[Soiltexture-commits] r88 - in pkg/soiltexture/inst: . doc
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Jan 9 11:08:05 CET 2014
Author: jmoeys
Date: 2014-01-09 11:08:05 +0100 (Thu, 09 Jan 2014)
New Revision: 88
Added:
pkg/soiltexture/inst/text.transf.R
Removed:
pkg/soiltexture/inst/doc/soiltexture_vignette.Rnw
pkg/soiltexture/inst/doc/soiltexture_vignette.bib
pkg/soiltexture/inst/doc/transformations.Rnw
Log:
Deleted: pkg/soiltexture/inst/doc/soiltexture_vignette.Rnw
===================================================================
--- pkg/soiltexture/inst/doc/soiltexture_vignette.Rnw 2014-01-09 10:06:44 UTC (rev 87)
+++ pkg/soiltexture/inst/doc/soiltexture_vignette.Rnw 2014-01-09 10:08:05 UTC (rev 88)
@@ -1,3661 +0,0 @@
-% +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+
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-
-\documentclass[a4paper]{article}
-
-\title{The soil texture wizard:\\R functions for plotting,
- classifying, transforming and exploring soil texture data}
-
-\author{Julien Moeys}
-% In case of changes, also change the 'PDF setup' and
-% 'cited as follow'
-
-
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-% Load Sweave and color, in order to modify
-% sweave's environments:
-
-\RequirePackage{Sweave} % ,sweave,color,placeins,rotating,subfig
-%\usepackage{underscore}
-\SweaveOpts{width=14,height=14,keep.source=TRUE}
-% Also modified in the document
-
-% \VignetteIndexEntry{The soil texture wizard: a tutorial}
-% \VignetteDepends{soiltexture}
-% \VignetteDepends{xtable}
-% \VignetteKeyword{soil}
-% \VignetteKeyword{texture}
-% \VignetteKeyword{plot}
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- frame = leftline, % vert line on the left
- framerule = 0.50mm % width of the vert line
-} %
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-} %
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-% formatcom = \color{blue} % new text color
-% } %
-
-% Modify the spacing between R code and R outputs:
-\fvset{listparameters={\setlength{\topsep}{0pt}}}
-\renewenvironment{Schunk}{\vspace{\topsep}}{\vspace{\topsep}}
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-
-%%% PDF setup -- fill in the title
-% \usepackage[dvipdfm, bookmarks, colorlinks, breaklinks, %
-% pdftitle={The soil texture wizard:R functions for plotting, classifying, transforming and exploring soil texture data},%
-% pdfauthor={Julien MOEYS}]{hyperref}
-% \hypersetup{linkcolor=MidnightBlue, citecolor=MidnightBlue,
-% filecolor=MidnightBlue,urlcolor=MidnightBlue}
-% From: http://malecki.wustl.edu/sweaveTemplate.Rnw
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-% +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+
-% | Beginning of the real document |
-% +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+
-
-% Don't forget to add this to path:
-% C:\Program Files\_SCIENCE\R_PROJECT\share\texmf
-
-\usepackage{Sweave}
-\begin{document}
-\bibliographystyle{plain}
-
-
-% \graphicspath{{INOUT/}}
-
-
-%INVISIBLY sets a few options for Sweave :: KEEP THIS
-<<echo=FALSE>>=
-# Set a few Sweave options:
-options(
- width = 65, # width of R output
- prompt = " ", # Sign preceding R input in R-GUI
- continue = " " # same, but after 2nd line
-) #
-
-# The working directory:
-# setwd("C:/_RTOOLS/SWEAVE_WORK/SOIL_TEXTURES/rforge/pkg/soiltexture/inst/doc/INOUT")
-
-# And load the xtable package:
-if( !"xtable" %in% .packages(all.available = TRUE) )
-{ #
- message( paste( sep = "",
- "The xtable package is not present in your R install:\n",
- "R will now try to connect to one package server\n",
- "and propose you a list of package to download\n",
- "and install: Choose 'xtable' from the list"
- ) ) #
- utils:::menuInstallPkgs()
-} #
-require( "xtable" )
-@
-
-% \SweaveOpts{width=14,height=14,keep.source=TRUE}
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-\maketitle
-
-
-
-% +~~~~~~~~~~~~~~~~~~~~~~~~~~~~+
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-
-
-
-<<echo=FALSE,results=hide,quiet=TRUE>>=
