[Soiltexture-commits] r80 - / pkg/soiltexture pkg/soiltexture/R pkg/soiltexture/inst/doc pkg/soiltexture/man pkg/soiltexture/tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Sep 12 18:14:49 CEST 2012
Author: jmoeys
Date: 2012-09-12 18:14:49 +0200 (Wed, 12 Sep 2012)
New Revision: 80
Added:
pkg/soiltexture/NEWS
Modified:
1_RCMDBUILD.bat
pkg/soiltexture/DESCRIPTION
pkg/soiltexture/R/soiltexture.R
pkg/soiltexture/inst/doc/soiltexture_vignette.Rnw
pkg/soiltexture/man/TT.DJ.col.Rd
pkg/soiltexture/man/TT.add.Rd
pkg/soiltexture/man/TT.auto.set.Rd
pkg/soiltexture/man/TT.axis.arrows.Rd
pkg/soiltexture/man/TT.baseplot.Rd
pkg/soiltexture/man/TT.blr.ps.lim.Rd
pkg/soiltexture/man/TT.blr.tx.check.Rd
pkg/soiltexture/man/TT.check.ps.lim.Rd
pkg/soiltexture/man/TT.check.ps.lim.Xm.Rd
pkg/soiltexture/man/TT.chemometrics.alr.Rd
pkg/soiltexture/man/TT.classes.Rd
pkg/soiltexture/man/TT.classes.tbl.Rd
pkg/soiltexture/man/TT.col2hsv.Rd
pkg/soiltexture/man/TT.contour.Rd
pkg/soiltexture/man/TT.css2xy.Rd
pkg/soiltexture/man/TT.data.test.Rd
pkg/soiltexture/man/TT.data.test.X.Rd
pkg/soiltexture/man/TT.dataset.Rd
pkg/soiltexture/man/TT.deg2rad.Rd
pkg/soiltexture/man/TT.dia2phi.Rd
pkg/soiltexture/man/TT.edges.Rd
pkg/soiltexture/man/TT.gen.op.set.Rd
pkg/soiltexture/man/TT.geo.get.Rd
pkg/soiltexture/man/TT.geo.set.Rd
pkg/soiltexture/man/TT.get.Rd
pkg/soiltexture/man/TT.grid.Rd
pkg/soiltexture/man/TT.ifelse.Rd
pkg/soiltexture/man/TT.image.Rd
pkg/soiltexture/man/TT.iwd.Rd
pkg/soiltexture/man/TT.kde2d.Rd
pkg/soiltexture/man/TT.lines.Rd
pkg/soiltexture/man/TT.locator.Rd
pkg/soiltexture/man/TT.mahalanobis.Rd
pkg/soiltexture/man/TT.normalise.sum.Rd
pkg/soiltexture/man/TT.normalise.sum.X.Rd
pkg/soiltexture/man/TT.par.op.set.Rd
pkg/soiltexture/man/TT.phi2dia.Rd
pkg/soiltexture/man/TT.plot.Rd
pkg/soiltexture/man/TT.points.Rd
pkg/soiltexture/man/TT.points.in.classes.Rd
pkg/soiltexture/man/TT.polygon.area.Rd
pkg/soiltexture/man/TT.polygon.centroids.Rd
pkg/soiltexture/man/TT.set.Rd
pkg/soiltexture/man/TT.str.Rd
pkg/soiltexture/man/TT.switch.Rd
pkg/soiltexture/man/TT.text.Rd
pkg/soiltexture/man/TT.text.transf.Rd
pkg/soiltexture/man/TT.text.transf.X.Rd
pkg/soiltexture/man/TT.text.transf.Xm.Rd
pkg/soiltexture/man/TT.ticks.Rd
pkg/soiltexture/man/TT.ticks.lab.Rd
pkg/soiltexture/man/TT.vertices.plot.Rd
pkg/soiltexture/man/TT.vertices.tbl.Rd
pkg/soiltexture/man/TT.xy.grid.Rd
pkg/soiltexture/man/TT.xy2css.Rd
pkg/soiltexture/man/soiltexture-package.Rd
pkg/soiltexture/tests/TT.plot.R
soiltexture_compile.R
soiltexture_transformations_compile.R
Log:
New version of the Australian texture triangle
Modified: 1_RCMDBUILD.bat
===================================================================
--- 1_RCMDBUILD.bat 2012-03-08 10:35:18 UTC (rev 79)
+++ 1_RCMDBUILD.bat 2012-09-12 16:14:49 UTC (rev 80)
@@ -2,5 +2,5 @@
cd \
cd "C:\_R_PACKAGES\soiltexture\pkg"
echo R_QPDF="qpdf -dPDFSETTINGS=/ebook"
-R CMD build --compact-vignettes soiltexture
+R CMD build --compact-vignettes="gs" soiltexture
pause
Modified: pkg/soiltexture/DESCRIPTION
===================================================================
--- pkg/soiltexture/DESCRIPTION 2012-03-08 10:35:18 UTC (rev 79)
