-## Not run: zstatus <- zeligDepStatus(lib.loc="~/.R/mylibrary")
-\end{ExampleCode}
-\end{Examples}
-
-\end{document}
diff --git a/inst/doc/commandsRd/zeligDepUpdate.pdf b/inst/doc/commandsRd/zeligDepUpdate.pdf
deleted file mode 100644
index da2c208..0000000
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diff --git a/inst/doc/commandsRd/zeligDepUpdate.tex b/inst/doc/commandsRd/zeligDepUpdate.tex
deleted file mode 100644
index b0047dc..0000000
--- a/inst/doc/commandsRd/zeligDepUpdate.tex
+++ /dev/null
@@ -1,67 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt zeligDepUpdate}: Download Zelig Dependencies Packages}\label{ss:zeligDepUpdate}
-\keyword{documentation}{zeligDepUpdate}
-\begin{Description}\relax
-Compares the packages in Zelig-matrix of dependencies to the
-locally installed packages. Finds local packages that have lower
-versions than in the corresponding row of the Zelig-matrix.
-Also, finds packages that \pkg{Zelig} required but are not
-installed locally.
-Downloads packages that are locally installed with lower versions and
-those from the Zelig-matrix that are not installed.
-The download repository is taken from either the default
-\code{\var{repos}} argument or from the \sQuote{URL} column of
-the Zelig-matrix of dependencies.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}
-zeligDepUpdate(destdir = NULL, installWithVers = FALSE, lib.loc = NULL,
-repos = "http://cran.r-project.org")
-\end{verbatim}
-\end{Usage}
-\begin{Arguments}
-\begin{ldescription}
-\item[\code{destdir}] directory to store the compress source-codes of
-packages that are downloaded from web repositories.
-\item[\code{installWithVers}] if TRUE, will invoke the install of the
-package such that it can be referenced by package version.
-\item[\code{lib.loc}] character vector describing the location of R
-library trees to search through (and update packages therein).
-\item[\code{repos}] character vector, the base URL(s) of the repositories to
-use, i.e. the URL of the CRAN master such as
-"http://cran.r-project.org", which is the default, or its Statlib
-mirror, "http://lib.stat.cmu.edu/R/CRAN". Can be NULL to install
-from local zip files.
-\end{ldescription}
-\end{Arguments}
-\begin{Value}
-No return value.
-\end{Value}
-\begin{Note}\relax
-Installs first level dependencies packages of \pkg{Zelig} using R function
-\code{install.packages} with the variable \code{\var{dependencies}} set
-equal to TRUE. If the installed packages have versions higher than the
-corresponding entry in Zelig-matrix, they are reported with a
-message. If the R version in the local environment is different from
-the R version that \pkg{Zelig} depends on, then, it is reported with a message and no futher action is taken.
-\end{Note}
-\begin{Author}\relax
-Ferdinand Alimadhi and Elena Villalon
-\end{Author}
-\begin{References}\relax
-King, Gary. Zelig: Everyones Statistical Software.
-\url{http://gking.harvard.edu/zelig}.
-\end{References}
-\begin{SeeAlso}\relax
-\code{\LinkA{zeligDepStatus}{zeligDepStatus}}
-\code{\LinkA{install.packages}{install.packages}}
-\end{SeeAlso}
-\begin{Examples}
-\begin{ExampleCode}
-##checks all libraries curently know for packages
-## Not run: zeligDepUpdate()
-##finds packages only in lib.loc
-## Not run: zeligDepUpdate(lib.loc="~/.R/mylibrary")
-\end{ExampleCode}
-\end{Examples}
-
-\end{document}
diff --git a/inst/doc/commandsRd/zeligVDC.pdf b/inst/doc/commandsRd/zeligVDC.pdf
deleted file mode 100644
index a4f599a..0000000
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diff --git a/inst/doc/commandsRd/zeligVDC.tex b/inst/doc/commandsRd/zeligVDC.tex
deleted file mode 100644
index e614c46..0000000
--- a/inst/doc/commandsRd/zeligVDC.tex
+++ /dev/null
@@ -1,63 +0,0 @@
-\include{zinput} \begin{document}\section{{\tt zeligDescribeModelXML}: Zelig interface functions}\label{ss:zeligDescribeModelXML}
-\aliasA{zeligGetSpecial}{zeligDescribeModelXML}{zeligGetSpecial}
-\aliasA{zeligInstalledModels}{zeligDescribeModelXML}{zeligInstalledModels}
-\aliasA{zeligListModels}{zeligDescribeModelXML}{zeligListModels}
-\aliasA{zeligModelDependency}{zeligDescribeModelXML}{zeligModelDependency}
-\keyword{IO}{zeligDescribeModelXML}
-\keyword{print}{zeligDescribeModelXML}
-\begin{Description}\relax
-Zelig interface functions. Used by VDC DSB to communicate with Zelig.
-\end{Description}
-\begin{Usage}
-\begin{verbatim}
- zeligDescribeModelXML(modelName,force=FALSE,schemaVersion="1.1")
- zeligInstalledModels(inZeligOnly=TRUE,schemaVersion="1.1")
- zeligListModels(inZeligOnly=TRUE)
- zeligModelDependency(modelName,repos)
- zeligGetSpecial(modelName)
-\end{verbatim}
-\end{Usage}
-\begin{Arguments}
-\begin{ldescription}
-\item[\code{modelName}] Name of model as returned by zeligInstalledModels or zeligListModels.
-\item[\code{inZeligOnly}] Flag, include only models in official Zelig distribution
-\item[\code{repos}] URL of default repository to use
-\item[\code{schemaVersion}] version of Zelig schema
-\item[\code{force}] generate a description even if no custom description supplied
-\end{ldescription}
-\end{Arguments}
-\begin{Value}
-Use zeligInstalledModels and zeligListModels to determine what models are available in zelig
-for a particular schema level. Use zmodel2string(zeligDescribeModel()) to generate an XML
-instance describing a model. Use zeligModelDependencies to generate a list of package
-dependencies for models. Use zeligGetSpecial to get the name special function, if any,
-to apply to the outcome variables. All functions return NULL if results are
-not available for that model.