-old.wd <- getwd()
-
-# setwd("C:/_RTOOLS/SWEAVE_WORK/SOIL_TEXTURES/rforge/pkg/soiltexture/inst/doc/INOUT")
-
-#if( !("soiltexture" %in% as.character( installed.packages()[,1] )) )
-#{ #
-# suppressMessages(
-# install.packages(
-# pkgs = "soiltexture"
-# # repos = "http://R-Forge.R-project.org"
-# ) #
-# ) #
-#} #
-
-#require(
-# package = "soiltexture",
-# character.only = TRUE,
-# quietly = TRUE
-#) #
-
-# setwd(old.wd)
-
-library( "soiltexture" )
-@
-
-
-
-% +~~~~~~~~~~~~~~~~~~~~~~~~~~~~+
-% | Front page image:
-
-<<COVERFIG,include=false,echo=FALSE,fig=TRUE>>=
-TT.plot(class.p.bg.col=T,class.sys="USDA.TT",main=NA)
-@
-
-\begin{figure}[b]
-\centering
-\includegraphics{soiltexture_vignette-COVERFIG}
-\end{figure}
-
-\clearpage
-
-% +~~~~~~~~~~~~~~~~~~~~~~~~~~~~+
-% | Table of Content:
-\tableofcontents
-
-
-
-% +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+
-\section{About this document}
-
-
-
-\subsection{Why creating 'The soil texture wizard'?}
-
-\textbf{Officially}: \textit{The Soil Texture Wizard} R functions
-are an attempt to provide a generic toolbox for soil texture data
-in R. These functions can (1) plot soil texture data (2) classify
-soil texture data, (3) transform soil texture data from and to
-different systems of particle size classes, and (4) provide some
-tools to 'explore' soil texture data (in the sense of a
-statistical visual analysis). All there tools are designed to be
-inherently multi-triangles, multi-geometry and multi-particle
-sizes classification\\
-
-\textbf{Officiously}: What was initially a slight reshape of R
-PLOTRIX package (by J. Lemon and B. Bolker), for my personal use%
-\footnote{It was also an excellent way to learn R.},
-to add the French 'Aisne' soil texture triangle, gradually
-skidded and ended up in a totally reshaped and extended code
-(over a 3 year period). There is unfortunately no compatibility
-at all between the two codes.\\
-
-
-
-\subsection{About R}
-
-
-This document is about functions (and package project) written in
-R "language and environment for statistical computing" (\texttt{http://www.R-project.org})
-(\cite{RDCT2009}), and has been generated with
-\Sexpr{R.Version()$version.string}.\\
-
-R website: <\texttt{http://www.R-project.org}>\\
-
-If you don't know about R, it is never too later to start...\\
-
-
-
-\subsection{About the author}
-
-I am an agriculture engineer, soil scientist and R programmer.
-See my website for more details (\texttt{http://julienmoeys.free.fr/}).\\
-
-The R functions presented in this document may not always conform
-to the 'best R programming practices', they are nevertheless
-programmed carefully, well checked, and should work efficiently
-for most uses.\\
-
-At this stage of development, some bugs should still be expected.
-The code has been written in 3 years, and tested quite extensively
-since then, but it has never been used by other people. If you
-find some bugs, please contact me at: \texttt{jules\_78-soiltexture at AT@yahoo.fr}.
-
-
-% \begin{figure}[h]
-% \centering
-% \includegraphics[width=108px,viewport=0 0 382 25]{%
-% julienmoeysmailaddress-382-25.png}
-% \end{figure}
-
-
-
-\subsection{Credits and License}
-
-This document, as well as this \textbf{document} source code
-(written in Sweave \footnote{\texttt{http://en.wikipedia.org/wiki/Sweave}},
-R \footnote{\texttt{http://www.r-project.org}} and
-\LaTeX \footnote{\texttt{http://en.wikipedia.org/wiki/LaTeX}}) are
-licensed under a \textbf{Creative
-Commons By-SA 3.0 unported \footnote{\texttt{http://creativecommons.org/licenses/by-sa/3.0/}}}.
-
-
-% \begin{figure}[h]
-% \centering
-% \includegraphics[width=88px,viewport=0 0 88 31]{%
-% CC-By-SA-nonported-88x31.PNG}
-% \end{figure}
-
-
-In short, this means (\textit{extract from the abovementioned url at
-creativecommons.org}):
-
-\begin{itemize}
- \item You are free to:
- \begin{itemize}
- \item \textbf{to Share} - to copy, distribute and
- transmit the work;
- \item \textbf{to Remix} - to adapt the work.