+++ pkg/soiltexture/DESCRIPTION 2012-09-12 16:14:49 UTC (rev 80)
@@ -1,6 +1,6 @@
Package: soiltexture
-Version: 1.2.9
-Date: 2012-03-07
+Version: 1.2.10
+Date: 2012-09-12
Title: Functions for soil texture plot, classification and transformation
Author: Julien MOEYS <jules_m78-soiltexture at yahoo.fr>, contributions from Wei Shangguan.
Maintainer: Julien MOEYS <jules_m78-soiltexture at yahoo.fr>
Added: pkg/soiltexture/NEWS
===================================================================
--- pkg/soiltexture/NEWS (rev 0)
+++ pkg/soiltexture/NEWS 2012-09-12 16:14:49 UTC (rev 80)
@@ -0,0 +1,165 @@
+The Soil Texture Wizard
+change log. From 2009/10/09. Most recent changes first / on top.
+Julien MOEYS
+-----------------------------------------------------------------------------------------
+
+o version 1.2.10
+
+ 20120912 Implemented a new version of the Australian soil texture classification
+ (AU2.TT)
+
+o version 1.2.9
+
+ 20120307 Removed a useless usage of installed.packages()
+ 20120308 Compact the vignettes before R CMD build
+
+o version 1.2.8
+
+ 20120125 New attempt to fix xtable package dependence in the vignette.
+
+o version 1.2.7
+
+ 20120106 no visible change (fixed package dependance in vignette) + corrected TT.plot()
+ example for Spanish language.
+
+o version 1.2.6
+
+ 20111112 Added the German (GDR) texture triangle for forest soils:
+ "Standortserkundungsanweisung SEA 1974 (DE)"
+
+o older versions
+
+ 20111109 New attempt to fix problems while loading the Polish texture triangle
+ under Mac/Darwin and freeBSD.
+
+ 20111101 Fixed a potential infinite loop problem in the texture transformation
+ functions based on "drc"
+
+ 20111101 Improved handling / loading of the Polish triangle (is not working under
+ Mac). Added the polih triangle to the vignette.
+
+ 20100610 New function TT.polygon.centroids() used for a smater calculation
+ of the texture class centroid for better placement of the texture
+ classes labels (used by TT.classes(), itself used by TT.plot()).
+
+ 20100607 Added the Romanian texture triangle to the list of pre-defined texture
+ triangles, and the Romanian language to the list of possible languages
+ for the texture triangle title and axis labels. many thanks to
+ Rosca Bogdan (Romanian Academy, Iasi Branch, Geography team) for providing
+ the code and translation.
+
+ 20100513 Accuracy problems detected in TT.points.in.classes() for texture data
+ located right on the boundary of the triangle (or some texture classes),
+ with some digits after the decimal: due to non-exact trigonometric
+ calculations (around 1E-15), these points may not be classified
+ as on the border, or even belonging to the texture class. These
+ accuracy problems can be partially fixed by a new parameter of
+ TT.points.in.classes(), 'texture2xy' that can be set to FALSE in
+ order to get more accurate classifications. Other accuracy problems
+ still remains, but this time in the underlying point.in.polygon()
+ function. There is no easy fix to this:
+ <https://stat.ethz.ch/pipermail/r-help/2010-May/239035.html>
+ No fix are planned in the close future to fix this error.
