[Vegan-commits] r2562 - pkg/vegan/inst/doc
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Jul 13 21:59:23 CEST 2013
Author: jarioksa
Date: 2013-07-13 21:59:23 +0200 (Sat, 13 Jul 2013)
New Revision: 2562
Added:
pkg/vegan/inst/doc/vegan.sty
Removed:
pkg/vegan/inst/doc/veganjss.sty
Modified:
pkg/vegan/inst/doc/decision-vegan.Rnw
pkg/vegan/inst/doc/diversity-vegan.Rnw
pkg/vegan/inst/doc/intro-vegan.Rnw
Log:
vignettes use standard amsart document style instead of hacked jss style
Modified: pkg/vegan/inst/doc/decision-vegan.Rnw
===================================================================
--- pkg/vegan/inst/doc/decision-vegan.Rnw 2013-07-12 12:19:57 UTC (rev 2561)
+++ pkg/vegan/inst/doc/decision-vegan.Rnw 2013-07-13 19:59:23 UTC (rev 2562)
@@ -1,33 +1,18 @@
% -*- mode: noweb; noweb-default-code-mode: R-mode; -*-
%\VignetteIndexEntry{Design decisions and implementation}
-\documentclass[article,nojss]{jss}
-\usepackage{veganjss} % package options and redefinitions
-\usepackage{amsmath}
-%\usepackage{ucs}
-%\usepackage[utf8x]{inputenc}
-%\usepackage[T1]{fontenc}
-\usepackage{sidecap}
-\usepackage[english]{babel} % kluge to avoid visible ~ in Figure~1.
-\renewcommand{\floatpagefraction}{0.8}
+\documentclass[a4paper,10pt]{amsart}
+\usepackage{vegan} % package options and redefinitions
+\usepackage[round]{natbib}
\renewcommand{\cite}{\citep}
-\newcommand{\R}{\textsf{R}}
\author{Jari Oksanen}
\title{Design decisions and implementation details in vegan}
-\Abstract{
- This document describes design decisions, and discusses implementation
-and algorithmic details in some vegan functions. The proper FAQ is
-another document.
- }
-\Keywords{parallel processing, nestdness, matrix temperature,
- community null models, scaling of PCA and RDA, WA and LC scores}
- %% hijack Address for version info
-\Address{$ $Id$ $
+
+\date{$ $Id$ $
processed with vegan
\Sexpr{packageDescription("vegan", field="Version")}
in \Sexpr{R.version.string} on \today}
-\Footername{About this version}
%% need no \usepackage{Sweave.sty}
\begin{document}
@@ -39,7 +24,14 @@
options("prompt" = "R> ", "continue" = "+ ")
require(vegan)
@
+\maketitle
+\begin{abstract}
+ This document describes design decisions, and discusses implementation
+and algorithmic details in some vegan functions. The proper FAQ is
+another document.
+\end{abstract}
+
\tableofcontents
\section{Parallel processing}
@@ -95,7 +87,7 @@
The \code{mc.cores} option is defined in the \pkg{parallel} package,
but it is usually unset in which case \pkg{vegan} will default to
non-parallel computation. The \code{mc.cores} option can be set by
-the environmental variable \code{MC_CORES} when the \pkg{parallel}
+the environmental variable \verb|MC_CORES| when the \pkg{parallel}
package is loaded.
\R{} allows\footnote{Since \R{} version 2.15.0.}
@@ -249,7 +241,7 @@
will mean creating and stopping socket clusters even when a
default cluster is set if \code{mc.cores} is not
\code{NULL}. Please note that the \code{mc.cores} is only set from
- the environmental variable \code{MC_CORES} when you load the
+ the environmental variable \verb|MC_CORES| when you load the
\pkg{parallel} package, and it is always unset before first
\code{require(parallel)}. \footnote{The behaviour of
\code{mc.cores} option is untested in Windows.}
@@ -798,6 +790,7 @@
primarily WA scores in plotting. However, the user makes the ultimate
choice, since both scores are available.
+\bibliographystyle{plainnat}
\bibliography{vegan}
\end{document}
Modified: pkg/vegan/inst/doc/diversity-vegan.Rnw
===================================================================
--- pkg/vegan/inst/doc/diversity-vegan.Rnw 2013-07-12 12:19:57 UTC (rev 2561)
+++ pkg/vegan/inst/doc/diversity-vegan.Rnw 2013-07-13 19:59:23 UTC (rev 2562)
@@ -1,39 +1,14 @@
% -*- mode: noweb; noweb-default-code-mode: R-mode; -*-
%\VignetteIndexEntry{Diversity analysis in vegan}
-\documentclass[article,nojss]{jss}
-\usepackage{veganjss} %% vegan setup
-\usepackage{ucs}
-\usepackage[utf8x]{inputenc}
-\usepackage[T1]{fontenc}
-\usepackage{sidecap}
-\usepackage{amsmath}
-\usepackage{amssymb} % \gtrapprox
-\usepackage[english]{babel} % kluge to avoid visible ~ in Figure~1
+\documentclass[a4paper,10pt]{amsart}
+\usepackage{vegan} %% vegan setup
\title{Vegan: ecological diversity} \author{Jari Oksanen}
-\Abstract{ This document explains diversity related methods in
- \pkg{vegan}. The methods are briefly described, and the equations
- used them are given often in more detail than in their help
- pages. The methods discussed include common diversity indices and
- rarefaction, families of diversity indices, species abundance
- models, species accumulation models and beta diversity, extrapolated
- richness and probability of being a member of the species pool. The
- document is still incomplete and does not cover all diversity
- methods in \pkg{vegan}.}
-\Keywords{diversity, Shannon, Simpson, R{\'e}nyi, Hill number,
- Tsallis, rarefaction, species accumulation, beta diversity, species
- abundance, Fisher alpha, Fisher logarithmic series, Preston
- log-normal model, species abundance models, Whittaker plots,
- extended richness, taxonomic diversity, functional divesity, species
- pool}
-
-%% misuse next for scm data
-\Address{$ $Id$ $
+\date{$ $Id$ $
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}
@@ -47,6 +22,18 @@
options("prompt" = "R> ", "continue" = "+ ")
@
+\maketitle
+\begin{abstract}
+ This document explains diversity related methods in
+ \pkg{vegan}. The methods are briefly described, and the equations
+ used them are given often in more detail than in their help
+ pages. The methods discussed include common diversity indices and
+ rarefaction, families of diversity indices, species abundance
+ models, species accumulation models and beta diversity, extrapolated
+ richness and probability of being a member of the species pool. The
+ document is still incomplete and does not cover all diversity
+ methods in \pkg{vegan}.