- \end{itemize}
- \item Under the following conditions:
- \begin{itemize}
- \item \textbf{Attribution} - You must attribute the work
- in the manner specified by the author or licensor (but
- not in any way that suggests that they endorse you or
- your use of the work);
- \item \textbf{Share Alike} - If you alter, transform, or
- build upon this work, you may distribute the resulting
- work only under the same, similar or a compatible
- license.
- \end{itemize}
-\end{itemize}
-
-'The soil texture wizard' R \textbf{functions} are licensed under
-a Affero GNU General Public License Version 3 (\texttt{http://www.gnu.org/licenses/agpl.html}).\\
-
-Given the fact that a lot of the work presented here has been done
-on my free time, and given its highly permissive license, \textbf{%
-this document is provided with NO responsibilities, guarantees or
-supports from the author or his employer} (Swedish University of
-Agricultural Sciences).\\
-
-Please notice that the R software itself is licensed under a GNU
-General Public License Version 2, June 1991.\\
-
-This tutorial has been created with the (great) \textbf{Sweave}
-tool, from Friedrich Leisch (\cite{SWEAVE2002}). Sweave allows the
-smooth integration of R code and R output (including figures) in
-a \LaTeX document.
-
-
-
-% +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+
-\section{Introduction: About soil texture, texture triangles
- and texture classifications}
-
-
-
-% +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+
-\subsection{What are soil granulometry and soil texture(s)?}
-
-\textbf{Soil granulometry} is the repartition of soil solid
-particles between (a range of) particle sizes. As the range of
-particle sizes is in fact continuous, they have been subdivided
-into different \textbf{particle size classes}.\\
-
-The most common subdivision of soil granulometry into classes is
-the \textbf{fine earth}, for particles ranging from \textbf{0 to
-2mm (2000$\mu$m)}, and \textbf{coarse particles}, for
-particles bigger than \textbf{2mm}. Only the fine earth interests
-us in this document, although the study of soil granulometry can
-be extended to the coarse fraction (for stony soils).\\
-
-\textbf{Fine earth} is generally (but not always; see below) divided
-into \textbf{3 particle size classes: clay (fine particles), silt
-(medium size particles) and sand (coarser particles in the fine
-earth)}. All soil scientists use the range \textbf{0-2$\mu$m} for
-\textbf{clay}. So silt lower limit is also always
-\textbf{2$\mu$m}. But the convention for \textbf{silt / sand}
-particle size limit \textbf{varies from country to country}.
-\textbf{Silt} particle size range can be \textbf{2-20$\mu$m}
-(Atterberg system\cite{MINASNY2001AJSR}\cite{RICHER2008INRA};
-'International system'; ISSS\footnote{ISSS: International Society
-of Soil Science. Now IUSS (\texttt{www.iuss.org}), International
-Union of Soil Science}\label{ISSSSIZE}. The ISSS particle size
-system should not be confused with the ISSS texture triangle (See
-\ref{ISSSTRIANGLE}, p. \pageref{ISSSTRIANGLE}); Australia\footnote{%%%
-Strangely, only a
-small number of countries have adopted the so called
-'international system'}\cite{MINASNY2001AJSR}; Japan%
-\cite{RICHER2008INRA}), \textbf{2-50$\mu$m} (FAO\footnote{%
-Food and Agriculture Organization of the United Nations
-(\texttt{www.fao.org})}; USA; France\cite{MINASNY2001AJSR}%
-\cite{RICHER2008EGS}), \textbf{2-60$\mu$m}
-(UK and Sweden\cite{RICHER2008INRA}) or \textbf{2-63$\mu$m}
-(Germany, Austria, Denmark and The Netherlands%
-\cite{RICHER2008INRA}). Logically, \textbf{sand} particle size
-range also varies accordingly to these systems:
-\textbf{20-2000$\mu$m}, \textbf{50-2000$\mu$m},
-\textbf{60-2000$\mu$meters} or \textbf{63-2000$\mu$meters}.\\
