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Modifications for check, rebuild vignette

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1 parent 8f00570 commit 7b2454db7cfc952425b8673045f324066e314790 @cameronbracken committed Mar 15, 2012
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1 .Rinstignore
@@ -0,0 +1 @@
+doc/fig*[.]pdf$
View
251 ChangeLog
@@ -1,3 +1,245 @@
+commit 8f00570ea40b0bba322c246e4e0c4333a96f8c50
+Author: cameronbracken <cameron.bracken@gmail.com>
+Date: Thu Mar 15 00:19:27 2012 -0700
+
+ Update NEWS and DESCRIPTION for new version 1.3.0
+
+ DESCRIPTION | 51 ++++++++++++++++++++++++++++++++++-----------------
+ NEWS | 14 +++++++++++++-
+ 2 files changed, 47 insertions(+), 18 deletions(-)
+
+commit 63652515e771b9e1e7a6a519cb07d1c07fb3a098
+Merge: 9ec3a2d f339a64
+Author: cameronbracken <cameron.bracken@gmail.com>
+Date: Wed Mar 14 23:25:44 2012 -0700
+
+ Merge branch 'master' of github.com:cameronbracken/pgfSweave
+
+commit 9ec3a2d0bcc0402a0b88025f18d3511815fcd61b
+Author: cameronbracken <cameron.bracken@gmail.com>
+Date: Wed Mar 14 23:23:02 2012 -0700
+
+ Roxegenize docs
+
+ NAMESPACE | 15 ++--
+ R/pgfSweave.R | 1 +
+ R/pgfSweaveDriver.R | 10 ++-
+ man/pgfSweave.Rd | 170 +++++++++++++++++++++++++++---------------------
+ man/pgfSweaveDriver.Rd | 157 ++++++++++++++++++++++++---------------------
+ 5 files changed, 198 insertions(+), 155 deletions(-)
+
+commit 184c07a447677a54341e92dea2494286f2372c04
+Merge: cb36897 bf5b655
+Author: cameronbracken <cameron.bracken@gmail.com>
+Date: Wed Mar 14 22:38:04 2012 -0700
+
+ Merge branch 'docs'
+
+commit cb3689772db07d3a8d65ecda639a7f7107495ea4
+Author: cameronbracken <cameron.bracken@gmail.com>
+Date: Wed Mar 14 22:18:45 2012 -0700
+
+ Fix link in docs, fixed GH-35
+
+ man/pgfSweaveDriver.Rd | 2 +-
+ 1 files changed, 1 insertions(+), 1 deletions(-)
+
+commit cea3c877827bc1a7b7b4e47548ee43fc4b75c814
+Author: cameronbracken <cameron.bracken@gmail.com>
+Date: Wed Mar 14 22:13:54 2012 -0700
+
+ Dont automatically install command line script, it is against the rules. Modify the install scrip to be called from a regular session so the user can install it themselves later.
+
+ NEWS | 7 ++++++-
+ R/pgfSweave.R | 4 ++++
+ exec/install-script.R | 7 +++----
+ src/Makevars | 6 ------
+ src/dummy.c | 8 --------
+ 5 files changed, 13 insertions(+), 19 deletions(-)
+
+commit 4d4f44bc633f840e61c0054dbf2d13f560ad5e52
+Author: cameronbracken <cameron.bracken@gmail.com>
+Date: Wed Mar 14 22:01:04 2012 -0700
+
+ Get rid of .onAttach, it didnt do anything and get rid of package loading in .onLoad
+
+ R/zzz.R | 14 --------------
+ 1 files changed, 0 insertions(+), 14 deletions(-)
+
+commit f339a643406dbb7a7ecd9ec9b249b02163543f35
+Merge: 9cc0095 d5b04a6
+Author: Cameron Bracken <cameron.bracken@gmail.com>
+Date: Sun Feb 26 19:10:25 2012 -0800
+
+ Merge pull request #39 from psibre/master
+
+ xelatex example updates
+
+commit d5b04a651d5fdab7704722c61660db5d56779c5e
+Author: Ingmar Steiner <ingmar.steiner@inria.fr>
+Date: Mon Feb 13 13:03:03 2012 +0100
+
+ modified xelatex example further,
+
+ particularly for use with fontspec (practically ubiquitous in xelatex documents)
+ Note: the actual fonts used (Times, Courier) may not be available everywhere.
+
+ For details on the potential ae conflict of Sweave and fontspec, see, e.g., http://www.theresearchkitchen.com/archives/118
+
+ inst/example/pgfSweave-xelatex-example.Rnw | 31 +++++++++++++++++++--------
+ 1 files changed, 22 insertions(+), 9 deletions(-)
+
+commit 871fc2171ee70439dce79b3e93bf3f197e350dfd
+Author: Ingmar Steiner <ingmar.steiner@inria.fr>
+Date: Mon Feb 13 11:49:52 2012 +0100
+
+ updated xelatex example and softened warning;
+
+ if xelatex is called with -8bit option, generated makefile is not malformed, and does not need to be hacked with sed or perl
+
+ see for example, http://tex.stackexchange.com/a/14776
+
+ inst/example/Makefile | 9 +++++++--
+ inst/example/pgfSweave-xelatex-example.Rnw | 5 ++---
+ 2 files changed, 9 insertions(+), 5 deletions(-)
+
+commit 9cc009512dd0968a17ba056deab5b56b55a58534
+Author: cameronbracken <cameron.bracken@gmail.com>
+Date: Thu Dec 1 14:51:54 2011 -0700
+
+ Importing cacheSweave doesnt work, need a dependency
+
+ DESCRIPTION | 2 +-
+ NAMESPACE | 3 +--
+ 2 files changed, 2 insertions(+), 3 deletions(-)
+
+commit 6e2d0a3858a883e87bc4d1648c917e7880d9b20c
+Author: cameronbracken <cameron.bracken@gmail.com>
+Date: Thu Dec 1 14:51:12 2011 -0700
+
+ Add support for figs.only option to Sweave (TRUE by defualt)
+
+ R/pgfSweaveDriver.R | 5 +++--
+ 1 files changed, 3 insertions(+), 2 deletions(-)
+
+commit 413d1d6404669a190c27541e6357feca7520f9f0
+Author: cameronbracken <cameron.bracken@gmail.com>
+Date: Mon Aug 22 12:39:35 2011 -0600
+
+ Add global option pgfSweaveNoHighlight to disable printing of highlight definitions (they are currently always printed.)