+ Thanks to Wei Shangguan (see below) for pointing this 'bug'.
+
+ 20100513 Added the ISSS (not to be confused with the 'Australian ISSS')
+ texture triangle to the
+ list of pre-defined texture triangles. Many thanks to Wei Shangguan,
+ PhD from the School of geography of Beijing normal university
+ for providing the code of the triangle.
+
+ 20100416 Added the Canadian texture triangle to the list of pre-defined
+ texture triangles.
+
+ 20100409 Created an r-forge page for the package and uploaded it to SCM
+ http://r-forge.r-project.org/scm/?group_id=740
+
+ 20100409 Finished documenting the function TT.plot with inlinedocs. Package
+ successfully compiled.
+
+ 20091221 The parameter 'fg' is now defunct, and replaced by 'col' that accepts
+ several values (while fg only accepts one). 'fg' still exists as an
+ option, but shouldn't produce any effect.
+
+ 20091119 Simplified some redundant code in TT.css2xy(), the function that
+ transforms clay silt sand data into x-y coordinates.
+
+ 20091118 Corrected a bug in the function TT.normalise.sum() (that couldn't
+ handle data.frames)
+
+ 20091014 Added the Belgian soil texture triangle to the list of pre-defined
+ texture triangles (now 8).
+
+ 20091013 The TT.mahalanobis() function can now compute a grid of the Mahalanobis
+ distance on log-ratio trasnformation of soil texture data. New option
+ alr, default = FALSE, can be set to TRUE for alr transformation.
+
+ 20091013 Added TT.chemometrics.alr(), for additive log-ratio trasnformation of
+ soil texture data. This is a copy of the alr() function in the chemometrics
+ package, with minor modifications for soil texture data. Used internally
+ in TT.mahalanobis().
+
+ 20091011 Added TT.normalise.sum(), that normalise the sum of the 3 texture classes
+ to text.sum (100%).
+
+ 20091011 The options 'pow' and 'q.max.dist' are now set to 0.5 and 50 respectively.
+ This is a stronger smoothing than the previous values.
+
+ 20091011 TT.iwd() has now a 'q.max.dist' option user to determin 'max.dist' if this
+ last is set to NULL. max.dist is the maximum euclidian distance, between
+ a grid point and a data point. If the distance between the grid point and
+ the data point is higher than max.dist, this point is not used to calculate
+ the iwd value. max.dist default value is
+ quantile( x = euclidian.distances, probs = q.max.dist )
+
+ 20091011 The option value 'z.type = "map"' is now deprecated in TT.plot(). Replaced
+ by TT.iwd() and TT.image(), called outside TT.plot().
+
+ 20091011 TT.as.image() internal function deprecated. now inside TT.iwd()
+
+ 20091011 TT.image.shade() internal function deprecated. now inside TT.iwd()
+
+ 20091011 TT.iwd.image() renamed to TT.iwd(). The function now output a list with
+ a x y grid and z value matrix, ready to be plotted by TT.image(). The
+ function is not plotting the image any more.
+
+ 20091011 TT.iwd() internal function is deprecated. The name will be attributed to
+ TT.iwd.image()
+
+ 20091010 TT.baseplot() now has a geo option.
+
+ 20091010 TT.kde2d() function created. Wrapper for MASS function kde2d(), but
+ customized for texture triangles. Results can be displayed by
+ TT.contour(), TT.image(), contour() or image().
+
+ 20091010 TT.image() function created. Wrapped for image(), but customized
+ for texture triangles. Used to display x-y-z list data in the same
+ format as 'x' in contour() or image().
+
+ 20091010 TT.contour() function created. Wrapped for contour(), but customized
+ for texture triangles. Used to display x-y-z list data in the same
+ format as 'x' in contour() or image().
+
+ 20091010 TT.mahalanobis() function created. Wrapper for the function mahalanobis(),
+ but customized for texture triangles. Results can be displayed by
+ TT.contour(), TT.image() [see above], contour() or image(). Calculates the
+ Mahalanobis distance for 2 of the 3 texture classes, on a regular x-y grid,
+ backtransformed into clay silt sand, used to calculate the Mahalanobis
+ distance.