-\end{Value}
-\begin{Author}\relax
-Micah Altman
-\email{thedata-users\@lists.sourceforge.net}
-\url{http://thedata.org}
-\end{Author}
-\begin{SeeAlso}\relax
-\LinkA{zelig}{zelig}
-\end{SeeAlso}
-\begin{Examples}
-\begin{ExampleCode}## Not run:
- # show all available models
- zeligListModels(inZeligOnly=FALSE)
- # show installed models
- zeligInstalledModels()
- # show dependency for normal.bayes
- zeligModelDependency("normal.bayes","http://cran.r-project.org/")
- # description of logit
- cat(zeligDescribeModelXML("ologit"))
- # special function for factor analysis
- zeligGetSpecial("factor.mix")
-## End(Not run)
-
-
-\end{ExampleCode}
-\end{Examples}
-
-\end{document}
diff --git a/inst/doc/commandsRd/zinput.tex b/inst/doc/commandsRd/zinput.tex
deleted file mode 100644
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--- a/inst/doc/commandsRd/zinput.tex
+++ /dev/null
@@ -1,41 +0,0 @@
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<a href="http://www.olivialau.org">Olivia Lau</a>
<br /><br />
<!-- rbuild: replace 'Version:' '</b>' version -->
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diff --git a/inst/doc/ls.net.pdf b/inst/doc/ls.net.pdf
index 1e83a2a..8780a3f 100644
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diff --git a/inst/doc/ls.pdf b/inst/doc/ls.pdf
index ddaf490..56ba663 100644
Binary files a/inst/doc/ls.pdf and b/inst/doc/ls.pdf differ
diff --git a/inst/doc/makeDocs b/inst/doc/makeDocs
index 6605b71..40a83d8 100755
--- a/inst/doc/makeDocs
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@@ -170,10 +170,10 @@ cat zeligheader.html zeligmodels.html zeligfooter.html > zelig.html
#rm models.txt
## do some cleanup
-rm -f *.aux *.toc *.log *.out *.blg *.bbl
+rm -f *.aux *.toc *.out *.blg *.bbl #*.log
## clean commandsRd directory
-rm -f commandsRd/*.aux commandsRd/*.out commandsRd/*.log
+rm -f commandsRd/*.aux commandsRd/*.out commandsRd/*.log commandsRd/*.tex
## clean statis folder
rm -f static/*.aux static/*.out static/*.log static/*.tex static/Rd.sty static/zinput.*
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diff --git a/inst/doc/ologit.pdf b/inst/doc/ologit.pdf
index 0c6d9f8..f7df62f 100644
Binary files a/inst/doc/ologit.pdf and b/inst/doc/ologit.pdf differ
diff --git a/inst/doc/oprobit.Rnw b/inst/doc/oprobit.Rnw
index ba6174e..98b1c6b 100644
--- a/inst/doc/oprobit.Rnw
+++ b/inst/doc/oprobit.Rnw
@@ -205,7 +205,7 @@ below.
\item {\tt predictors}: an $n \times (J-1)$ matrix of the linear
predictors $x_i \beta_j$.
\item {\tt residuals}: an $n \times (J-1)$ matrix of the residuals.
- \itme {\tt zeta}: a vector containing the estimated class boundaries.
+ \item {\tt zeta}: a vector containing the estimated class boundaries.
\item {\tt df.residual}: the residual degrees of freedom.
\item {\tt df.total}: the total degrees of freedom.
\item {\tt rss}: the residual sum of squares.
diff --git a/inst/doc/oprobit.bayes.log b/inst/doc/oprobit.bayes.log
new file mode 100644
index 0000000..27ba2cd
--- /dev/null
+++ b/inst/doc/oprobit.bayes.log
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BT
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ET
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BT
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ET
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BT
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ET
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BT
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ET
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BT
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ET
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BT
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ET
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Q q
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0.75 w
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1 J
1 j
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BT
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ET
BT
-/F2 1 Tf 12.00 0.00 -0.00 12.00 139.87 253.44 Tm (0.30) Tj
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diff --git a/inst/doc/vigpics/coxph-ExamplePlot2.pdf b/inst/doc/vigpics/coxph-ExamplePlot2.pdf
index 34f236f..a83f3bb 100644
--- a/inst/doc/vigpics/coxph-ExamplePlot2.pdf
+++ b/inst/doc/vigpics/coxph-ExamplePlot2.pdf
@@ -2,10 +2,10 @@
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index c5efba3..01820ff 100644
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diff --git a/inst/doc/whatsnew.tex b/inst/doc/whatsnew.tex
index 5e9af1b..678ef68 100644
--- a/inst/doc/whatsnew.tex
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few days.
\begin{itemize}
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\item {3.4-7} (Oct 23, 2009): Stable release for R 2.9.2
Fixed .net models \\
-\begin{itemize}
\item {3.4-6} (May 22, 2009): Stable release for R 2.9
Added quantile regression model (quantile) \\
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+
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+
+ (./zelig.bbl)
+! pdfTeX warning (ext4): destination with the same identifier (name{page.1}) ha
+s been already used, duplicate ignored
+<to be read again>
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+ [1
+
+]
+\openout2 = `acknowledgments.aux'.
+
+ (./acknowledgments.tex) [2
+
+] (./intro.tex
+Chapter 1.
+
+Package natbib Warning: Citation `KinTomWit00' undefined on input line 41.
+
+
+Package natbib Warning: Citation `KinHonJos01' undefined on input line 57.
+
+
+Package natbib Warning: Citation `King95' undefined on input line 62.
+
+[3
+
+
+] [4]
+Overfull \hbox (25.97044pt too wide) in paragraph at lines 125--133
+[]\T1/aer/m/n/12 Please di-rect in-quiries and prob-lems about Zelig to our lis
+t-serv at []zelig at lists.gking.harvard.edu[].
+ []
+
+(./citeZelig.tex)) [5] [6
+
+] (./install.tex
+Chapter 2.
+
+Overfull \hbox (7.46567pt too wide) in paragraph at lines 46--54
+\T1/aer/m/n/12 down-load the lat-est []in-staller for Win-dows[] at [][]$\T1/ae
+tt/m/n/12 http : / / cran . us . r-[]project . org / bin / windows /
+ []
+
+[7
+
+] [8] [9] [10]
+
+LaTeX Warning: Characters dropped after `\end{verbatim}' on input line 237.
+
+[11] [12] [13]
+Overfull \hbox (1034.93843pt too wide) in paragraph at lines 416--416
+ []\T1/aett/m/n/12 % rm Zelig_XX.tar.gz zoo_XX.tar.gz sandwich_XX.tar.gz MCMCpa
+ck_XX.tar.gz coda_XX.tar.gz lattice_XX.tar.gz mvtnorm_XX.tar.gz mvtnorm_XX.tar.
+gz VGAM_XX.tar.gz sna_XX.tar.gz systemfit_XX.tar.gz nnet_XX.tar.gz gee_XX.tar.