+
+ Set the options to any other value than NULL to disable printing of the definitions e.g. options(pgfSweaveNoHighlight=TRUE)
+
+ R/pgfSweaveDriver.R | 42 ++++++++++++++++++++++--------------------
+ 1 files changed, 22 insertions(+), 20 deletions(-)
+
+commit bf5b65532c9ed6f9f88d876fc2c88ecfc74cd0f2
+Author: cameronbracken <cameron.bracken@gmail.com>
+Date: Mon Aug 22 12:37:20 2011 -0600
+
+ Roxygenize docs
+
+ R/pgfSweave.R | 110 ++++++++++++++++++++++++++++++++++++++++++++++++++-
+ R/pgfSweaveDriver.R | 57 ++++++++++++++++++++++++++
+ 2 files changed, 166 insertions(+), 1 deletions(-)
+
+commit fc21a9d22861f6739d8765aa3330ca498093cfd0
+Author: cameronbracken <cameron.bracken@gmail.com>
+Date: Fri Jul 8 14:20:41 2011 -0600
+
+ Can now specify your installed PGF version in your .Rprofile to circumvent the check at startup, `options(pgfversion = "2.10")`; This gets the package load time down to a bare minimum, the rest of the time is from loading other packages:
+
+ $Rcpp
+ [1] 0.314
+
+ $parser
+ [1] 0.044
+
+ $codetools
+ [1] 0.029
+
+ $formatR
+ [1] 0.029
+
+ $filehash
+ [1] 0.094
+
+ $stashR
+ [1] 0.067
+
+ $tikzDevice
+ [1] 0.094
+
+ $highlight
+ [1] 0.088
+
+ $pgfSweave
+ [1] 0.044
+
+ packs <- c('Rcpp', 'parser', 'codetools', 'formatR', 'filehash',
+ 'tikzDevice', 'highlight', 'stashR', 'pgfSweave')
+ ti <- list()
+ for(p in packs)
+ ti[[p]] <- system.time(suppressPackageStartupMessages(library(p,character.only=TRUE)))
+
+ R/zzz.R | 25 +++++++++++++++++++------
+ 1 files changed, 19 insertions(+), 6 deletions(-)
+
+commit 9264763b9dae55c032e23018001cb57fd6bcb83d
+Author: cameronbracken <cameron.bracken@gmail.com>
+Date: Fri Jul 8 13:16:17 2011 -0600
+
+ Move optparse to 'Enhances' and add a check for it in the command line
+ script.
+
+ DESCRIPTION | 4 +++-
+ exec/pgfsweave | 1 +
+ exec/pgfsweave-script.R | 3 ++-
+ 3 files changed, 6 insertions(+), 2 deletions(-)
+
+commit f1e4d03c3ab7e9014b6a22dd695f4cf5007a5649
+Author: cameronbracken <cameron.bracken@gmail.com>
+Date: Tue May 31 12:25:29 2011 -0600
+
+ Fix spacing bug for highlight=F, tidy=T, wasn't caught with previous spacing fixes, GH-31
+
+ R/pgfSweaveDriver.R | 3 ---
+ 1 files changed, 0 insertions(+), 3 deletions(-)
+
+commit 54e1c783f5162251c9eb2c7fed997cf931f43bc7
+Merge: e13ae66 ec0225e
+Author: cameronbracken <cameron.bracken@gmail.com>
+Date: Sat May 28 17:39:22 2011 -0600
+
+ Merge branch 'master' of github.com:cameronbracken/pgfSweave
+
+commit e13ae6680c28237ba79e509a1e95a4fea425ac3f
+Author: cameronbracken <cameron.bracken@gmail.com>
+Date: Sat May 28 17:22:17 2011 -0600
+
+ Fix typos in the vignette
+
+ ChangeLog | 110 ++++++++++++
+ inst/doc/figs/fig-normalSweave.pdf | Bin 2839 -> 12554 bytes
+ inst/doc/figs/fig-pgfSweave-hist.pgf | 180 +++++++++++---------
+ inst/doc/figs/fig-pgfSweave-tikz-hist.pdf | Bin 28507 -> 35472 bytes
+ inst/doc/figs/fig-pgfSweave-tikz-hist.tikz | 77 +++++----
+ inst/doc/pgfSweave-example-tex.in | 26 ++--
+ inst/doc/pgfSweave-example.pdf | Bin 78304 -> 77979 bytes
+ inst/doc/pgfSweave.Rnw | 58 +++---
+ inst/doc/pgfSweave.pdf | Bin 279712 -> 289790 bytes
+ .../vignette-src/pgfSweave-vignette-source.Rnw | 6 +-
+ 10 files changed, 294 insertions(+), 163 deletions(-)
+
+commit ec0225ef4a84f66a77023760ba1f3c742d68ad55
+Merge: 29a4b9a 50566c1
+Author: Cameron Bracken <cameron.bracken@gmail.com>
+Date: Mon May 9 11:52:35 2011 -0700
+
+ Merge pull request #30 from lq/master
+
+ caching does not work properly when keep.source=TRUE
+
commit 29a4b9ae44804fda444c3f8fd4b04c94a1a84bce
Author: cameronbracken <cameron.bracken@gmail.com>
Date: Wed May 4 16:29:09 2011 -0600
@@ -7,6 +249,15 @@ Date: Wed May 4 16:29:09 2011 -0600
R/pgfSweaveDriver.R | 4 +++-
1 files changed, 3 insertions(+), 1 deletions(-)
+commit 50566c11734cb8719c0b33c06df7578711259a32
+Author: Qiang Li <liqiang@picb.ac.cn>
+Date: Wed May 4 01:11:42 2011 +0800
+
+ fixed: keep.source breaks cache
+
+ R/cacheSweaveUnexportedFunctions.R | 2 +-
+ 1 files changed, 1 insertions(+), 1 deletions(-)
+
commit 0cdf5785592ee6b94a40aeb72ed91253cac51b37
Merge: c53f9f8 dada019
Author: Cameron Bracken <cameron.bracken@gmail.com>
View
2 NAMESPACE
@@ -1,5 +1,5 @@
export(pgfSweave)
-export(pgfSweaveDriver)
+export(pgfSweaveSetup)
import(utils)
importFrom(digest,digest)
importFrom(formatR,deparse.tidy)