-
-\textbf{Silt} class is sometimes divided into \textbf{fine silts}
-and \textbf{coarse silts}, and \textbf{sand} class is sometimes
-divided into \textbf{fine sand} and \textbf{coarse sand}, but in
-this document / package, we only focus on clay / silt / sand
-classes.\\
-
-Below is a scheme representing the different particle size
-classes used in France (with Cl for Clay, FiSi for Fine Silt,
-CoSi for Coarse Silt, FiSa for Fine Sand, CoSa for Coarse Sand,
-Gr for Gravels and St for Stones). The figure is adapted
-from Moeys 2007\cite{MOEYS2007}, and based on information from
-Baize \& Jabiol 1995\cite{BAIZE1995}. The particle size axis
-(abscissa) is log-scale:
-
-
-\SweaveOpts{width=14,height=4,keep.source=TRUE}
-<<echo=FALSE,fig=TRUE,include=TRUE>>=
-bornes <- c(0,2,20,50,200,2e3,20e3)
-noms <- c("Cl","FiSi","CoSi","FiSa","CoSa","Gr","St")
-txt.b <- expression( 0*mu*m, 2*mu*m, 20*mu*m, 50*mu*m, 200*mu*m, 2*'mm', 2*'cm')
-
-tmp <- data.frame(bornes,noms) # ,txt.b
-#tmp$"txt.b" <- as.character(tmp$"txt.b")
-
-par( "mar"=c(4,1,1,1)+0.1 ) # c(bottom, left, top, right)
-
-plot(
- x = tmp$"bornes"[-1],
- y = rep(1,dim(tmp[-1,])[1]),
- type = "n",
- main = "",
- xlab = "Soil particule sizes",
- ylab = "",
- yaxt = "n", xaxt = "n",
- log = "x",
- xlim = c(0.2,75e3),
- bty = "n",
- cex.lab = 2
-) #
-
-abline(v=tmp$"bornes",lty=3,lwd=c(2,4,2,4,2,4,2))
-abline(h=par("usr")[3:4],lty=1,lwd=4)
-
-mtext(
- text = txt.b[-1],
- side = 1,
- line = rep(
- c(0.5,1.25),
- (dim(tmp)[1]-1)/2
- ), #
- at = tmp$"bornes"[-1],
- cex = 2
-) #
-
-xtxt <- (tmp$"bornes"[1:(length(tmp$"bornes"))]+c(tmp$"bornes"[2:length(tmp$"bornes")],75e3))/2
-
-text(x=xtxt,y=rep(1,length(xtxt)),labels=tmp$"noms",cex=2)
-@
-\SweaveOpts{width=14,height=14,keep.source=TRUE}
-
-
-Soil particles -- and each soil particle size class -- occupy a
-given volume in the soil, and have a given mass. They are
-nevertheless generally not expressed as 'absolute' volumetric
-quantities\footnote{for instance kilograms of clay per liters of
-soil', or 'liters of clay per liter of soil'}. They are expressed
-as \textbf{'relative abundance'}, that is \textbf{kilograms of
-particles of a given class per kilograms of fine earth}. These
-measurements are also always made on dehydrated soil samples
-(dried slightly above $100^{\circ}\mathrm{C}$), in order to be
-independent from soil water content (which varies a lot in time
-and space).\\
-
-\textbf{Soil texture} is defined as the relative abundance of the
-3 particle size classes: clay, silt and sand\footnote{But some
-systems define for than 3 particle size classes for soil texture}.\\
-
-\textit{In summary}, important information to know when talking
-about soil texture (and using these functions):
-
-\begin{itemize}
- \item Soil's fine earth is generally (but not always) divided
- into 3 soil texture classes:
- \begin{itemize}
- \item Clay;
- \item Silt;
- \item Sand.
- \end{itemize}
- \item The silt / sand limit varies:
- \begin{itemize}
- \item 20$\mu$m; or
- \item 50$\mu$m; or
- \item 60$\mu$m; or
- \item 63$\mu$m.
- \end{itemize}
- \item Soil texture measurement do have a specific unit and a
- corresponding 'sum of the 3 texture classes', that is
- constant:
- \begin{itemize}
- \item in \% or $g.100g^{-1}$ (sum: 100); or
- \item in fraction $[-]$ or $kg.kg^{-1}$ (sum: 1); or
- \item in $g.kg^{-1}$ (sum: 1000);
- \end{itemize}
-\end{itemize}
-
-
-\textbf{More than 3 particle size classes?}\\
-
-Some country have a particle size classes system that differ from
-the common 'clay silt sand' triplet. Sweden is using a system
-with 4 particle size classes: Ler [0-2$\mu$m], Mj\"ala [2-20$\mu$m],
-Mo [20-200$\mu$m] and Sand [200-2000$\mu$m] (See table 1 p.9 in
-Lidberg 2009\cite{LIDBERG2009}).