+
+ 20091010 Added TT.xy.grid() that generates a regular grid on the
+ x-y axis. Made after part of kde2d
+
+ 20091009 Modified TT.plot() function so it accepts an optionnal 'geo' option and an
+ 'add' option that behaves like plot(add=TRUE) when non-null. This is intended
+ to allow overplotting a soil texture triangle over a background plotted by
+ another function (i.e. heat map, contour map etc.)
+
+ 20091009 Added TT.locator(). This function is equivalent to the locator() function,
+ except that it returns clay silt sand coordinates instead.
+
+ 20091009 Added TT.xy2css() a function to convert x-y coordinates into clay silt sand.
+
+ 20091009 renamed TT.arrows() to TT.axis.arrows().
+
+
Modified: pkg/soiltexture/R/soiltexture.R
===================================================================
--- pkg/soiltexture/R/soiltexture.R 2012-03-08 10:35:18 UTC (rev 79)
+++ pkg/soiltexture/R/soiltexture.R 2012-09-12 16:14:49 UTC (rev 80)
@@ -872,6 +872,63 @@
text.sum = 100
), #
#
+ "AU2.TT" = list( # Australian TRIANGLE PARAMETERS :
+ main = "Autralia (AU)",
+ #
+ # The coordinates of this triangle were kindly provided by Budiman Minasni
+ # as a replacememnt for the original implementation of the Australian
+ # texture triangle.
+ #
+ # The list below specify the CSS coordinates of the different POINTS
+ # that are used to draw soil texture classes. One points can be
+ # used by several classes :
+ # P01 P02 P03 P04 P05 P06 P07
+ # P08 P09 P10 P11 P12 P13 P14
+ # P15 P16 P17 P18 P19
+ "tt.points" = data.frame(
+ "CLAY" = c( 0.510, 0.300, 0.400, 0.750, 1.000, 0.400, 0.260,
+ 0.260, 0.000, 0.000, 0.120, 0.085, 0.000, 0.000,
+ 0.080, 0.100, 0.210, 0.170, 0.260 ),
+ "SILT" = c( 0.000, 0.070, 0.250, 0.250, 0.000, 0.600, 0.740,
+ 0.250, 0.250, 1.000, 0.250, 0.040, 0.075, 0.000,
+ 0.000, 0.130, 0.100, 0.000, 0.000 ),
+ "SAND" = c( 0.490, 0.630, 0.350, 0.000, 0.000, 0.000, 0.000,
+ 0.490, 0.750, 0.000, 0.630, 0.875, 0.925, 1.000,
+ 0.920, 0.770, 0.690, 0.830, 0.740 )
+ ), #
+ #
+ #
+ # Abreviations; Names of the texture cl; Points marking the class limits (points specified above)
+ "tt.polygons" = list(
+ "C" = list( "name" = "Clay", "points" = c(01, 02, 03, 04, 05, 01) ),
+ "ZC" = list( "name" = "Silty clay", "points" = c(03, 06, 04, 03) ),
+ "ZCL" = list( "name" = "Silty clay loam", "points" = c(08, 07, 06, 03, 08) ),
+ "ZL" = list( "name" = "Silty loam", "points" = c(09, 10, 07, 08, 11, 09) ),
+ "LS" = list( "name" = "Loamy sand", "points" = c(13, 09, 11, 12) ),
+ "S" = list( "name" = "Sand", "points" = c(14, 13, 12, 15, 14) ),
+ "SL" = list( "name" = "Sandy loam", "points" = c(15, 16, 17, 18, 15) ),
+ "L" = list( "name" = "Loam", "points" = c(16, 11, 08, 17, 16) ),
+ "SCL" = list( "name" = "Sandy clay loam", "points" = c(18, 17, 02, 19, 18) ),
+ "CL" = list( "name" = "Clay loam", "points" = c(17, 08, 03, 02) ),
+ "SC" = list( "name" = "Sandy clay", "points" = c(19, 02, 01, 19) )