View
27 R/pgfSweaveDriver.R
@@ -22,7 +22,15 @@
## Heavily relies on functions of cacheSweave but reimplements the
## Sweave driver function.
-
+pgfSweaveDriver <- function() {
+ list(
+ setup = pgfSweaveSetup,
+ runcode = pgfSweaveRuncode,
+ writedoc = pgfSweaveWritedoc,
+ finish = utils::RweaveLatexFinish,
+ checkopts = pgfSweaveOptions
+ )
+}
#' The Sweave driver for pgfSweave
#'
@@ -35,6 +43,7 @@
#' pdf.
#'
#' @aliases pgfSweaveDriver pgfSweaveSetup
+#' @rdname pgfSweaveDriver
#' @param file A connection or a character string giving the name of the Sweave
#' file to load.
#' @param syntax See \code{\link{RweaveLatex}}
@@ -58,7 +67,9 @@
#' package.
#' @param tidy Should echo'd code be cleaned up with the
#' \code{\link[formatR]{tidy.source}} function from the
-#' \code{\link[formatR]{formatR}} package.
+#' \pkg{formatR} package.
+#' @param concordance \code{\link{RweaveLatex}}
+#' @param figs.only \code{\link{RweaveLatex}}
#' @return Nothing useful returned.
#' @note \itemize{ \item For myfile.Rnw, Make sure to call the command
#' \\code{pgfrealjobname{myfile}} in the LaTeX header. \item Calling
@@ -84,17 +95,7 @@
#' @importFrom tools texi2dvi
#' @importFrom tikzDevice tikz
#' @importFrom formatR tidy.source parse.tidy deparse.tidy
-#' @export
-pgfSweaveDriver <- function() {
- list(
- setup = pgfSweaveSetup,
- runcode = pgfSweaveRuncode,
- writedoc = pgfSweaveWritedoc,
- finish = utils::RweaveLatexFinish,
- checkopts = pgfSweaveOptions
- )
-}
-
+#' @export
#source('R/cacheSweaveUnexportedFunctions.R')
#source('R/utilities.R')
View
33 inst/doc/Sweave.sty
@@ -1,33 +0,0 @@
-\NeedsTeXFormat{LaTeX2e}
-\ProvidesPackage{Sweave}{}
-
-\RequirePackage{ifthen}
-\newboolean{Sweave@gin}
-\setboolean{Sweave@gin}{true}
-\newboolean{Sweave@ae}
-\setboolean{Sweave@ae}{true}
-
-\DeclareOption{nogin}{\setboolean{Sweave@gin}{false}}
-\DeclareOption{noae}{\setboolean{Sweave@ae}{false}}
-\ProcessOptions
-
-\RequirePackage{graphicx,fancyvrb}
-\IfFileExists{upquote.sty}{\RequirePackage{upquote}}{}
-
-\ifthenelse{\boolean{Sweave@gin}}{\setkeys{Gin}{width=0.8\textwidth}}{}%
-\ifthenelse{\boolean{Sweave@ae}}{%
- \RequirePackage[T1]{fontenc}
- \RequirePackage{ae}
-}{}%
-
-\DefineVerbatimEnvironment{Sinput}{Verbatim}{fontshape=sl}
-\DefineVerbatimEnvironment{Soutput}{Verbatim}{}
-\DefineVerbatimEnvironment{Scode}{Verbatim}{fontshape=sl}
-
-\newenvironment{Schunk}{}{}
-
-\newcommand{\Sconcordance}[1]{%
- \ifx\pdfoutput\undefined%
- \csname newcount\endcsname\pdfoutput\fi%
- \ifcase\pdfoutput\special{#1}%
- \else\immediate\pdfobj{#1}\fi}
View
BIN inst/doc/fig-normalSweave.pdf
Binary file not shown.