-Ler corresponds to clay. When considering the International or
-Australian particle size system (silt-sand limit 20$\mu$m), Mj\"ala
-is silt, and 'Mo + Sand' is sand. When considering other systems
-with a silt-sand limit at 50$\mu$m, 60$\mu$m or 63$\mu$m, Mj\"ala
-is ~fine-silt, Mo is ~'coarse-silt + fine sand', and Sand is
-~coarse-sand.\\
-
-'The Soil Texture Wizard' has been made for systems with 3
-particle size classes (clay, silt and sand), \textbf{because soil
-texture triangles have 3 sides, and thus can only represent
-texture data that are divided into 3 particle size classes}.
-There are methods to estimate 3 particle size classes when more
-classes are presented in the data (although the best is to
-measure texture so it also can fit a system with 3 particle size
-classes system).
-
-
-
-% +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+
-\subsection{What are soil texture triangle and classes}
-
-Soil texture triangles are also called \textbf{soil texture
-diagrams}.\\
-
-Soil texture can be plotted on a \textbf{ternary plot} (also
-called triangle plot). In a ternary plot, 3D coordinates, which
-sum is constant, are projected in the 2D space, using simple
-trigonometry rules. The texture of a soil sample can be plotted
-inside a texture triangle, as shown in the example below for
-the texture 45\% clay, 38\% silt and 17\% sand:
-
-
-<<echo=FALSE,fig=TRUE,include=TRUE>>=
-TT.plot(
- class.sys = "none",
- tri.data = data.frame(
- "CLAY" = 45,
- "SILT" = 38,
- "SAND" = 17
- ), #
- main = NA
-) #
-@
-
-
-When mapping soil, field pedologists usually estimate texture by
-manipulating a moist (but not saturated) soil sample in their
-hand. Depending on the relative importance of clay silt and sand,
-the mechanical properties of the soil (plasticity, stickyness,
-roughness) varies. Pedologists have 'classified' clay silt and
-sand relative abundance as a function of what they could feel in
-the field: they have divided the 'soil texture space' into
-classes.\\
-
-\textbf{Soil particle size classes (clay, silt and sand)} should
-not be confused with \textbf{soil texture classes}. While the
-first are ranges of particle sizes, the latter are defined by a
-'range of clay, silt and sand' (see the graph below). Soil
-texture should not be confused with the concept of \textbf{soil
-structure}, that concerns the way these particles are arranged
-together (or not) into peds, clods and aggregates (etc.) of
-different size and shape\footnote{In the same way bricks and
-cement (the texture) can be arranged into a house (the structure)}.
-This document does not deal with soil structure.\\
-
-Soil texture classes are convenient to represent soil texture
-on soil maps\footnote{It is more easy to represent 1 variable,
-soil texture class, than 3 variables: clay silt and sand}, and
-there use is quite broad (soil description, soil classification,
-pedogenesis, soil functional properties, pedotransfer functions,
-etc.). One of these texture classification systems is the FAO
-system. Here is the representation of the same point as in the
-graph above, but with the FAO soil classification system on the
-background.
-
-<<echo=FALSE,fig=TRUE,include=TRUE>>=
-TT.plot(
- class.sys = "FAO50.TT",
- tri.data = data.frame(
- "CLAY" = 45,
- "SILT" = 38,
- "SAND" = 17
- ), #
- main = NA
-) #
-@
-
-The soil texture class symbols are:
-
-<<echo=FALSE>>=
-library( "xtable" )
-@
-
-<<echo=FALSE,results=tex>>=
-tex.tbl <- TT.classes.tbl( class.sys = "FAO50.TT" )
-xtable(
- x = tex.tbl[,-3], #
- caption = "Texture classes of the FAO system / triangle",
- label = NULL
-) #
-@
-
-The main characteristics of the graph (texture triangle) are:
-
-\begin{itemize}
- \item 3 Axis, graduated from 0 to 100\%, each of them
- carrying 1 particle size class.
- \begin{itemize}
- \item Sand on the bottom axis;
- \item Clay on the left axis;
- \item Silt on the right axix.
- \end{itemize}
- \item It is possible to permute clay, silt and sand axis, but
- this choice depend on the particle size classification used.
- \item Inside the triangle, the lines of equi-values for a
- given axis/particle size class are ALWAYS parallel to the
- (other) axis that intersect the axis of interest at 'zero'
- (minimum value).
- \item The 3 axis intersect each other in 3 submits, that are
- characterized by an \textbf{angle}. In the example above, all
- 3 angles are 60 degrees. But other angles are possible,
- depending on the soil texture classification used. It is for
- instance possible to have a 90 degrees angle on the left, and
- 45 degrees angles on the top and on the right (right-angled
- triangle).