+gz mgcv_XX.tar.gz[]
+ []
+
+
+LaTeX Warning: Reference `table.compat' on page 14 undefined on input line 455.
+
+
+) (./syntax.tex [14]
+Chapter 3.
+[15
+
+]
+LaTeX Font Info: Try loading font information for TS1+aer on input line 72.
+ (/usr/lib64/R/share/texmf/ts1aer.fd
+File: ts1aer.fd
+)
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+(Font) Font shape `TS1/cmr/m/n' tried instead on input line 72.
+LaTeX Font Info: Try loading font information for TS1+aett on input line 87.
+
+ (/usr/lib64/R/share/texmf/ts1aett.fd
+File: ts1aett.fd
+)
+LaTeX Font Info: Try loading font information for TS1+cmtt on input line 87.
+
+(/usr/share/texmf/tex/latex/base/ts1cmtt.fd
+File: ts1cmtt.fd 1999/05/25 v2.5h Standard LaTeX font definitions
+)
+LaTeX Font Info: Font shape `TS1/aett/m/n' in size <12> not available
+(Font) Font shape `TS1/cmtt/m/n' tried instead on input line 87.
+ [16]
+
+LaTeX Warning: Characters dropped after `\end{verbatim}' on input line 92.
+
+[17]
+Overfull \hbox (17.68726pt too wide) in paragraph at lines 159--161
+[]\T1/aer/m/n/12 If your dataset is in a \T1/aer/bx/n/12 tab- or space-delimite
+d .txt file\T1/aer/m/n/12 , use \T1/aett/m/n/12 read.table("mydata.txt")
+ []
+
+
+Overfull \hbox (3.71233pt too wide) in paragraph at lines 169--169
+ []\T1/aett/m/n/12 > library(foreign) # Load the fore
+ign package.
+ []
+
+
+Overfull \hbox (3.71233pt too wide) in paragraph at lines 171--171
+ []\T1/aett/m/n/12 > spss.data <- read.spss("mydata.sav", to.data.frame = TRUE)
+ # For SPSS.[]
+ []
+
+
+Overfull \hbox (3.71233pt too wide) in paragraph at lines 182--182
+ []\T1/aett/m/n/12 > library(Zelig) # Loads the Ze
+lig library.
+ []
+
+[18] [19]
+Overfull \hbox (5.18848pt too wide) in paragraph at lines 282--282
+[]\T1/aett/m/n/12 > logic <- c(TRUE, FALSE, TRUE, TRUE, TRUE) # Creates \TS1/cm
+tt/m/n/12 `\T1/aett/m/n/12 logic\TS1/cmtt/m/n/12 ' \T1/aett/m/n/12 (5 T/F value
+s).[]
+ []
+
+
+Overfull \hbox (5.1774pt too wide) in paragraph at lines 283--283
+[]\T1/aett/m/n/12 > var1 <- 10:20 # All integers be
+tween 10 and 20.[]
+ []
+
+
+Overfull \hbox (3.7234pt too wide) in paragraph at lines 300--300
+ []\T1/aett/m/n/12 > var3 <- log(var2) - 2*var1 # Create \TS1/cmtt/m/n/12
+`\T1/aett/m/n/12 var3\TS1/cmtt/m/n/12 ' \T1/aett/m/n/12 using math operations.[
+]
+ []
+
+[20]
+Overfull \hbox (5.21063pt too wide) in paragraph at lines 366--366
+[]\T1/aett/m/n/12 > var <- data$var1 # Copies \TS1/cmtt/m/n/12 `\
+T1/aett/m/n/12 var1\TS1/cmtt/m/n/12 ' \T1/aett/m/n/12 from \TS1/cmtt/m/n/12 `\T
+1/aett/m/n/12 data\TS1/cmtt/m/n/12 '\T1/aett/m/n/12 , creating \TS1/cmtt/m/n/12
+ `\T1/aett/m/n/12 var\TS1/cmtt/m/n/12 '\T1/aett/m/n/12 .[]
+ []
+
+
+LaTeX Warning: Characters dropped after `\end{verbatim}' on input line 367.
+
+[21]
+Overfull \hbox (5.21063pt too wide) in paragraph at lines 376--376
+[]\T1/aett/m/n/12 > data$new.var <- var # Generate \TS1/cmtt/m/n/12
+ `\T1/aett/m/n/12 new.var\TS1/cmtt/m/n/12 ' \T1/aett/m/n/12 in \TS1/cmtt/m/n/12
+ `\T1/aett/m/n/12 data\TS1/cmtt/m/n/12 ' \T1/aett/m/n/12 using \TS1/cmtt/m/n/12
+ `\T1/aett/m/n/12 var\TS1/cmtt/m/n/12 '\T1/aett/m/n/12 .[]
+ []
+
+
+LaTeX Warning: Characters dropped after `\end{verbatim}' on input line 383.
+
+
+Overfull \hbox (3.7234pt too wide) in paragraph at lines 402--402
+ []\T1/aett/m/n/12 > x == y # Only the 3rd \TS1/c
+mtt/m/n/12 `\T1/aett/m/n/12 x\TS1/cmtt/m/n/12 ' \T1/aett/m/n/12 exactly equals[
+]
+ []
+
+
+Overfull \hbox (9.89136pt too wide) in paragraph at lines 419--419
+ [] \T1/aett/m/n/12 [1] FALSE FALSE FALSE FALSE TRUE # than its counte
+rpart in \TS1/cmtt/m/n/12 `\T1/aett/m/n/12 y\TS1/cmtt/m/n/12 '\T1/aett/m/n/12 .
+[]
+ []
+
+
+Overfull \hbox (9.89136pt too wide) in paragraph at lines 429--429
+ []\T1/aett/m/n/12 [1] TRUE TRUE FALSE TRUE FALSE # less than their counter
+parts in \TS1/cmtt/m/n/12 `\T1/aett/m/n/12 y\TS1/cmtt/m/n/12 '\T1/aett/m/n/12 .