View
234 inst/doc/fig-pgfSweave-hist.pgf
@@ -0,0 +1,234 @@
+% Created by Eps2pgf 0.7.0 (build on 2008-08-24) on Thu Mar 15 00:30:59 PDT 2012
+\begin{pgfpicture}
+\pgfpathmoveto{\pgfqpoint{0cm}{0cm}}
+\pgfpathlineto{\pgfqpoint{7.62cm}{0cm}}
+\pgfpathlineto{\pgfqpoint{7.62cm}{7.62cm}}
+\pgfpathlineto{\pgfqpoint{0cm}{7.62cm}}
+\pgfpathclose
+\pgfusepath{clip}
+\begin{pgfscope}
+\begin{pgfscope}
+\end{pgfscope}
+\begin{pgfscope}
+\pgfpathmoveto{\pgfqpoint{0cm}{0cm}}
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+\pgfpathclose
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+\begin{pgfscope}
+\definecolor{eps2pgf_color}{rgb}{0,0,0}\pgfsetstrokecolor{eps2pgf_color}\pgfsetfillcolor{eps2pgf_color}
+\pgftext[x=4.327cm,y=6.529cm,rotate=0]{Histogram of rnorm(10000)}
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BIN inst/doc/fig-pgfSweave-tikz-hist.pdf
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77 inst/doc/figs/fig-pgfSweave-tikz-hist.tikz → inst/doc/fig-pgfSweave-tikz-hist.tikz
@@ -1,21 +1,18 @@
-% Created by tikzDevice version 0.6.1 on 2011-05-05 17:32:21
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BIN inst/doc/figs/fig-normalSweave.pdf
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BIN inst/doc/figs/fig-pgfSweave-hist.pdf
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248 inst/doc/figs/fig-pgfSweave-hist.pgf
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-\pgfpathlineto{\pgfqpoint{4.927cm}{3.303cm}}
-\pgfpathlineto{\pgfqpoint{5.17cm}{3.303cm}}
-\pgfpathlineto{\pgfqpoint{5.17cm}{2.7cm}}
-\pgfpathclose
-\pgfusepath{stroke}
-\pgfsetdash{}{0cm}
-\pgfpathmoveto{\pgfqpoint{5.17cm}{2.7cm}}
-\pgfpathlineto{\pgfqpoint{5.17cm}{2.927cm}}
-\pgfpathlineto{\pgfqpoint{5.414cm}{2.927cm}}
-\pgfpathlineto{\pgfqpoint{5.414cm}{2.7cm}}
-\pgfpathclose
-\pgfusepath{stroke}
-\pgfsetdash{}{0cm}
-\pgfpathmoveto{\pgfqpoint{5.414cm}{2.7cm}}
-\pgfpathlineto{\pgfqpoint{5.414cm}{2.771cm}}
-\pgfpathlineto{\pgfqpoint{5.657cm}{2.771cm}}
-\pgfpathlineto{\pgfqpoint{5.657cm}{2.7cm}}
-\pgfpathclose
-\pgfusepath{stroke}
-\pgfsetdash{}{0cm}
-\pgfpathmoveto{\pgfqpoint{5.657cm}{2.7cm}}
-\pgfpathlineto{\pgfqpoint{5.657cm}{2.711cm}}
-\pgfpathlineto{\pgfqpoint{5.901cm}{2.711cm}}
-\pgfpathlineto{\pgfqpoint{5.901cm}{2.7cm}}
-\pgfpathclose
-\pgfusepath{stroke}
-\pgfsetdash{}{0cm}
-\pgfpathmoveto{\pgfqpoint{5.901cm}{2.7cm}}
-\pgfpathlineto{\pgfqpoint{5.901cm}{2.7cm}}
-\pgfpathlineto{\pgfqpoint{6.144cm}{2.7cm}}
-\pgfpathlineto{\pgfqpoint{6.144cm}{2.7cm}}
-\pgfpathclose
-\pgfusepath{stroke}
-\pgfsetdash{}{0cm}
-\pgfpathmoveto{\pgfqpoint{6.144cm}{2.7cm}}
-\pgfpathlineto{\pgfqpoint{6.144cm}{2.701cm}}
-\pgfpathlineto{\pgfqpoint{6.387cm}{2.701cm}}
-\pgfpathlineto{\pgfqpoint{6.387cm}{2.7cm}}
-\pgfpathclose
-\pgfusepath{stroke}
-\end{pgfscope}
-\end{pgfscope}
-\end{pgfpicture}
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BIN inst/doc/figs/fig-pgfSweave-tikz-hist.pdf
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17 inst/doc/pgfSweave-example-tex.in
@@ -363,6 +363,7 @@
\newcommand{\hlkwd}[1]{\textcolor[rgb]{0,0,0.51}{#1}}
\newenvironment{Hinput}{\begin{trivlist}\item}{\end{trivlist}}
+\usepackage[utf8]{inputenc}
\usepackage{tikz}
\usetikzlibrary{external}
@@ -376,7 +377,6 @@
\begin{document}
-
\maketitle
This example is identical to that in the Sweave manual and is intended to
introduce pgfSweave and highlight the basic differences. Please refer to
@@ -395,17 +395,11 @@ into a \LaTeX{} document:
\normalfont
\hspace*{\fill}\\
\hlstd{}\ttfamily\noindent