- \item The 3 axis have a \textbf{direction} of increasing
- texture abundance. This direction is often referred as
- 'clock' or 'anticlock', but they can also be directed 'inside'
- the triangle in some cases. In the example
- above, all the axis are clockwise: texture increase when
- rotating in the opposite direction as a clock.
- \item \textbf{Labeled ticks} are placed at regular intervals
- (10\%) on the texture triangle axes, apart if the axis is
- directed inside the triangle. Ticks can be placed at irregular
- intervals if they are placed at each value taken by the
- texture class polygons vertices (This is a smart
- representation, unfortunately not implemented here).
- \item An \textbf{broken arrow} is drawn 'parallel' to each
- axis. The first part indicate the direction of increasing
- value, and the second, broken, part indicates the direction of
- the equi-value for that axis/texture class.
- \item The \textbf{axis labels} indicates the texture class
- concerned, and should ideally remind the particle size limits,
- because these limits are of crucial importance when (re)using
- soil texture data (Silt and Sand does not exactly mean the
- same particle size limits everywhere).
- \item \textbf{Soil texture class boundaries} are drawn inside
- the triangle. They are 2D representation of 3D limits. They
- are generally \textbf{labeled} with soil texture class
- abbreviations (or full names).
- \item Inside the triangle frame, a grid can be represented,
- for each ticks and ticks label drawn outside the triangle.
-\end{itemize}
-
-
-
-% +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+
-\section{Installing the package}
-
-
-
-% +~~~~~~~~~~~~~~~~~~~~~~~~~~~~+
-\subsection{Installing the package from r-forge}
-
-
-The Soil Texture Wizard is now available on CRAN
-\footnote{\texttt{http://cran.r-project.org/package=soiltexture}}
-and r-forge \footnote{\texttt{http://r-forge.r-project.org/}}, under
-the project name "soiltexture". The package can be installed from
-CRAN with the following commands:
-
-
-<<echo=TRUE,eval=FALSE>>=
-install.packages( pkgs = "soiltexture" )
-@
-
-
-And \textbf{if you have the latest R version} installed, and want
-the latest development version of the package, from r-forge, type
-the following commands:
-
-
-<<echo=TRUE,eval=FALSE>>=
-install.packages(
- pkgs = "soiltexture",
- repos = "http://R-Forge.R-project.org"
-) #
-@
-
-
-It can then be loaded with the following command:
-
-
-<<echo=TRUE>>=
-require( soiltexture )
-@
-
-
-If you get bored of the package, you can unload it and uninstall
-it with the following commands:
-
-
-<<echo=TRUE,eval=FALSE>>=
-detach( package:soiltexture )
-remove.packages( "soiltexture" )
-@
-
-
-If you don't have the latest R version, please try to install the
-package from the binaries. In the next section, an example is given
-for R under MS Windows systems (Zip binaries).
-
-
-
-% % +~~~~~~~~~~~~~~~~~~~~~~~~~~~~+
-% \subsection{Installing the package from Windows binaries (.zip)}
-
-
-% To install and load the package directly from
-% \href{"http://r-forge.r-project.org/bin/windows/contrib/2.10/soiltexture_1.0.zip"}%%%
-% {r-forge zip binaries},
-% you can type the following command:
-
-
-% <<echo=TRUE,eval=FALSE>>=
-% download.file(
-% url =
-% "http://r-forge.r-project.org/bin/windows/contrib/2.10/soiltexture_1.0.zip",
-% destfile = file.path( getwd(), "soiltexture_1.0.zip" )
-% ) #
-% #
-% install.packages(
-% pkgs = file.path( getwd(), "soiltexture_1.0.zip" ),
-% repos = NULL
-% ) #
-% #
-% file.remove( "soiltexture_1.0.zip" )
-% @
-
-
-% \textbf{Where 2.10 should be replaced by the latest stable R
-% version and 1.0 by the latest package version on r-forge}.
-
-
-
-% % +~~~~~~~~~~~~~~~~~~~~~~~~~~~~+
-% \subsection{Load the latest package sources}
-
-
-% If all the options above failed to intall the soiltexture package,
-% you can still load the
-% \href{http://r-forge.r-project.org/plugins/scmsvn/viewcvs.php/*checkout*/pkg/soiltexture/R/soiltexture.r?root=soiltexture}%%%
-% {latest package sources} in R by using the
-% following command:
-
-
-% <<echo=TRUE,eval=FALSE>>=
-% source(
-% paste(
-% sep = "",
-% "http://r-forge.r-project.org/scm/viewvc.php/*checkout*",
-% "/pkg/soiltexture/R/soiltexture.R?&root=soiltexture"
-% ) #
-% ) #
-% @
-
-
-% The examples shown in this vignette are ran with these sources.