+[]
+ []
+
+[22]
+Overfull \hbox (3.7234pt too wide) in paragraph at lines 461--461
+ []\T1/aett/m/n/12 > v1 <- a > 3 # Creates the matrix \TS1/c
+mtt/m/n/12 `\T1/aett/m/n/12 v1\TS1/cmtt/m/n/12 ' \T1/aett/m/n/12 (T/F values).[
+]
+ []
+
+
+Overfull \hbox (3.7234pt too wide) in paragraph at lines 462--462
+ []\T1/aett/m/n/12 > v2 <- b > 3 # Creates the matrix \TS1/c
+mtt/m/n/12 `\T1/aett/m/n/12 v2\TS1/cmtt/m/n/12 ' \T1/aett/m/n/12 (T/F values).[
+]
+ []
+
+
+Overfull \hbox (3.7234pt too wide) in paragraph at lines 463--463
+ []\T1/aett/m/n/12 > v1 & v2 # Checks if the (i,j) value
+ in \TS1/cmtt/m/n/12 `\T1/aett/m/n/12 v1\TS1/cmtt/m/n/12 ' \T1/aett/m/n/12 and[
+]
+ []
+
+
+Overfull \hbox (3.7234pt too wide) in paragraph at lines 464--464
+ [] \T1/aett/m/n/12 [,1] [,2] [,3] [,4] # \TS1/cmtt/m/n/12 `\T1/ae
+tt/m/n/12 v2\TS1/cmtt/m/n/12 ' \T1/aett/m/n/12 are both TRUE. Because columns[
+]
+ []
+
+
+Overfull \hbox (9.89136pt too wide) in paragraph at lines 465--465
+ []\T1/aett/m/n/12 [1,] FALSE TRUE TRUE FALSE # 2-4 of \TS1/cmtt/m/n/12
+`\T1/aett/m/n/12 v1\TS1/cmtt/m/n/12 ' \T1/aett/m/n/12 are TRUE, and columns 1-3
+[]
+ []
+
+[23]
+Overfull \hbox (5.1774pt too wide) in paragraph at lines 501--501
+[]\T1/aett/m/n/12 > var3 <- var1 < var2 # Creates a vector of n T
+/F observations.[]
+ []
+
+
+Overfull \hbox (5.19955pt too wide) in paragraph at lines 530--530
+[]\T1/aett/m/n/12 > var1[var1 == "don\TS1/cmtt/m/n/12 '\T1/aett/m/n/12 t know"]
+ <- NA # Replaces all "don\TS1/cmtt/m/n/12 '\T1/aett/m/n/12 t know"\TS1/cmtt/
+m/n/12 '\T1/aett/m/n/12 s with NA\TS1/cmtt/m/n/12 '\T1/aett/m/n/12 s.[]
+ []
+
+[24]) (./Zcommands.tex [25]
+Chapter 4.
+<xymatrix 3x5 368> [26
+
+]
+
+Package natbib Warning: Citation `KinZen06' on page 27 undefined on input line
+51.
+
+
+Package natbib Warning: Citation `KinZen07' on page 27 undefined on input line
+52.
+
+
+Package natbib Warning: Citation `StoKinZen05' on page 27 undefined on input li
+ne 52.
+
+[27]
+Overfull \hbox (3.71233pt too wide) in paragraph at lines 92--92
+ []\T1/aett/m/n/12 > z.out <- zelig(vote ~ race + educate, model = "logit", dat
+a = turnout)[]
+ []
+
+
+Overfull \hbox (9.88028pt too wide) in paragraph at lines 96--96
+ []\T1/aett/m/n/12 > summary(s.out) # Numer
+ical summary.[]
+ []
+
+
+Overfull \hbox (9.88028pt too wide) in paragraph at lines 97--97
+ []\T1/aett/m/n/12 > plot(s.out) # Graph
+ical summary.[]
+ []
+
+
+Overfull \hbox (3.71233pt too wide) in paragraph at lines 103--103
+ []\T1/aett/m/n/12 > z.out <- zelig(vote ~ race + educate, model = "logit", dat
+a = turnout)[]
+ []
+
+
+Package natbib Warning: Citation `SchSla01' on page 28 undefined on input line
+109.
+
+[28]
+Overfull \hbox (3.71233pt too wide) in paragraph at lines 141--141
+ []\T1/aett/m/n/12 > z.out <- zelig(vote ~ race + educate, model = "logit", dat
+a = turnout)[]
+ []
+
+[29]
+Overfull \hbox (9.88028pt too wide) in paragraph at lines 224--226
+[]\T1/aett/m/n/12 x.out <- setx(z.out, fn = list(numeric = mean, ordered = medi
+an, others =
+ []
+
+
+Package natbib Warning: Citation `HoImaKin07' on page 30 undefined on input lin
+e 253.
+
+
+Package natbib Warning: Citation `KinAltBur90' on page 30 undefined on input li
+ne 256.
+
+
+Package natbib Warning: Citation `King97' on page 30 undefined on input line 26
+0.
+
+
+Package natbib Warning: Citation `AdoKinHer03' on page 30 undefined on input li
+ne 260.
+
+
+Package natbib Warning: Citation `GelKin94a' on page 30 undefined on input line
+ 265.
+
+
+Package natbib Warning: Citation `KinMurSal04' on page 30 undefined on input li
+ne 274.
+
+[30]
+Overfull \hbox (4.8902pt too wide) in paragraph at lines 292--292
+ []\T1/aett/m/n/12 > z.out <- zelig(vote ~ age + race, model = "logit", data =
+turnout)[]
+ []
+
+[31]
+Overfull \hbox (9.88028pt too wide) in paragraph at lines 374--376
+[]\T1/aett/m/n/12 s.out <- sim(z.out, x = x.out, x1 = NULL, num = c(1000, 100),
+ bootstrap =
+ []
+
+[32]
+Overfull \hbox (0.73853pt too wide) in paragraph at lines 401--412
+[]\T1/aer/m/n/12 Zelig sim-u-lates pa-ram-e-ters from clas-si-cal \T1/aer/m/it/
+12 max-i-mum like-li-hood \T1/aer/m/n/12 mod-els us-ing asymp-
+ []
+
+[33]
+
+LaTeX Warning: Reference `ls' on page 34 undefined on input line 485.
+
+
+LaTeX Warning: Reference `normal' on page 34 undefined on input line 491.
+
+
+LaTeX Warning: Reference `normal.bayes' on page 34 undefined on input line 498.
+
+
+
+LaTeX Warning: Reference `netls' on page 34 undefined on input line 503.
+
+
+LaTeX Warning: Reference `tobit' on page 34 undefined on input line 509.
+
+
+LaTeX Warning: Reference `tobit.bayes' on page 34 undefined on input line 512.
+
+
+LaTeX Warning: Reference `arima' on page 34 undefined on input line 516.
+
+[34]
+
+LaTeX Warning: Reference `factor.bayes' on page 35 undefined on input line 519.
+
+
+
+LaTeX Warning: Reference `logit' on page 35 undefined on input line 526.
+
+
+LaTeX Warning: Reference `relogit' on page 35 undefined on input line 530.
+
+
+LaTeX Warning: Reference `logit.bayes' on page 35 undefined on input line 536.