-\hlprompt{\usebox{\hlnormalsizeboxgreaterthan}{\ }}\hlfunctioncall{print}\hlkeyword{(}\hlfunctioncall{kruskal.test}\hlkeyword{(}\hlsymbol{Ozone}{\ }\hlkeyword{\urltilda{}}{\ }\hlsymbol{Month}\hlkeyword{,}{\ }\hlargument{data}{\ }\hlargument{=}{\ }\hlsymbol{airquality}\hlkeyword{)}\hlkeyword{)}{\ }{\ }\hlcomment{\usebox{\hlnormalsizeboxhash}{\ }and{\ }another}\mbox{}
+\hlprompt{\usebox{\hlnormalsizeboxgreaterthan}{\ }}\hlfunctioncall{print}\hlkeyword{(}\hlfunctioncall{kruskal.test}\hlkeyword{(}\hlsymbol{Ozone}{\ }\hlkeyword{\urltilda{}}{\ }\hlsymbol{Month}\hlkeyword{,}{\ }\hlargument{data}{\ }\hlargument{=}{\ }\hlsymbol{airquality}\hlkeyword{)}\hlkeyword{)}{\ }\hlkeyword{\usebox{\hlnormalsizeboxpercent}InLiNe\usebox{\hlnormalsizeboxunderscore}IdEnTiFiEr\usebox{\hlnormalsizeboxpercent}}\hspace*{\fill}\\
+\hlstd{}\hlprompt{+{\ }}{\ }{\ }{\ }{\ }\hlstring{"\usebox{\hlnormalsizeboxhash}{\ }and{\ }another"}\mbox{}
\normalfont
\end{Hinput}
-\begin{Soutput}
- Kruskal-Wallis rank sum test
-
-data: Ozone by Month
-Kruskal-Wallis chi-squared = 29.2666, df = 4, p-value = 6.901e-06
-\end{Soutput}
-
\end{Schunk}
\noindent which shows that the location parameter of the Ozone distribution varies
@@ -417,11 +411,10 @@ significantly from month to month. Finally we include a boxplot of the data:
{\pgfkeys{/pgf/images/include external/.code={\includegraphics[width=3in]{#1}}}
\begin{Schunk}
\begin{Hinput}\ttfamily\noindent
-\hlprompt{\usebox{\hlnormalsizeboxgreaterthan}{\ }}\hlfunctioncall{boxplot}\hlkeyword{(}\hlsymbol{Ozone}{\ }\hlkeyword{\urltilda{}}{\ }\hlsymbol{Month}\hlkeyword{,}{\ }\hlargument{data}{\ }\hlargument{=}{\ }\hlsymbol{airquality}\hlkeyword{,}{\ }\hlargument{main}{\ }\hlargument{=}{\ }\hlstring{"Ozone{\ }distribution"}\hlkeyword{,}\hspace*{\fill}\\
-\hlstd{}\hlprompt{+{\ }}{\ }{\ }{\ }{\ }\hlargument{xlab}{\ }\hlargument{=}{\ }\hlstring{"Month"}\hlkeyword{,}{\ }\hlargument{ylab}{\ }\hlargument{=}{\ }\hlstring{"Concentration"}\hlkeyword{)}\mbox{}
+\hlprompt{\usebox{\hlnormalsizeboxgreaterthan}{\ }}{\ }{\ }\hlfunctioncall{boxplot}\hlkeyword{(}\hlsymbol{Ozone}{\ }\hlkeyword{\urltilda{}}{\ }\hlsymbol{Month}\hlkeyword{,}{\ }\hlargument{data}{\ }\hlargument{=}{\ }\hlsymbol{airquality}\hlkeyword{,}\hspace*{\fill}\\
+\hlstd{}\hlprompt{+{\ }}{\ }{\ }{\ }{\ }\hlargument{main}\hlargument{=}\hlstring{\usebox{\hlnormalsizeboxsinglequote}Ozone{\ }distribution\usebox{\hlnormalsizeboxsinglequote}}\hlkeyword{,}\hlargument{xlab}\hlargument{=}\hlstring{\usebox{\hlnormalsizeboxsinglequote}Month\usebox{\hlnormalsizeboxsinglequote}}\hlkeyword{,}\hlargument{ylab}\hlargument{=}\hlstring{\usebox{\hlnormalsizeboxsinglequote}Concentration\usebox{\hlnormalsizeboxsinglequote}}\hlkeyword{)}\mbox{}
\normalfont
-
\end{Hinput}
\end{Schunk}
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BIN inst/doc/pgfSweave-example.pdf
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59 inst/doc/pgfSweave.Rnw
@@ -397,7 +397,6 @@
\begin{document}
-
%% Cache all of the code chunks and generate external figures by default
%% the pgfSweave defaults are pdf=FALSE and eps=FALSE and pgf=FALSE and tikz=TRUE.
%% to get normal Sweave behavior set pgf=FALSE and external=FALSE
@@ -666,36 +665,39 @@ The original code in the chunk looks like:
Normal:
\begin{Schunk}
\begin{Sinput}
-> x <- numeric(100)
-> for (i in 1:100) {
-+ x[i] <- rnorm(1)
-+ }
-> y <- rnorm(100)
-> plot(x, y)
+> # here is a comment
+> x <- numeric(100)
+> for( i in 1:100){
++ x[i] <- rnorm(1)
++ }
+> # OR
+> y <- rnorm(100) # and another comment
+> plot(x,y)
\end{Sinput}
\end{Schunk}
With Highlighting:
\begin{Schunk}