-
-
-
-% % +~~~~~~~~~~~~~~~~~~~~~~~~~~~~+
-% \subsection{Set the work directory}
-
-
-% Here is the working directory we are using in this package vignette
-% (choose the one you like...):
-
-% <<echo=TRUE>>=
-% # setwd("C:/_RTOOLS/SWEAVE_WORK/SOIL_TEXTURES/rforge/pkg/soiltexture/inst/doc/INOUT")
-% @
-
-
-
-% +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+
-\section{Plotting soil texture triangles and classification
- systems}
-
-The package comes with 8 predefined soil texture triangles. Empty %%% THINGS TO CHECK HERE: NB TRIANGLES
-(i.e. without soil textures data) soil texture triangles can be
-plotted, in order to obtain smart representation of the soil
-texture classification. Of course, it is also possible to plot
-'classification free' texture triangles.
-
-
-
-% +~~~~~~~~~~~~~~~~~~~~~~~~~~~~+
-\subsection{An empty soil texture triangle}
-
-Below is the code to display an empty triangle (without
-classification and without data):
-
-
-<<echo=TRUE,fig=TRUE,include=TRUE>>=
-TT.plot( class.sys = "none" )
-@
-
-
-The option \texttt{class.sys} (characters) determines the soil
-texture classification system used. If set to \texttt{'none'},
-an empty soil texture triangle is plotted.\\
-
-Without further options, the plotted default soil texture
-triangle has the same geometry as the FAO, USDA or French 'Aisne'
-soil texture triangles (i.e. all axis are clockwise, all angles
-are 60 degrees, sand is on the bottom axe, clay on the left and
-silt on the right).\\
-
-The default unit is always percentage (0 to 100\%). It is also
-equivalent to $g.100g^{-1}$.
-
-
-
-% +~~~~~~~~~~~~~~~~~~~~~~~~~~~~+
-\subsection{The USDA soil texture classification}
-
-To display a USDA texture triangle, type:
-
-
-<<echo=TRUE,fig=TRUE,include=TRUE>>=
-TT.plot( class.sys = "USDA.TT" )
-@
-
-
-When the option \texttt{class.sys} is set to \texttt{"USDA.TT"},
-a soil texture triangle with USDA classification system is used.\\
-
-The USDA soil texture triangle has been built considering a
-silt - sand limit of
-\Sexpr{TT.get("USDA.TT")[["base.css.ps.lim"]][3]}$\mu$meters.\\
-
-See the table for soil texture classes symbols.\\
-
-
-<<echo=FALSE,results=tex>>=
-tex.tbl <- TT.classes.tbl( class.sys = "USDA.TT" )
-xtable(
- x = tex.tbl[,-3], #
- caption = "Texture classes of the USDA system / triangle",
- label = NULL
-) #
-@
-
-
-The reference used to digitize this triangle is the Soil Survey
-Manual (Soil Survey Staff 1993\cite{USDA1993}).
-
-\clearpage % otherwise the table may 'eats' next triangle
-
-
-
-% +~~~~~~~~~~~~~~~~~~~~~~~~~~~~+
-\subsection{The FAO soil texture classification (also known as
- 'European Soil map', or 'HYPRES')}
-
-To display a FAO / HYPRES texture triangle, type:
-
-
-<<echo=TRUE,fig=TRUE,include=TRUE>>=
-TT.plot( class.sys = "FAO50.TT" )
-@
-
-
-De Forges et al. 2008\cite{RICHER2008EGS} pointed out the fact
-that the silt-sand particle size limit that is officially related
-to the FAO soil texture triangle has changed over time, 50$\mu$m,
-then 63$\mu$m, and then again 50$\mu$m for some projects.
-We here consider that the FAO / EU Soil map / HYPRES soil texture
-triangle has a silt - sand limit of
-\Sexpr{TT.get("FAO50.TT")[["base.css.ps.lim"]][3]}$\mu$m. As this
-choice is somehow arbitrary, we have named the 'FAO' option
-\texttt{"FAO50.TT"} in order to avoid any confusion. It will be
-explained later in the document how it is possible to add a custom
-texture triangle to the existing list, that could for instance be
-used to configure an FAO texture triangle with another silt -
-sand limit.\\
-
-See the table for soil texture classes symbols.\\
-
-
-<<echo=FALSE,results=tex>>=
-tex.tbl <- TT.classes.tbl( class.sys = "FAO50.TT" )
-xtable(
- x = tex.tbl[,-3], #
- caption = "Texture classes of the FAO system / triangle",
- label = NULL
-) #
-@
-
-
-The references used to digitize this triangle is the texture
-triangle provided by the HYPRES project web site
-(\cite{HYPRES2009}). The The Canadian Soil Information System
-(CanSIS) also provides some details on this triangle
-(\cite{CANSIS2009}).