+
+
+LaTeX Warning: Reference `probit' on page 35 undefined on input line 539.
+
+
+LaTeX Warning: Reference `probit.bayes' on page 35 undefined on input line 543.
+
+
+
+LaTeX Warning: Reference `netlogit' on page 35 undefined on input line 548.
+
+
+LaTeX Warning: Reference `blogit' on page 35 undefined on input line 554.
+
+
+LaTeX Warning: Reference `bprobit' on page 35 undefined on input line 558.
+
+
+LaTeX Warning: Reference `irt1d' on page 35 undefined on input line 561.
+
+
+LaTeX Warning: Reference `irtkd' on page 35 undefined on input line 564.
+
+[35]
+
+LaTeX Warning: Reference `ologit' on page 36 undefined on input line 576.
+
+
+LaTeX Warning: Reference `oprobit' on page 36 undefined on input line 579.
+
+
+LaTeX Warning: Reference `oprobit.bayes' on page 36 undefined on input line 582
+.
+
+
+LaTeX Warning: Reference `factor.ord' on page 36 undefined on input line 586.
+
+
+LaTeX Warning: Reference `mlogit' on page 36 undefined on input line 595.
+
+
+LaTeX Warning: Reference `mlogit.bayes' on page 36 undefined on input line 599.
+
+
+
+LaTeX Warning: Reference `poisson' on page 36 undefined on input line 612.
+
+
+LaTeX Warning: Reference `poisson.bayes' on page 36 undefined on input line 618
+.
+
+
+LaTeX Warning: Reference `negbin' on page 36 undefined on input line 622.
+
+[36]
+
+LaTeX Warning: Reference `gamma' on page 37 undefined on input line 636.
+
+
+LaTeX Warning: Reference `exp' on page 37 undefined on input line 640.
+
+
+LaTeX Warning: Reference `weibull' on page 37 undefined on input line 646.
+
+
+LaTeX Warning: Reference `lognorm' on page 37 undefined on input line 657.
+
+
+LaTeX Warning: Reference `ei.hier' on page 37 undefined on input line 679.
+
+
+LaTeX Warning: Reference `ei.dynamic' on page 37 undefined on input line 682.
+
+
+LaTeX Warning: Reference `eiRxC' on page 37 undefined on input line 684.
+
+
+Package natbib Warning: Citation `King95' undefined on input line 708.
+
+[37] [38]
+Overfull \hbox (5.1774pt too wide) in paragraph at lines 792--792
+[]\T1/aett/m/n/12 # Check that the expected values are identical. You may do t
+his for each qi.[]
+ []
+
+
+LaTeX Warning: Characters dropped after `\end{verbatim}' on input line 794.
+
+) (./graphs.tex [39]
+Chapter 5.
+[40
+
+] [41]
+Overfull \hbox (5.97571pt too wide) in paragraph at lines 111--111
+[]\T1/aer/bx/n/17.28 Adding Points, Lines, and Leg-ends to Ex-ist-ing Plots
+ []
+
+[42] [43] <figs/sample1.pdf, id=786, 451.6875pt x 289.08pt>
+File: figs/sample1.pdf Graphic file (type pdf)
+
+<use figs/sample1.pdf> [44 <./figs/sample1.pdf>]
+<figs/sample2.pdf, id=800, 325.215pt x 252.945pt>
+File: figs/sample2.pdf Graphic file (type pdf)
+ <use figs/sample2.pdf>
+Overfull \hbox (5.1774pt too wide) in paragraph at lines 234--234
+[]\T1/aett/m/n/12 > lines(density(turnout$income)) # Adds the kern
+el density line.[]
+ []
+
+
+LaTeX Warning: Characters dropped after `\end{verbatim}' on input line 235.
+
+[45 <./figs/sample2.pdf>]
+
+Package natbib Warning: Citation `KatKin99' undefined on input line 252.
+
+
+LaTeX Warning: Reference `ternary' on page 46 undefined on input line 252.
+
+
+LaTeX Warning: Reference `ternary' on page 46 undefined on input line 254.
+
+<figs/ternary.pdf, id=814, 289.08pt x 289.08pt>
+File: figs/ternary.pdf Graphic file (type pdf)
+ <use figs/ternary.pdf> [46 <./figs/ternary.pdf>]
+
+Package natbib Warning: Citation `KinZen02' undefined on input line 268.
+
+
+LaTeX Warning: Reference `ROC' on page 47 undefined on input line 269.
+
+<figs/roc.pdf, id=829, 289.08pt x 289.08pt>
+File: figs/roc.pdf Graphic file (type pdf)
+ <use figs/roc.pdf> [47 <./figs/roc.pdf>]
+
+Package natbib Warning: Citation `KinTomWit00' undefined on input line 282.
+
+<figs/vertci.pdf, id=844, 433.62pt x 289.08pt>
+File: figs/vertci.pdf Graphic file (type pdf)
+ <use figs/vertci.pdf>) [48 <./figs/vertci.pdf>] [49
+
+] (./robjects.tex
+Chapter 6.