\begin{Hinput}\ttfamily\noindent
-\hlprompt{\usebox{\hlnormalsizeboxgreaterthan}{\ }}\hlsymbol{x}{\ }\hlassignement{\usebox{\hlnormalsizeboxlessthan}-}{\ }\hlfunctioncall{numeric}\hlkeyword{(}\hlnumber{100}\hlkeyword{)}\mbox{}
+\hlprompt{\usebox{\hlnormalsizeboxgreaterthan}{\ }}{\ }{\ }{\ }{\ }{\ }{\ }{\ }{\ }\hlcomment{\usebox{\hlnormalsizeboxhash}{\ }here{\ }is{\ }a{\ }comment}\hspace*{\fill}\\
+\hlstd{}\hlprompt{\usebox{\hlnormalsizeboxgreaterthan}{\ }}{\ }{\ }{\ }{\ }\hlsymbol{x}{\ }\hlassignement{\usebox{\hlnormalsizeboxlessthan}-}{\ }\hlfunctioncall{numeric}\hlkeyword{(}\hlnumber{100}\hlkeyword{)}\mbox{}
\normalfont
\hspace*{\fill}\\
\hlstd{}\ttfamily\noindent
-\hlprompt{\usebox{\hlnormalsizeboxgreaterthan}{\ }}\hlkeyword{for}{\ }\hlkeyword{(}\hlsymbol{i}{\ }\hlkeyword{in}{\ }\hlnumber{1}\hlkeyword{:}\hlnumber{100}\hlkeyword{)}{\ }\hlkeyword{\usebox{\hlnormalsizeboxopenbrace}}\hspace*{\fill}\\
-\hlstd{}\hlprompt{+{\ }}{\ }{\ }{\ }{\ }\hlsymbol{x}\hlkeyword{[}\hlsymbol{i}\hlkeyword{]}{\ }\hlassignement{\usebox{\hlnormalsizeboxlessthan}-}{\ }\hlfunctioncall{rnorm}\hlkeyword{(}\hlnumber{1}\hlkeyword{)}\hspace*{\fill}\\
-\hlstd{}\hlprompt{+{\ }}\hlkeyword{\usebox{\hlnormalsizeboxclosebrace}}\mbox{}
+\hlprompt{\usebox{\hlnormalsizeboxgreaterthan}{\ }}{\ }{\ }{\ }{\ }\hlkeyword{for}\hlkeyword{(}{\ }\hlsymbol{i}{\ }\hlkeyword{in}{\ }\hlnumber{1}\hlkeyword{:}\hlnumber{100}\hlkeyword{)}\hlkeyword{\usebox{\hlnormalsizeboxopenbrace}}\hspace*{\fill}\\
+\hlstd{}\hlprompt{+{\ }}{\ }{\ }{\ }{\ }{\ }{\ }{\ }{\ }\hlsymbol{x}\hlkeyword{[}\hlsymbol{i}\hlkeyword{]}{\ }\hlassignement{\usebox{\hlnormalsizeboxlessthan}-}{\ }\hlfunctioncall{rnorm}\hlkeyword{(}\hlnumber{1}\hlkeyword{)}\hspace*{\fill}\\
+\hlstd{}\hlprompt{+{\ }}{\ }{\ }{\ }{\ }\hlkeyword{\usebox{\hlnormalsizeboxclosebrace}}\mbox{}
\normalfont
\hspace*{\fill}\\
\hlstd{}\ttfamily\noindent
-\hlprompt{\usebox{\hlnormalsizeboxgreaterthan}{\ }}\hlsymbol{y}{\ }\hlassignement{\usebox{\hlnormalsizeboxlessthan}-}{\ }\hlfunctioncall{rnorm}\hlkeyword{(}\hlnumber{100}\hlkeyword{)}\mbox{}
+\hlprompt{\usebox{\hlnormalsizeboxgreaterthan}{\ }}{\ }{\ }{\ }{\ }{\ }{\ }{\ }{\ }\hlcomment{\usebox{\hlnormalsizeboxhash}{\ }OR}\hspace*{\fill}\\
+\hlstd{}\hlprompt{\usebox{\hlnormalsizeboxgreaterthan}{\ }}{\ }{\ }{\ }{\ }\hlsymbol{y}{\ }\hlassignement{\usebox{\hlnormalsizeboxlessthan}-}{\ }\hlfunctioncall{rnorm}\hlkeyword{(}\hlnumber{100}\hlkeyword{)}{\ }{\ }\hlcomment{\usebox{\hlnormalsizeboxhash}{\ }and{\ }another{\ }comment}\mbox{}
\normalfont
\hspace*{\fill}\\
\hlstd{}\ttfamily\noindent
-\hlprompt{\usebox{\hlnormalsizeboxgreaterthan}{\ }}\hlfunctioncall{plot}\hlkeyword{(}\hlsymbol{x}\hlkeyword{,}{\ }\hlsymbol{y}\hlkeyword{)}\mbox{}
+\hlprompt{\usebox{\hlnormalsizeboxgreaterthan}{\ }}{\ }{\ }{\ }{\ }\hlfunctioncall{plot}\hlkeyword{(}\hlsymbol{x}\hlkeyword{,}\hlsymbol{y}\hlkeyword{)}\mbox{}
\normalfont
-
\end{Hinput}
\end{Schunk}
@@ -705,24 +707,22 @@ Version 1.1.0 of \pkg{pgfSweave} introduced the \code{tidy} option. This functi
Default (highlighting only, cleaned up with parse):
\begin{Schunk}
\begin{Hinput}\ttfamily\noindent
-\hlprompt{\usebox{\hlnormalsizeboxgreaterthan}{\ }}\hlsymbol{x}{\ }\hlassignement{\usebox{\hlnormalsizeboxlessthan}-}{\ }\hlfunctioncall{numeric}\hlkeyword{(}\hlnumber{100}\hlkeyword{)}\mbox{}
+\hlprompt{\usebox{\hlnormalsizeboxgreaterthan}{\ }}{\ }{\ }{\ }{\ }{\ }{\ }{\ }{\ }\hlcomment{\usebox{\hlnormalsizeboxhash}{\ }here{\ }is{\ }a{\ }comment}\hspace*{\fill}\\