+ ), #
+ #
+ # Triangle specific parameters for triangle geometry / appearance
+ # See general parameters above for detailed description of them
+ blr.clock = c(F,T,NA),
+ tlr.an = c(45,90,45),
+ #
+ blr.tx = c("SAND","CLAY","SILT"),
+ #
+ base.css.ps.lim = c(0,2,20,2000),
+ tri.css.ps.lim = c(0,2,20,2000),
+ #
+ unit.ps = quote(bold(mu) * bold('m')),
+ unit.tx = quote(bold('%')),
+ #
+ text.sum = 100
+ ), #
+ #
"BE.TT" = list( # Belgian TRIANGLE PARAMETERS :
#
main = "Belgium (BE)",
Modified: pkg/soiltexture/inst/doc/soiltexture_vignette.Rnw
===================================================================
--- pkg/soiltexture/inst/doc/soiltexture_vignette.Rnw 2012-03-08 10:35:18 UTC (rev 79)
+++ pkg/soiltexture/inst/doc/soiltexture_vignette.Rnw 2012-09-12 16:14:49 UTC (rev 80)
@@ -142,23 +142,25 @@
# 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"
- ) #
- ) #
-} #
+#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
-) #
+#require(
+# package = "soiltexture",
+# character.only = TRUE,
+# quietly = TRUE
+#) #
# setwd(old.wd)
+
+library( "soiltexture" )
@
@@ -1157,19 +1159,19 @@
<<echo=TRUE,fig=TRUE,include=TRUE>>=
-TT.plot( class.sys = "AU.TT" )
+TT.plot( class.sys = "AU2.TT" )
@
The Australian soil texture classification has been built
considering a silt - sand limit of
-\Sexpr{TT.get("AU.TT")[["base.css.ps.lim"]][3]}$\mu$meters.\\
+\Sexpr{TT.get("AU2.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 = "AU.TT" )
+tex.tbl <- TT.classes.tbl( class.sys = "AU2.TT" )
xtable(
x = tex.tbl[,-3], #
caption = "Texture classes of the Australian system / triangle",
@@ -1177,14 +1179,19 @@
) #
@
+The clay silt sand coordinates of the vertices of this triangle have been kindly
+provided by Budiman Minasny. This should correct the small errors in the previous
+implementation of the triangle (\texttt{AU.TT}). The previous version is still
+available for eventual backward compatibility (but it is not presented here any
+more).\\
-There are probably small errors in the exact placement of some
-texture classes vertices (expected to be 1 or 2\% of the 'exact
-value'), due to technical difficulties for reproducing precisely
-this triangle (reproduced after both Minasny and McBratney
-2001\cite{MINASNY2001AJSR}, and Holbeche 2008\cite{HOLBECHE2008}
-(brochure 'Soil Texture-Laboratory Method' from soilquality.org.au
-\footnote{texttt{http://soilquality.org.au}}).\\
+% There are probably small errors in the exact placement of some
+% texture classes vertices (expected to be 1 or 2\% of the 'exact
+% value'), due to technical difficulties for reproducing precisely
+% this triangle (reproduced after both Minasny and McBratney
+% 2001\cite{MINASNY2001AJSR}, and Holbeche 2008\cite{HOLBECHE2008}
+% (brochure 'Soil Texture-Laboratory Method' from soilquality.org.au
+% \footnote{texttt{http://soilquality.org.au}}).\\