-
-\clearpage % otherwise the table may 'eats' next triangle
-
-
-
-% +~~~~~~~~~~~~~~~~~~~~~~~~~~~~+
-\subsection{The French 'Aisne' soil texture classification}
-
-To display a French 'Aisne' texture triangle, type:
-
-
-<<echo=TRUE,fig=TRUE,include=TRUE>>=
-TT.plot( class.sys = "FR.AISNE.TT" )
-@
-
-
-The French Aisne soil texture triangle has been built
-considering a silt - sand limit of
-\Sexpr{TT.get("FR.AISNE.TT")[["base.css.ps.lim"]][3]}$\mu$meters.\\
-
-See the table for soil texture classes symbols\footnote{In
-classes 14 and 15, 'leger' should be replaced by 'l\'eger'. R (and
-Sweave) can not display french accents easily, and I found no easy
-trics for displaying them.}.\\
-
-
-<<echo=FALSE,results=tex>>=
-tex.tbl <- TT.classes.tbl( class.sys = "FR.AISNE.TT" )
-xtable(
- x = tex.tbl[,-3], #
- caption = "Texture classes of the French 'Aisne' system / triangle",
- label = NULL
-) #
-@
-
-The references used for digising this triangle is Baize and
-Jabiol 1995\cite{BAIZE1995} and Jamagne 1967\cite{JAMAGNE1967}.
-This triangle may be referred as the 'Triangle des textures de la
-Chambre d'Agriculture de l'Aisne' (en: texture triangle of the
-Aisne extension service).
-
-\clearpage % otherwise the table may 'eats' next triangle
-
-
-
-% +~~~~~~~~~~~~~~~~~~~~~~~~~~~~+
-\subsection{The French 'GEPPA' soil texture classification}
-
-To display a French 'GEPPA' texture triangle, type:
-
-
-<<echo=TRUE,fig=TRUE,include=TRUE>>=
-TT.plot( class.sys = "FR.GEPPA.TT" )
-@
-
-
-The French GEPPA soil texture triangle has been built
-considering a silt - sand limit of
-\Sexpr{TT.get("FR.GEPPA.TT")[["base.css.ps.lim"]][3]}$\mu$meters.\\
-
-See the table for soil texture classes symbols.\\
-
-
-<<echo=FALSE,results=tex>>=
-tex.tbl <- TT.classes.tbl( class.sys = "FR.GEPPA.TT" )
-xtable(
- x = tex.tbl[,-3], #
- caption = "Texture classes of the French 'GEPPA' system / triangle",
- label = NULL
-) #
-@
-
-
-This triangle has been digitized after
-\texttt{sols-de-bretagne.fr} 2009\cite{SOLBRETAGNE2009}. The
-website refers to an illustration from Baize and Jabiol 1995%
-\cite{BAIZE1995}. 'GEPPA' means 'Groupe d'Etude pour les
-Probl\`emes de P\'edologie Appliqu\'ee' (en: Group for the study of
-applied pedology problems / questions).
-
-\clearpage % otherwise the table may 'eats' next triangle
-
-
-
-% +~~~~~~~~~~~~~~~~~~~~~~~~~~~~+
-\subsection{The German Bodenartendiagramm (B.K. 1994) soil
- texture classification}
-
-To display a German Bodenartendiagramm (BK 1994) texture triangle,
-type:
-
-
-<<echo=TRUE,fig=TRUE,include=TRUE>>=
-TT.plot( class.sys = "DE.BK94.TT" )
-@
-
-
-The German Bodenartendiagramm (BK 1994) soil texture triangle has
-been built considering a silt - sand limit of
-\Sexpr{TT.get("DE.BK94.TT")[["base.css.ps.lim"]][3]}$\mu$meters.\\
-
-See the table for soil texture classes symbols.\\
-
-
-<<echo=FALSE,results=tex>>=
-tex.tbl <- TT.classes.tbl( class.sys = "DE.BK94.TT" )
-xtable(
- x = tex.tbl[,-3], #
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/soiltexture -r 88
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