+\hlstd{}\hlprompt{\usebox{\hlnormalsizeboxgreaterthan}{\ }}{\ }{\ }{\ }{\ }\hlsymbol{x}{\ }\hlassignement{\usebox{\hlnormalsizeboxlessthan}-}{\ }\hlfunctioncall{numeric}\hlkeyword{(}\hlnumber{100}\hlkeyword{)}{\ }{\ }\hlcomment{\usebox{\hlnormalsizeboxhash}{\ }here{\ }is{\ }a{\ }comment}\mbox{}
\normalfont
\hspace*{\fill}\\
\hlstd{}\ttfamily\noindent
-\hlprompt{\usebox{\hlnormalsizeboxgreaterthan}{\ }}\hlkeyword{for}{\ }\hlkeyword{(}\hlsymbol{i}{\ }\hlkeyword{in}{\ }\hlnumber{1}\hlkeyword{:}\hlnumber{100}\hlkeyword{)}{\ }\hlkeyword{\usebox{\hlnormalsizeboxopenbrace}}\hspace*{\fill}\\
-\hlstd{}\hlprompt{+{\ }}{\ }{\ }{\ }{\ }\hlsymbol{x}\hlkeyword{[}\hlsymbol{i}\hlkeyword{]}{\ }\hlassignement{\usebox{\hlnormalsizeboxlessthan}-}{\ }\hlfunctioncall{rnorm}\hlkeyword{(}\hlnumber{1}\hlkeyword{)}\hspace*{\fill}\\
-\hlstd{}\hlprompt{+{\ }}\hlkeyword{\usebox{\hlnormalsizeboxclosebrace}}\mbox{}
+\hlprompt{\usebox{\hlnormalsizeboxgreaterthan}{\ }}{\ }{\ }{\ }{\ }\hlkeyword{for}\hlkeyword{(}{\ }\hlsymbol{i}{\ }\hlkeyword{in}{\ }\hlnumber{1}\hlkeyword{:}\hlnumber{100}\hlkeyword{)}\hlkeyword{\usebox{\hlnormalsizeboxopenbrace}}{\ }\hlsymbol{x}\hlkeyword{[}\hlsymbol{i}\hlkeyword{]}{\ }\hlassignement{\usebox{\hlnormalsizeboxlessthan}-}{\ }\hlfunctioncall{rnorm}\hlkeyword{(}\hlnumber{1}\hlkeyword{)}\hlkeyword{\usebox{\hlnormalsizeboxclosebrace}}\mbox{}
\normalfont
\hspace*{\fill}\\
\hlstd{}\ttfamily\noindent
-\hlprompt{\usebox{\hlnormalsizeboxgreaterthan}{\ }}\hlsymbol{z}{\ }\hlassignement{\usebox{\hlnormalsizeboxlessthan}-}{\ }\hlfunctioncall{rnorm}\hlkeyword{(}\hlnumber{100}\hlkeyword{)}\mbox{}
+\hlprompt{\usebox{\hlnormalsizeboxgreaterthan}{\ }}{\ }{\ }{\ }{\ }\hlsymbol{z}{\ }\hlassignement{\usebox{\hlnormalsizeboxlessthan}-}{\ }\hlfunctioncall{rnorm}\hlkeyword{(}\hlnumber{100}\hlkeyword{)}{\ }{\ }\hlcomment{\usebox{\hlnormalsizeboxhash}{\ }and{\ }another{\ }comment}\mbox{}
\normalfont
\hspace*{\fill}\\
\hlstd{}\ttfamily\noindent
-\hlprompt{\usebox{\hlnormalsizeboxgreaterthan}{\ }}\hlfunctioncall{plot}\hlkeyword{(}\hlsymbol{x}\hlkeyword{,}{\ }\hlsymbol{z}\hlkeyword{)}\mbox{}
+\hlprompt{\usebox{\hlnormalsizeboxgreaterthan}{\ }}{\ }{\ }{\ }{\ }\hlfunctioncall{plot}\hlkeyword{(}\hlsymbol{x}\hlkeyword{,}\hlsymbol{z}\hlkeyword{)}\mbox{}
\normalfont
-
\end{Hinput}
\end{Schunk}
@@ -745,7 +745,6 @@ Normal with \code{keep.source=T} (highlighting only, not cleaned up):
\hlprompt{\usebox{\hlnormalsizeboxgreaterthan}{\ }}{\ }{\ }{\ }{\ }\hlfunctioncall{plot}\hlkeyword{(}\hlsymbol{x}\hlkeyword{,}\hlsymbol{z}\hlkeyword{)}\mbox{}
\normalfont
-
\end{Hinput}
\end{Schunk}
@@ -755,11 +754,10 @@ Only Tidying:
> # here is a comment
> x <- numeric(100) # here is a comment
> for (i in 1:100) {
- x[i] <- rnorm(1)
-}
++ x[i] <- rnorm(1)
++ }
> y <- rnorm(100) # and another comment
> plot(x, y)
-
\end{Sinput}
\end{Schunk}
@@ -787,7 +785,6 @@ With Tidying and highlighting:
\hlprompt{\usebox{\hlnormalsizeboxgreaterthan}{\ }}\hlfunctioncall{plot}\hlkeyword{(}\hlsymbol{x}\hlkeyword{,}{\ }\hlsymbol{y}\hlkeyword{)}\mbox{}
\normalfont
-
\end{Hinput}
\end{Schunk}
@@ -895,14 +892,12 @@ The process that \pkg{pgfSweave} uses when caching and externalization are turne
\section{Consistency in style between graphics and text}
%% initial calculations
-
In Figure \ref{normalSweave}, notice the inconsistency in font and size between the default \lang{R} output and the default \LaTeX{} output. Fonts and font sizes can be changed from \lang{R} but it is hard to be precise. What if you decide to change the font and and point size of your entire document? In Figure \ref{pgfSweave-hist} and \ref{pgfSweave-tikz-hist} the text is consistent with the rest of the document.