\clearpage % otherwise the table may 'eats' next triangle
@@ -1558,7 +1565,7 @@
# Plot the triangles
TT.plot(
- class.sys = "AU.TT",
+ class.sys = "AU2.TT",
class.p.bg.col = TRUE
) #
Modified: pkg/soiltexture/man/TT.DJ.col.Rd
===================================================================
--- pkg/soiltexture/man/TT.DJ.col.Rd 2012-03-08 10:35:18 UTC (rev 79)
+++ pkg/soiltexture/man/TT.DJ.col.Rd 2012-09-12 16:14:49 UTC (rev 80)
@@ -6,16 +6,8 @@
\description{A function to obtaine a weight average 'mix' of different colors!}
-\usage{
+\usage{TT.DJ.col(cl, w, gray.l = FALSE)}
-TT.DJ.col(cl,
-
-w,
-
-gray.l = FALSE)
-
-}
-
\arguments{
\item{cl}{
Modified: pkg/soiltexture/man/TT.add.Rd
===================================================================
--- pkg/soiltexture/man/TT.add.Rd 2012-03-08 10:35:18 UTC (rev 79)
+++ pkg/soiltexture/man/TT.add.Rd 2012-09-12 16:14:49 UTC (rev 80)
@@ -8,18 +8,10 @@
to add a new texture triangle definition.}
-\usage{
+\usage{TT.add(..., par.list = "TT.par", bkp.par.list = "TT.par.bkp",
-TT.add(...,
+ par.env = TT.env)}
-par.list = "TT.par",
-
-bkp.par.list = "TT.par.bkp",
-
-par.env = TT.env)
-
-}
-
\arguments{
\item{\dots}{
Modified: pkg/soiltexture/man/TT.auto.set.Rd
===================================================================
--- pkg/soiltexture/man/TT.auto.set.Rd 2012-03-08 10:35:18 UTC (rev 79)
+++ pkg/soiltexture/man/TT.auto.set.Rd 2012-09-12 16:14:49 UTC (rev 80)
@@ -6,18 +6,10 @@
\description{Retrieve and set default values for parameters (par() or not), when NULL.}
-\usage{
+\usage{TT.auto.set(fun = sys.function(which = -1), assign.op = TRUE,
-TT.auto.set(fun = sys.function(which = -1),
+ p.env = parent.frame(), set.par = TRUE)}
-assign.op = TRUE,
-
-p.env = parent.frame(),
-
-set.par = TRUE)
-
-}
-
\arguments{
\item{fun}{
Modified: pkg/soiltexture/man/TT.axis.arrows.Rd
===================================================================
--- pkg/soiltexture/man/TT.axis.arrows.Rd 2012-03-08 10:35:18 UTC (rev 79)
+++ pkg/soiltexture/man/TT.axis.arrows.Rd 2012-09-12 16:14:49 UTC (rev 80)
@@ -6,56 +6,22 @@
\description{Plot the axis' arrows of a texture triangle plot. }
-\usage{
+\usage{TT.axis.arrows(geo, css.lab = NULL, a.l = TT.get("arrows.lims"),
-TT.axis.arrows(geo,
+ a.h.s = TT.get("arrows.head.shift"), a.t.s = TT.get("arrows.text.shift"),
-css.lab = NULL,
+ a.t.s2 = TT.get("arrows.text.shift2"), a.b.s = TT.get("arrows.base.shift"),
-a.l = TT.get("arrows.lims"),
+ text.tol = NULL, text.sum = NULL, blr.clock = NULL, tlr.an = NULL,
-a.h.s = TT.get("arrows.head.shift"),
+ base.css.ps.lim = NULL, tri.sum.tst = FALSE, tri.pos.tst = FALSE,
-a.t.s = TT.get("arrows.text.shift"),
+ lwd.lab = NULL, arrows.lty = NULL, col.lab = NULL, font.lab = NULL,
-a.t.s2 = TT.get("arrows.text.shift2"),
+ cex.lab = NULL, family.op = NULL, unit.ps = NULL, unit.tx = NULL,
-a.b.s = TT.get("arrows.base.shift"),
+ lang = NULL)}
-text.tol = NULL,
-