+
+Overfull \hbox (3.71233pt too wide) in paragraph at lines 27--27
+ []\T1/aett/m/n/12 > 2 > 3 # Basic logical operations,
+including >,[]
+ []
+
+
+Overfull \hbox (9.88028pt too wide) in paragraph at lines 29--29
+ [] \T1/aett/m/n/12 # <= (less than or equals)
+, == (exactly[]
+ []
+
+
+Overfull \hbox (3.71233pt too wide) in paragraph at lines 31--31
+ []\T1/aett/m/n/12 > 3 >= 2 && 100 == 1000/10 # Advanced logical operation
+s, including[]
+ []
+
+
+Overfull \hbox (9.88028pt too wide) in paragraph at lines 32--32
+ [] \T1/aett/m/n/12 [1] TRUE # & (and), && (if and only
+ if), | (or),[]
+ []
+
+[50
+
+]
+Overfull \hbox (34.5521pt too wide) in paragraph at lines 78--78
+ []\T1/aett/m/n/12 > a <- 1:5 # Creates a vector of integers from
+ 1 to 5 inclusive[]
+ []
+
+
+Overfull \hbox (3.7234pt too wide) in paragraph at lines 84--84
+ []\T1/aett/m/n/12 > a[5] <- 3.14 # Inserts 3.14 as the 5th value in th
+e vector \TS1/cmtt/m/n/12 `\T1/aett/m/n/12 a\TS1/cmtt/m/n/12 '[]
+ []
+
+
+Overfull \hbox (34.5521pt too wide) in paragraph at lines 85--85
+ []\T1/aett/m/n/12 > a[5:7] <- c(2, 4, 7) # Replaces the 5th through 7th values
+ with 2, 4, and 7[]
+ []
+
+[51]
+Overfull \hbox (28.38968pt too wide) in paragraph at lines 112--112
+ []\T1/aett/m/n/12 > x <- c("like", "dislike", "hate", "like", "don\TS1/cmtt/m/
+n/12 '\T1/aett/m/n/12 t know", "like", "dislike")[]
+ []
+
+
+Overfull \hbox (11.05815pt too wide) in paragraph at lines 144--144
+ [] \T1/aett/m/n/12 [,1] [,2] [,3] # Note that when assigning a ve
+ctor to a[]
+ []
+
+[52]
+Overfull \hbox (17.23718pt too wide) in paragraph at lines 154--154
+ []\T1/aett/m/n/12 > y <- c(55, 33, 12) # Creates another vector \TS1/c
+mtt/m/n/12 `\T1/aett/m/n/12 y\TS1/cmtt/m/n/12 ' \T1/aett/m/n/12 of 3 values.[]
+
+ []
+
+
+Overfull \hbox (11.05815pt too wide) in paragraph at lines 155--155
+ []\T1/aett/m/n/12 > rbind(x, y) # Creates a 2 x 3 matrix. Note
+ that row[]
+ []
+
+
+Overfull \hbox (11.05815pt too wide) in paragraph at lines 159--159
+ []\T1/aett/m/n/12 > cbind(x, y) # Creates a 3 x 2 matrix. Note
+ that the[]
+ []
+
+
+Overfull \hbox (3.71233pt too wide) in paragraph at lines 176--176
+ []\T1/aett/m/n/12 > loo[1,3] <- 13 # Inserts 13 as the value for row
+1, column 3.[]
+ []
+
+
+Overfull \hbox (9.88582pt too wide) in paragraph at lines 188--188
+ []\T1/aett/m/n/12 > a <- matrix(8, 2, 3) # Creates a 2 x 3 matrix popula
+ted with 8\TS1/cmtt/m/n/12 '\T1/aett/m/n/12 s.[]
+ []
+
+
+Overfull \hbox (9.88582pt too wide) in paragraph at lines 189--189
+ []\T1/aett/m/n/12 > b <- matrix(9, 2, 3) # Creates a 2 x 3 matrix popula
+ted with 9\TS1/cmtt/m/n/12 '\T1/aett/m/n/12 s.[]
+ []
+
+
+Overfull \hbox (16.05377pt too wide) in paragraph at lines 191--191
+ [] \T1/aett/m/n/12 , , 1 # level [,,1] populated with m
+atrix a (8\TS1/cmtt/m/n/12 '\T1/aett/m/n/12 s),[]
+ []
+
+
+Overfull \hbox (16.04823pt too wide) in paragraph at lines 195--195
+ [] \T1/aett/m/n/12 [2,] 8 8 8 # Use square brackets to extrac
+t values. For[]
+ []
+
+[53]
+Overfull \hbox (22.21619pt too wide) in paragraph at lines 197--197
+ [] \T1/aett/m/n/12 , , 2 # value in the first row of th
+e second level.[]
+ []
+
+
+Overfull \hbox (9.89136pt too wide) in paragraph at lines 230--230
+ []\T1/aett/m/n/12 > c[1, 2] # Pull out the value in the first row, second
+column of \TS1/cmtt/m/n/12 `\T1/aett/m/n/12 c\TS1/cmtt/m/n/12 '[]
+ []
+
+[54]
+
+LaTeX Warning: Characters dropped after `\end{verbatim}' on input line 252.
+
+
+Overfull \hbox (5.1774pt too wide) in paragraph at lines 268--268
+[]\T1/aett/m/n/12 > L[[4]] <- c(1, 4, 6, 8) # Inserts the vector into
+the 4th position[]
+ []
+
+
+LaTeX Warning: Characters dropped after `\end{verbatim}' on input line 272.
+
+
+Overfull \hbox (11.34535pt too wide) in paragraph at lines 291--291
+[]\T1/aett/m/n/12 > dat[1:10,] # Extracts observations 1-10 and all ass
+ociated variables
+ []
+
+[55]) (./programmingstatements.tex [56]
+Chapter 7.
+[57
+
+]
+Overfull \hbox (5.1774pt too wide) in paragraph at lines 84--84
+[]\T1/aett/m/n/12 > x <- array(dim = c(5,2,3)) # A 3D array of 3 stacked
+5 by 2 matrices.[]
+ []
+
+[58]
+
+LaTeX Warning: Characters dropped after `\end{verbatim}' on input line 128.
+
+
+LaTeX Warning: Characters dropped after `\end{verbatim}' on input line 147.
+
+[59]
+
+LaTeX Warning: Characters dropped after `\end{verbatim}' on input line 160.
+
+
+Overfull \hbox (36.4869pt too wide) in paragraph at lines 161--166
+\T1/aer/m/n/12 The sin-gle loop pro-ce-dure eval-u-ates each el-e-ment in \T1/a
+ett/m/n/12 idx \T1/aer/m/n/12 against the vec-tor \T1/aett/m/n/12 mydata$state\
+T1/aer/m/n/12 .
+ []
+
+
+Overfull \hbox (22.21619pt too wide) in paragraph at lines 186--186
+ []\T1/aett/m/n/12 z.out <- zelig(y ~ x1 + x2 + x3, by = "state", data = mydata
+, model = "ls")[]
+ []
+
+
+Overfull \hbox (28.38414pt too wide) in paragraph at lines 192--192
+ []\T1/aett/m/n/12 se <- array() # Initalize the empty
+ data structure.[]
+ []
+
+
+Overfull \hbox (22.21619pt too wide) in paragraph at lines 193--193
+ []\T1/aett/m/n/12 for (i in 1:50) { # vcov() creates the
+variance matrix[]
+ []
+
+
+Overfull \hbox (28.38414pt too wide) in paragraph at lines 194--194
+ [] \T1/aett/m/n/12 se[i] <- sqrt(vcov(z.out[[i]])[2,2]) # Since we have an in
+tercept, the 2nd[]
+ []
+
+
+Overfull \hbox (16.04823pt too wide) in paragraph at lines 195--195
+ []\T1/aett/m/n/12 } # diagonal value corr
+esponds to x1.[]
+ []
+
+[60]
+
+LaTeX Warning: Characters dropped after `\end{verbatim}' on input line 211.
+
+) (./newModels.tex [61]
+Chapter 8.