\begin{figure}[!ht]
\begin{minipage}{.45\linewidth}
\centering
-
-\includegraphics{figs/fig-normalSweave}
+\includegraphics{fig-normalSweave}
\caption{This is normal \pkg{Sweave}.}\label{normalSweave}
\end{minipage}
\begin{minipage}[!ht]{.45\linewidth}
@@ -911,8 +906,7 @@ The process that \pkg{pgfSweave} uses when caching and externalization are turne
\centering
-
-\input{figs/fig-pgfSweave-hist.pgf}
+\input{fig-pgfSweave-hist.pgf}
\caption{This is from \pkg{pgfSweave} with the \code{pgf} option.}\label{pgfSweave-hist}
\end{minipage}
\end{figure}
@@ -923,8 +917,7 @@ The process that \pkg{pgfSweave} uses when caching and externalization are turne
\centering
-
-\input{figs/fig-pgfSweave-tikz-hist.tikz}
+\input{fig-pgfSweave-tikz-hist.tikz}
\caption{This is from \pkg{pgfSweave} with the \code{tikz} option.}\label{pgfSweave-tikz-hist}
\end{figure}
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BIN inst/doc/pgfSweave.pdf
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14 inst/misc/vignette-src/Makefile
@@ -44,11 +44,11 @@ $(VIGNETTE_HANS_PDF): $(VIGNETTE_HANS_RNW)
$(VIGNETTE_DUMMY_RNW): $(EXAMPLE_PDF) $(VIGNETTE_SOURCE_PDF)
# Copy Sweave.sty
- cp Sweave.sty $(DOC_PATH)/
+ # cp Sweave.sty $(DOC_PATH)/
# Copy all the figures
- cp figs/*.pdf $(DOC_PATH)/figs/
- cp figs/*.pgf $(DOC_PATH)/figs/
- cp figs/*.tikz $(DOC_PATH)/figs/
+ cp *.pdf $(DOC_PATH)
+ cp *.pgf $(DOC_PATH)
+ cp *.tikz $(DOC_PATH)
# Copy all the example file to include but dont use .Rnw so they are not
# recognised as another vignette
cp -f $(EXAMPLE_PATH)/pgfSweave-example.Rnw \
@@ -78,14 +78,14 @@ $(EXAMPLE_PDF):
(cd $(EXAMPLE_PATH)/ ; make)
cleanall:
- rm -rf cache figs *.pdf $(RM_PATH).$(RM_SUFFIX) \
+ rm -rf cache *.pdf $(RM_PATH).$(RM_SUFFIX) \
$(DOC_PATH)/Sweave.sty $(DOC_PATH)/pgfSweave.Rnw $(DOC_PATH)/*.pdf \
- $(DOC_PATH)/figs/* tmp $(CHANGELOG)
+ tmp $(CHANGELOG)
(cd $(EXAMPLE_PATH) ; make clean)
(cd $(TEST_PATH) ; make clean)
clean:
- rm -rf cache figs *.pdf $(RM_PATH).$(BUILD_RM_SUFFIX) \
+ rm -rf cache *.pdf $(RM_PATH).$(BUILD_RM_SUFFIX) \
./pgfSweave-vignette-source.tex $(DOC_PATH)/pgfSweave.tex \
$(DOC_PATH)/pgfSweave_hans.tex tmp
(cd $(EXAMPLE_PATH) ; make cleanforbuild)
View
33 inst/misc/vignette-src/Sweave.sty
@@ -1,33 +0,0 @@
-\NeedsTeXFormat{LaTeX2e}
-\ProvidesPackage{Sweave}{}
-
-\RequirePackage{ifthen}
-\newboolean{Sweave@gin}
-\setboolean{Sweave@gin}{true}
-\newboolean{Sweave@ae}
-\setboolean{Sweave@ae}{true}
-
-\DeclareOption{nogin}{\setboolean{Sweave@gin}{false}}
-\DeclareOption{noae}{\setboolean{Sweave@ae}{false}}
-\ProcessOptions
-
-\RequirePackage{graphicx,fancyvrb}
-\IfFileExists{upquote.sty}{\RequirePackage{upquote}}{}
-
-\ifthenelse{\boolean{Sweave@gin}}{\setkeys{Gin}{width=0.8\textwidth}}{}%
-\ifthenelse{\boolean{Sweave@ae}}{%
- \RequirePackage[T1]{fontenc}
- \RequirePackage{ae}
-}{}%
-
-\DefineVerbatimEnvironment{Sinput}{Verbatim}{fontshape=sl}
-\DefineVerbatimEnvironment{Soutput}{Verbatim}{}
-\DefineVerbatimEnvironment{Scode}{Verbatim}{fontshape=sl}
-
-\newenvironment{Schunk}{}{}
-
-\newcommand{\Sconcordance}[1]{%
- \ifx\pdfoutput\undefined%
- \csname newcount\endcsname\pdfoutput\fi%
- \ifcase\pdfoutput\special{#1}%
- \else\immediate\pdfobj{#1}\fi}
View
4 inst/misc/vignette-src/pgfSweave-vignette-source.Rnw
@@ -35,13 +35,13 @@
require(cacheSweave)
setCacheDir("cache")
require(tikzDevice)
- if(!file.exists('figs')) dir.create('figs')
+ #if(!file.exists('figs')) dir.create('figs')
@
%% Cache all of the code chunks and generate external figures by default
%% the pgfSweave defaults are pdf=FALSE and eps=FALSE and pgf=FALSE and tikz=TRUE.
%% to get normal Sweave behavior set pgf=FALSE and external=FALSE
-\SweaveOpts{prefix.string=figs/fig,fig=T,eps=F,pdf=F,cache=T,tikz=T,external=T}
+\SweaveOpts{prefix.string=fig,fig=T,eps=F,pdf=F,cache=T,tikz=T,external=T}
\begin{center}
{\Large The \pkg{pgfSweave} Package}\\
View
15 man/pgfSweaveDriver.Rd
@@ -1,9 +1,14 @@
-\name{pgfSweaveDriver}
+\name{pgfSweaveSetup}
\alias{pgfSweaveDriver}
\alias{pgfSweaveSetup}
\title{The Sweave driver for pgfSweave}
\usage{
- pgfSweaveDriver()
+ pgfSweaveSetup(file, syntax, output = NULL,
+ quiet = FALSE, debug = FALSE, echo = TRUE, eval = TRUE,
+ split = FALSE, stylepath = TRUE, pdf = FALSE,
+ eps = FALSE, cache = FALSE, pgf = FALSE, tikz = TRUE,
+ external = FALSE, sanitize = FALSE, highlight = TRUE,
+ tidy = FALSE, concordance = FALSE, figs.only = TRUE)
}
\arguments{
\item{file}{A connection or a character string giving the
@@ -51,7 +56,11 @@
\item{tidy}{Should echo'd code be cleaned up with the
\code{\link[formatR]{tidy.source}} function from the
- \code{\link[formatR]{formatR}} package.}
+ \pkg{formatR} package.}
+
+ \item{concordance}{\code{\link{RweaveLatex}}}
+
+ \item{figs.only}{\code{\link{RweaveLatex}}}
}
\value{
Nothing useful returned.

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