-text.sum = NULL,
-
-blr.clock = NULL,
-
-tlr.an = NULL,
-
-base.css.ps.lim = NULL,
-
-tri.sum.tst = FALSE,
-
-tri.pos.tst = FALSE,
-
-lwd.lab = NULL,
-
-arrows.lty = NULL,
-
-col.lab = NULL,
-
-font.lab = NULL,
-
-cex.lab = NULL,
-
-family.op = NULL,
-
-unit.ps = NULL,
-
-unit.tx = NULL,
-
-lang = NULL)
-
-}
-
\arguments{
\item{geo}{
Modified: pkg/soiltexture/man/TT.baseplot.Rd
===================================================================
--- pkg/soiltexture/man/TT.baseplot.Rd 2012-03-08 10:35:18 UTC (rev 79)
+++ pkg/soiltexture/man/TT.baseplot.Rd 2012-09-12 16:14:49 UTC (rev 80)
@@ -10,52 +10,18 @@
'geo' parameters needed by these secondary functions.}
-\usage{
+\usage{TT.baseplot(geo = NULL, class.sys = "none", blr.clock = NULL,
-TT.baseplot(geo = NULL,
+ tlr.an = NULL, blr.tx = NULL, text.sum = NULL, base.css.ps.lim = NULL,
-class.sys = "none",
+ tri.sum.tst = NULL, tri.pos.tst = NULL, text.tol = NULL,
-blr.clock = NULL,
+ unit.ps = NULL, unit.tx = NULL, b.lim = NULL, l.lim = NULL,
-tlr.an = NULL,
+ main = NULL, new.mar = NULL, bg = NULL, fg = NULL, col = NULL,
-blr.tx = NULL,
+ cex.main = NULL, lang = NULL)}
-text.sum = NULL,
-
-base.css.ps.lim = NULL,
-
-tri.sum.tst = NULL,
-
-tri.pos.tst = NULL,
-
-text.tol = NULL,
-
-unit.ps = NULL,
-
-unit.tx = NULL,
-
-b.lim = NULL,
-
-l.lim = NULL,
-
-main = NULL,
-
-new.mar = NULL,
-
-bg = NULL,
-
-fg = NULL,
-
-col = NULL,
-
-cex.main = NULL,
-
-lang = NULL)
-
-}
-
\arguments{
\item{geo}{
Modified: pkg/soiltexture/man/TT.blr.ps.lim.Rd
===================================================================
--- pkg/soiltexture/man/TT.blr.ps.lim.Rd 2012-03-08 10:35:18 UTC (rev 79)
+++ pkg/soiltexture/man/TT.blr.ps.lim.Rd 2012-09-12 16:14:49 UTC (rev 80)
@@ -6,14 +6,8 @@
\description{Create a tabular version of clay silt sand particle size limits. }
-\usage{
+\usage{TT.blr.ps.lim(blr.tx, css.ps.lim)}
-TT.blr.ps.lim(blr.tx,
-
-css.ps.lim)
-
-}
-
\arguments{
\item{blr.tx}{
Modified: pkg/soiltexture/man/TT.blr.tx.check.Rd
===================================================================
--- pkg/soiltexture/man/TT.blr.tx.check.Rd 2012-03-08 10:35:18 UTC (rev 79)
+++ pkg/soiltexture/man/TT.blr.tx.check.Rd 2012-09-12 16:14:49 UTC (rev 80)
@@ -8,14 +8,8 @@
in blr.tx should be found in css.names and vice-versa.}
-\usage{
+\usage{TT.blr.tx.check(blr.tx, css.names)}
-TT.blr.tx.check(blr.tx,
-
-css.names)
-
-}
-
\arguments{
\item{blr.tx}{
Modified: pkg/soiltexture/man/TT.check.ps.lim.Rd
===================================================================
--- pkg/soiltexture/man/TT.check.ps.lim.Rd 2012-03-08 10:35:18 UTC (rev 79)
+++ pkg/soiltexture/man/TT.check.ps.lim.Rd 2012-09-12 16:14:49 UTC (rev 80)
@@ -8,18 +8,10 @@
5 tests performed.}
-\usage{
+\usage{TT.check.ps.lim(base.ps.lim, dat.ps.lim, ps.lim.length = c(4,
-TT.check.ps.lim(base.ps.lim,
+ 4))}
-dat.ps.lim,
-
-ps.lim.length = c(4,
-
-4))
-
-}
-
\arguments{