+\end{abstract}
\tableofcontents
Modified: pkg/vegan/inst/doc/intro-vegan.Rnw
===================================================================
--- pkg/vegan/inst/doc/intro-vegan.Rnw 2013-07-12 12:19:57 UTC (rev 2561)
+++ pkg/vegan/inst/doc/intro-vegan.Rnw 2013-07-13 19:59:23 UTC (rev 2562)
@@ -1,45 +1,15 @@
% -*- mode: noweb; noweb-default-code-mode: R-mode; -*-
%\VignetteIndexEntry{Introduction to ordination in vegan}
-\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{sidecap}
-\usepackage{amsmath}
-\usepackage[english]{babel} % kluge to avoid visible ~ in Figure~1
+\documentclass[a4paper,10pt]{amsart}
+\usepackage{vegan} % vegan settings
-\renewcommand{\floatpagefraction}{0.8}
-
-
\title{Vegan: an introduction to ordination}
-
\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
-\Address{$ $Id$ $
+\date{$ $Id$ $
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}
@@ -54,6 +24,22 @@
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}
\tableofcontents
\vspace{3ex}
Added: pkg/vegan/inst/doc/vegan.sty
===================================================================
--- pkg/vegan/inst/doc/vegan.sty (rev 0)
+++ pkg/vegan/inst/doc/vegan.sty 2013-07-13 19:59:23 UTC (rev 2562)
@@ -0,0 +1,22 @@
+%% typeset vegan vignettes
+\usepackage{amsmath}
+\usepackage{amssymb}
+\usepackage{ucs}
+\usepackage[utf8x]{inputenc}
+\usepackage[T1]{fontenc}
+\usepackage{sidecap}
+\setlength{\captionindent}{0pt} % sidecap needs this with amsart
+\usepackage[english]{babel} % kluge to avoid visible ~ in Figure~1.
+\renewcommand{\floatpagefraction}{0.8}
+\usepackage{Sweave}
+\usepackage{hyperref}
+%% macros
+\newcommand{\code}[1]{\texttt{#1}}
+\newcommand{\pkg}[1]{\textbf{#1}}
+\newcommand{\proglang}[1]{\textsf{#1}}
+\newcommand{\R}{\proglang{R}}
+\newcommand{\VAR}{\textsf{Var}}
+\newcommand{\COV}{\textsf{Cov}}
+%% smaller examples
+\renewenvironment{Schunk}{\par\small}{}
+
Deleted: pkg/vegan/inst/doc/veganjss.sty
===================================================================
--- pkg/vegan/inst/doc/veganjss.sty 2013-07-12 12:19:57 UTC (rev 2561)
+++ pkg/vegan/inst/doc/veganjss.sty 2013-07-13 19:59:23 UTC (rev 2562)
@@ -1,25 +0,0 @@
-%% macros to typeset vegan vignettes with jss.cls
-
-%% jss.cls does not collect toc info, but we redefine jss section and
-%% subsection commands to add contents line. Line of pdfbookmark can
-%% be removed, since toc is used for the purpose.
-\renewcommand{\jsssec}[2][default]{\vskip \preXLskip%
- %\pdfbookmark[1]{#1}{Section.\thesection.#1}%
- \refstepcounter{section}%
- \addcontentsline{toc}{section}{\protect\numberline{\thesection}#1}%
- \centerline{\textbf{\Large \thesection. #2}} \nopagebreak
- \vskip \postMskip \nopagebreak
-}
-\renewcommand{\jsssubsec}[2][default]{\vskip \preMskip%
- %\pdfbookmark[2]{#1}{Subsection.\thesubsection.#1}%
- \refstepcounter{subsection}%
- \addcontentsline{toc}{subsection}{\protect\numberline{\thesubsection}#1}%
- \textbf{\large \thesubsection. #2} \nopagebreak
- \vskip \postSskip \nopagebreak}
-
-%% do not use inconsolata fonts for code and examples: they are to be
-%% removed from CTAN
-%\usepackage{inconsolata}
-%% smaller examples
-\renewenvironment{Schunk}{\par\small}{}
-
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