+[62
+
+]
+Overfull \hbox (11.34535pt too wide) in paragraph at lines 48--48
+[]\T1/aett/m/n/12 # Given the formula above, programmers can use the following
+standard commands[]
+ []
+
+
+LaTeX Warning: Reference `categories' on page 63 undefined on input line 88.
+
+[63]
+
+LaTeX Warning: Reference `describe.mymodel' on page 64 undefined on input line
+112.
+
+
+Overfull \hbox (0.7662pt too wide) in paragraph at lines 115--115
+[]\T1/aer/bx/n/14.4 Single Re-sponse Vari-able Mod-els: Nor-mal Re-gres-sion Mo
+del
+ []
+
+
+Overfull \hbox (19.04494pt too wide) in paragraph at lines 123--127
+\T1/aer/m/n/12 im-plies two sets of pa-ram-e-ters in your model, and the fol-lo
+w-ing \T1/aett/m/n/12 describe.normal.regression()
+ []
+
+[64] [65]
+
+LaTeX Warning: Characters dropped after `\end{verbatim}' on input line 228.
+
+[66] [67] [68] [69] [70] [71] [72]
+Overfull \hbox (16.04823pt too wide) in paragraph at lines 588--588
+ []\T1/aett/m/n/12 X <- model.matrix(fml, data = D, shape = "stacked", eqn = c(
+"mu1", "mu2"))[]
+ []
+
+
+Overfull \hbox (3.71233pt too wide) in paragraph at lines 598--598
+ []\T1/aett/m/n/12 X <- model.matrix(fml, data = D, shape = "array", eqn = c("m
+u1", "mu2"))[]
+ []
+
+) (./addingModels.tex [73]
+Chapter 9.
+
+LaTeX Warning: `!h' float specifier changed to `!ht'.
+
+
+LaTeX Warning: Reference `describe.mymodel' on page 74 undefined on input line
+76.
+
+[74
+
+] [75]
+Overfull \hbox (39.2998pt too wide) in paragraph at lines 145--154
+\T1/aett/m/n/12 zelig2normal.regression()\T1/aer/m/n/12 , in-clud-ing the ex-tr
+a ar-gu-ments taken by \T1/aett/m/n/12 normal.regression()\T1/aer/m/n/12 ,
+ []
+
+
+Overfull \hbox (6.41313pt too wide) in paragraph at lines 145--154
+\T1/aer/m/n/12 but not by \T1/aett/m/n/12 zelig()\T1/aer/m/n/12 . All wrap-pers
+ must take the same stan-dard-ized ar-gu-ments (\T1/aett/m/n/12 formula\T1/aer/
+m/n/12 ,
+ []
+
+
+Overfull \hbox (58.76842pt too wide) in paragraph at lines 145--154
+\T1/aett/m/n/12 zelig() \T1/aer/m/n/12 call into the \T1/aett/m/n/12 normal.reg
+ression() \T1/aer/m/n/12 call. Ad-di-tional ar-gu-ments to \T1/aett/m/n/12 norm
+al.regression()\T1/aer/m/n/12 ,
+ []
+
+[76] [77]
+
+LaTeX Warning: Characters dropped after `\end{verbatim}' on input line 248.
+
+
+LaTeX Warning: Characters dropped after `\end{verbatim}' on input line 254.
+
+[78] [79] [80]
+
+LaTeX Warning: Reference `describe.mymodel' on page 81 undefined on input line
+396.
+
+[81] [82]
+Overfull \hbox (16.04823pt too wide) in paragraph at lines 475--475
+ []\T1/aett/m/n/12 \item The first difference in expected values, given when x1
+ is specified.[]
+ []
+
+) [83] [84
+
+] (./refman.tex
+Chapter 10.
+[85
+
+]
+\openout2 = `commandsRd/zelig.aux'.
+
+
+No file commandsRd/zelig.tex.
+\openout2 = `commandsRd/setx.aux'.
+
+No file commandsRd/setx.tex.
+\openout2 = `commandsRd/sim.aux'.
+
+No file commandsRd/sim.tex.
+\openout2 = `commandsRd/summary.aux'.
+
+No file commandsRd/summary.tex.
+\openout2 = `commandsRd/plot.zelig.aux'.
+
+No file commandsRd/plot.zelig.tex.
+\openout2 = `commands/print.aux'.
+
+(./commands/print.tex
+
+Package hyperref Warning: Token not allowed in a PDFDocEncoded string,
+(hyperref) removing `\<def>-command' on input line 1.
+
+
+Package hyperref Warning: Token not allowed in a PDFDocEncoded string,
+(hyperref) removing `\f at encoding' on input line 1.
+
+
+Package hyperref Warning: Token not allowed in a PDFDocEncoded string,
+(hyperref) removing `\<let>-command' on input line 1.
+
+
+Package hyperref Warning: Token not allowed in a PDFDocEncoded string,
+(hyperref) removing `\<def>-command' on input line 1.
+
+
+Package hyperref Warning: Token not allowed in a PDFDocEncoded string,
+(hyperref) removing `\f at family' on input line 1.
+
+
+Package hyperref Warning: Token not allowed in a PDFDocEncoded string,
+(hyperref) removing `\<def>-command' on input line 1.
+
+
+Package hyperref Warning: Token not allowed in a PDFDocEncoded string,
+(hyperref) removing `\f at series' on input line 1.
+
+
+Package hyperref Warning: Token not allowed in a PDFDocEncoded string,
+(hyperref) removing `\<def>-command' on input line 1.
+
+
+Package hyperref Warning: Token not allowed in a PDFDocEncoded string,
+(hyperref) removing `\f at shape' on input line 1.
+
+
+Package hyperref Warning: Token not allowed in a PDFDocEncoded string,
+(hyperref) removing `\<def>-command' on input line 1.
+
+
+Package hyperref Warning: Token not allowed in a PDFDocEncoded string,
+(hyperref) removing `\font at name' on input line 1.
+
+
+Package hyperref Warning: Token not allowed in a PDFDocEncoded string,
+(hyperref) removing `\T1/aett/m/n/17.28' on input line 1.
+
+
+Package hyperref Warning: Token not allowed in a PDFDocEncoded string,
+(hyperref) removing `\ignorespaces' on input line 1.
+
+) [86
+
+
+
+
+
+
+
+
+
+
+
+]
+\openout2 = `commandsRd/repl.aux'.
+
+
+No file commandsRd/repl.tex.
+Chapter 11.
+[87
+
+
+
+
+]
+\openout2 = `commands/matchit.aux'.
+
+ (./commands/matchit.tex
+
+Package hyperref Warning: Token not allowed in a PDFDocEncoded string,
+(hyperref) removing `\<def>-command' on input line 1.
