81 lines
2.6 KiB
Plaintext
81 lines
2.6 KiB
Plaintext
%\VignetteIndexEntry{Partition of Variation}
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%% This file rewrites Pierre Legendre's introduction and takes pages
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%% of Pierre Legendre's pdf documents and puts them together.
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\documentclass[10pt]{article}
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\usepackage{vegan} %% vegan setup
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\usepackage{pdfpages}
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\setkeys{Gin}{width=0.6\linewidth}
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\title{Diagrams and Procedures for Partition of Variation}
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\author{Pierre Legendre}
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\date{\footnotesize{
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processed with vegan \Sexpr{packageDescription("vegan", field="Version")}
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in \Sexpr{R.version.string} on \today}}
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\begin{document}
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%% Sweave document
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\SweaveOpts{strip.white=true}
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<<echo=false>>=
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par(mfrow=c(1,1))
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figset <- function() par(mar=c(4,4,1,1)+.1)
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options(SweaveHooks = list(fig = figset))
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library(vegan)
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labs <- paste("Table", 1:4)
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cls <- c("hotpink", "skyblue", "orange", "limegreen")
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@
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\maketitle
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\noindent Diagrams describing the partitions of variation of a
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response data table by two (Fig.~\ref{fig:part2}), three
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(Fig.~\ref{fig:part3}) and four tables (Fig.~\ref{fig:part4}) of
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explanatory variables. The fraction names [a] to [p] in the output of
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\code{varpart} function follow the notation in these Venn diagrams,
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and the diagrams were produced using the \code{showvarparts} function.
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%%%%%%%%%%%%%%%
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\begin{figure}[!ht]
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<<echo=FALSE,fig=TRUE>>=
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showvarparts(2, bg = cls, Xnames=labs)
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@
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\caption{3 regression/ canonical analyses and 3 subtraction equations
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are needed to estimate the $4\;(=2^2)$ fractions.
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[a] and [c] can be tested for significance (3 canonical analyses per
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permutation). Fraction [b] cannot be tested singly.}
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\label{fig:part2}
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\end{figure}
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%%%%%%%%%%%
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\begin{figure}[!ht]
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<<echo=FALSE,fig=TRUE>>=
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showvarparts(3, bg = cls, Xnames=labs)
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@
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\caption{7 regression/ canonical analyses and 10 subtraction equations
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are needed to estimate the $8\;(=2^3)$ fractions.
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[a] to [c] and subsets containing [a] to [c] can be tested for
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significance (4 canonical analyses per permutation to test [a] to
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[c]). Fractions [d] to [g] cannot be tested singly.}
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\label{fig:part3}
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\end{figure}
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%%%%%%%%%%%
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\begin{figure}[!ht]
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<<echo=FALSE,fig=TRUE>>=
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showvarparts(4, bg = cls, Xnames=labs)
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@
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\caption{15 regression/ canonical analyses and 27 subtraction equations
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are needed to estimate the $16\;(=2^4)$ fractions.
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[a] to [d] and subsets containing [a] to [d] can be tested for
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significance (5 canonical analyses per permutation to test [a] to
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[d]). Fractions [e] to [o] cannot be tested singly.}
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\label{fig:part4}
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\end{figure}
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\clearpage
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\setkeys{Gin}{width=\paperwidth}
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%% Add partitioning models 2-3 and 4.
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\includepdf[fitpaper=true,pages=-]{varpart23.pdf}
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\includepdf[fitpaper=true, pages=-]{varpart4.pdf}
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\end{document}
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