[Vegan-commits] r2248 - pkg/vegan/inst/doc

[noreply at r-forge.r-project.org]

Author: jarioksa
Date: 2012-08-15 09:14:51 +0200 (Wed, 15 Aug 2012)
New Revision: 2248

Removed:
   pkg/vegan/inst/doc/vegan.sty
Modified:
   pkg/vegan/inst/doc/intro-vegan.Rnw
   pkg/vegan/inst/doc/veganjss.sty
Log:
revert 2243,5: I think I know the solution to the latex problems

Modified: pkg/vegan/inst/doc/intro-vegan.Rnw
===================================================================
--- pkg/vegan/inst/doc/intro-vegan.Rnw	2012-08-13 15:16:20 UTC (rev 2247)
+++ pkg/vegan/inst/doc/intro-vegan.Rnw	2012-08-15 07:14:51 UTC (rev 2248)
@@ -1,16 +1,13 @@
 % -*- mode: noweb; noweb-default-code-mode: R-mode; -*-
 %\VignetteIndexEntry{Introduction to ordination in vegan}
-\documentclass[a4paper,10pt]{amsart}
-\usepackage{vegan}
-\usepackage{ucs}
+\documentclass[article,nojss]{jss}
+\usepackage{veganjss} % vegan settings
+\usepackage{ucs} %% needed for R output: signif stars etc, quotes
 \usepackage[utf8x]{inputenc}
 \usepackage[T1]{fontenc}
-\usepackage{graphicx}
 \usepackage{sidecap}
-\setlength{\captionindent}{0pt}
-\usepackage{url}
+\usepackage{amsmath}
 
-
 \renewcommand{\floatpagefraction}{0.8}
 
 
@@ -18,13 +15,32 @@
 
 \author{Jari Oksanen}
 
+\Abstract{The document describes typical, simple work pathways of
+  vegetation ordination. Unconstrained ordination uses as examples
+  detrended correspondence analysis and non-metric multidimensional
+  scaling, and shows how to interpret their results by fitting
+  environmental vectors and factors or smooth environmental surfaces
+  to the graph. The basic plotting command, and more advanced plotting
+  commands for congested plots are also discussed, as well as adding
+  items such as ellipses, convex hulls, and other items for
+  classes. The constrained ordination uses constrained (canonical)
+  correspondence analysis as an example. It is first shown how a model
+  is defined, then the document discusses model building and
+  signficance tests of the whole analysis, single constraints and
+  axes.}
 
+\Keywords{ordination, correspondence analysis, non-metric
+  multidimensional scaling, CCA, RDA, NMDS, fitted environmental
+  vector, fitted environmental surface, permutation tests}
+
 %% misuse of the address field for revision data
-\date{$ $Id$ $
+\Address{$ $Id$ $
   processed with vegan
 \Sexpr{packageDescription("vegan", field="Version")}
 in \Sexpr{R.version.string} on \today}
+\Footername{About this version}
 
+%% need no \usepackage{Sweave}
 \begin{document}
 
 \setkeys{Gin}{width=0.55\linewidth}
@@ -37,29 +53,6 @@
 options("prompt" = "R> ", "continue" = "+  ")
 @
 
-\maketitle
-
-\begin{abstract}
-  The document describes typical, simple work pathways of
-  vegetation ordination. Unconstrained ordination uses as examples
-  detrended correspondence analysis and non-metric multidimensional
-  scaling, and shows how to interpret their results by fitting
-  environmental vectors and factors or smooth environmental surfaces
-  to the graph. The basic plotting command, and more advanced plotting
-  commands for congested plots are also discussed, as well as adding
-  items such as ellipses, convex hulls, and other items for
-  classes. The constrained ordination uses constrained (canonical)
-  correspondence analysis as an example. It is first shown how a model
-  is defined, then the document discusses model building and
-  signficance tests of the whole analysis, single constraints and
-  axes.
-\end{abstract}
-
-\keywords{ordination, correspondence analysis, non-metric
-  multidimensional scaling, CCA, RDA, NMDS, fitted environmental
-  vector, fitted environmental surface, permutation tests}
-
-
 \tableofcontents
 
 \section*{~}

Deleted: pkg/vegan/inst/doc/vegan.sty
===================================================================
--- pkg/vegan/inst/doc/vegan.sty	2012-08-13 15:16:20 UTC (rev 2247)
+++ pkg/vegan/inst/doc/vegan.sty	2012-08-15 07:14:51 UTC (rev 2248)
@@ -1,7 +0,0 @@
-% vegan style: copy entries from jss.cls of the R distribution 
-\let\proglang=\textsf
-\makeatletter
-\newcommand\code{\bgroup\@makeother\_\@makeother\~\@makeother\$\@codex}
-\def\@codex#1{{\normalfont\ttfamily\hyphenchar\font=-1 #1}\egroup}
-\makeatother
-\newcommand{\pkg}[1]{{\fontseries{b}\selectfont #1}}
\ No newline at end of file

Modified: pkg/vegan/inst/doc/veganjss.sty
===================================================================
--- pkg/vegan/inst/doc/veganjss.sty	2012-08-13 15:16:20 UTC (rev 2247)
+++ pkg/vegan/inst/doc/veganjss.sty	2012-08-15 07:14:51 UTC (rev 2248)
@@ -20,5 +20,5 @@
 %% use inconsolata fonts for code and examples 
 \usepackage{inconsolata}
 %% smaller examples
-%\renewenvironment{Schunk}{\par\small}{}
+\renewenvironment{Schunk}{\par\small}{}