+
+
+Package hyperref Warning: Token not allowed in a PDFDocEncoded string,
+(hyperref) removing `\f at encoding' on input line 1.
+
+
+Package hyperref Warning: Token not allowed in a PDFDocEncoded string,
+(hyperref) removing `\<let>-command' on input line 1.
+
+
+Package hyperref Warning: Token not allowed in a PDFDocEncoded string,
+(hyperref) removing `\<def>-command' on input line 1.
+
+
+Package hyperref Warning: Token not allowed in a PDFDocEncoded string,
+(hyperref) removing `\f at family' on input line 1.
+
+
+Package hyperref Warning: Token not allowed in a PDFDocEncoded string,
+(hyperref) removing `\<def>-command' on input line 1.
+
+
+Package hyperref Warning: Token not allowed in a PDFDocEncoded string,
+(hyperref) removing `\f at series' on input line 1.
+
+
+Package hyperref Warning: Token not allowed in a PDFDocEncoded string,
+(hyperref) removing `\<def>-command' on input line 1.
+
+
+Package hyperref Warning: Token not allowed in a PDFDocEncoded string,
+(hyperref) removing `\f at shape' on input line 1.
+
+
+Package hyperref Warning: Token not allowed in a PDFDocEncoded string,
+(hyperref) removing `\<def>-command' on input line 1.
+
+
+Package hyperref Warning: Token not allowed in a PDFDocEncoded string,
+(hyperref) removing `\font at name' on input line 1.
+
+
+Package hyperref Warning: Token not allowed in a PDFDocEncoded string,
+(hyperref) removing `\T1/aett/m/n/17.28' on input line 1.
+
+
+Package hyperref Warning: Token not allowed in a PDFDocEncoded string,
+(hyperref) removing `\ignorespaces' on input line 1.
+
+
+Package natbib Warning: Citation `HoImaKin05b' on page 88 undefined on input li
+ne 6.
+
+[88
+
+] [89]
+
+Package natbib Warning: Citation `Imai05' on page 90 undefined on input line 14
+7.
+
+[90] [91]
+Overfull \hbox (5.78813pt too wide) in paragraph at lines 259--264
+\T1/aer/m/n/12 pack-age. See \T1/aett/m/n/12 help(fullmatch) \T1/aer/m/n/12 or
+[]http://www.stat.lsa.umich.edu/^^Cbbh/optmatch.html[]
+ []
+
+
+Overfull \hbox (5.78813pt too wide) in paragraph at lines 270--274
+\T1/aer/m/n/12 pack-age. See \T1/aett/m/n/12 help(fullmatch) \T1/aer/m/n/12 or
+[]http://www.stat.lsa.umich.edu/^^Cbbh/optmatch.html[]
+ []
+
+
+Overfull \hbox (164.73892pt too wide) in paragraph at lines 283--288
+\T1/aett/m/n/12 Matching \T1/aer/m/n/12 pack-age. See \T1/aett/m/n/12 help(GenM
+atch) \T1/aer/m/n/12 or []http://sekhon.polisci.berkeley.edu/library/Matching/h
+tml/GenMatch.html[]
+ []
+
+
+Overfull \hbox (39.64076pt too wide) in paragraph at lines 304--308
+[]\T1/aett/m/n/12 model\T1/aer/m/n/12 : the out-put of the model used to es-ti-
+mate the dis-tance mea-sure. \T1/aett/m/n/12 summary(m.out$model)
+ []
+
+[92]
+
+Package natbib Warning: Citation `HoImaKin07' undefined on input line 359.
+
+! Undefined control sequence.
+<argument> ...G., and Stuart, E. (2007), \enquote
+ {Matching as Nonparametric...
+l.359 \bibentry{HoImaKin07}
+
+?
+! Emergency stop.
+<argument> ...G., and Stuart, E. (2007), \enquote
+ {Matching as Nonparametric...
+l.359 \bibentry{HoImaKin07}
+
+End of file on the terminal!
+
+
+Here is how much of TeX's memory you used:
+ 8792 strings out of 94500
+ 109010 string characters out of 1176767
+ 203345 words of memory out of 1000000
+ 11192 multiletter control sequences out of 10000+50000
+ 68026 words of font info for 166 fonts, out of 500000 for 2000
+ 580 hyphenation exceptions out of 1000
+ 38i,15n,43p,259b,593s stack positions out of 1500i,500n,5000p,200000b,5000s
+PDF statistics:
+ 1171 PDF objects out of 300000
+ 439 named destinations out of 131072
+ 594 words of extra memory for PDF output out of 65536
+! ==> Fatal error occurred, the output PDF file is not finished!
diff --git a/inst/doc/zelig.pdf b/inst/doc/zelig.pdf
index 122d5be..d920d17 100644
Binary files a/inst/doc/zelig.pdf and b/inst/doc/zelig.pdf differ
diff --git a/inst/doc/zelig.tex b/inst/doc/zelig.tex
index e03d2fe..ebf27f1 100644
--- a/inst/doc/zelig.tex
+++ b/inst/doc/zelig.tex
@@ -22,7 +22,7 @@ Olivia Lau\thanks{Ph.D.\ Candidate, Department of Government, Harvard
\texttt{OLau at Fas.Harvard.Edu}).}}
% rbuild: replace 'Version ' '\\' Version
-\date{Version 3.4-7\\ \today}
+\date{Version 3.4-8\\ \today}
\begin{document}
\maketitle
diff --git a/man/plot.ci.Rd b/man/plot.ci.Rd
index 1fe414a..a264416 100644
--- a/man/plot.ci.Rd
+++ b/man/plot.ci.Rd
@@ -55,6 +55,10 @@ plot.ci(s.out, xlab = "Age in Years",
legend(45, 0.52, legend = c("College Education (16 years)",
"High School Education (12 years)"), col = c("blue","red"),
lty = c("solid"))
+
+## adding lines connecting point estimates
+lines(age.range, apply(s.out$qi$ev, 2, mean))
+lines(age.range, apply(s.out$qi$fd+s.out$qi$ev, 2, mean))
}
\seealso{
diff --git a/man/zeligVDC.Rd b/man/zeligVDC.Rd
index f077648..252517b 100644
--- a/man/zeligVDC.Rd
+++ b/man/zeligVDC.Rd
@@ -77,7 +77,7 @@ Micah Altman
}
-\seealso{ \link[pkg:Zelig]{zelig}}
+\seealso{ \link[Zelig]{zelig}}
\keyword{IO}
\keyword{print}
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-science/packages/r-cran-zelig.git
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