\item{base.ps.lim}{
Modified: pkg/soiltexture/man/TT.check.ps.lim.Xm.Rd
===================================================================
--- pkg/soiltexture/man/TT.check.ps.lim.Xm.Rd 2012-03-08 10:35:18 UTC (rev 79)
+++ pkg/soiltexture/man/TT.check.ps.lim.Xm.Rd 2012-09-12 16:14:49 UTC (rev 80)
@@ -8,18 +8,10 @@
4 tests performed.}
-\usage{
+\usage{TT.check.ps.lim.Xm(base.ps.lim, dat.ps.lim, ps.lim.length = c(4,
-TT.check.ps.lim.Xm(base.ps.lim,
+ 4))}
-dat.ps.lim,
-
-ps.lim.length = c(4,
-
-4))
-
-}
-
\arguments{
\item{base.ps.lim}{
Modified: pkg/soiltexture/man/TT.chemometrics.alr.Rd
===================================================================
--- pkg/soiltexture/man/TT.chemometrics.alr.Rd 2012-03-08 10:35:18 UTC (rev 79)
+++ pkg/soiltexture/man/TT.chemometrics.alr.Rd 2012-09-12 16:14:49 UTC (rev 80)
@@ -26,16 +26,8 @@
rather than column index.}
-\usage{
+\usage{TT.chemometrics.alr(X, divisorvar, css.names)}
-TT.chemometrics.alr(X,
-
-divisorvar,
-
-css.names)
-
-}
-
\arguments{
\item{X}{
Modified: pkg/soiltexture/man/TT.classes.Rd
===================================================================
--- pkg/soiltexture/man/TT.classes.Rd 2012-03-08 10:35:18 UTC (rev 79)
+++ pkg/soiltexture/man/TT.classes.Rd 2012-09-12 16:14:49 UTC (rev 80)
@@ -10,64 +10,22 @@
polygons.}
-\usage{
+\usage{TT.classes(geo, class.sys, tri.css.ps.lim = NULL, css.transf = NULL,
-TT.classes(geo,
+ text.transf.fun = NULL, trsf.add.opt1 = NULL, trsf.add.opt2 = NULL,
-class.sys,
+ text.tol = NULL, text.sum = NULL, base.css.ps.lim = NULL,
-tri.css.ps.lim = NULL,
+ blr.tx = NULL, blr.clock = NULL, tri.sum.tst = NULL, tri.pos.tst = NULL,
-css.transf = NULL,
+ bg = NULL, class.lab.col = NULL, class.p.bg.col = NULL, class.p.bg.hue = NULL,
-text.transf.fun = NULL,
+ class.line.col = NULL, class.lty = NULL, class.lab.show = NULL,
-trsf.add.opt1 = NULL,
+ cex.lab = NULL, font.lab = NULL, family.op = NULL, lwd.axis = NULL,
-trsf.add.opt2 = NULL,
+ col.axis = NULL, new.centroid = TRUE)}
-text.tol = NULL,
-
-text.sum = NULL,
-
-base.css.ps.lim = NULL,
-
-blr.tx = NULL,
-
-blr.clock = NULL,
-
-tri.sum.tst = NULL,
-
-tri.pos.tst = NULL,
-
-bg = NULL,
-
-class.lab.col = NULL,
-
-class.p.bg.col = NULL,
-
-class.p.bg.hue = NULL,
-
-class.line.col = NULL,
-
-class.lty = NULL,
-
-class.lab.show = NULL,
-
-cex.lab = NULL,
-
-font.lab = NULL,
-
-family.op = NULL,
-
-lwd.axis = NULL,
-
-col.axis = NULL,
-
-new.centroid = TRUE)
-
-}
-
\arguments{
\item{geo}{
Modified: pkg/soiltexture/man/TT.classes.tbl.Rd
===================================================================
--- pkg/soiltexture/man/TT.classes.tbl.Rd 2012-03-08 10:35:18 UTC (rev 79)
+++ pkg/soiltexture/man/TT.classes.tbl.Rd 2012-09-12 16:14:49 UTC (rev 80)
@@ -14,14 +14,8 @@
See also TT.vertices.plot().}
-\usage{
+\usage{TT.classes.tbl(class.sys = "FAO50.TT", collapse = NULL)}
-TT.classes.tbl(class.sys = "FAO50.TT",
-
-collapse = NULL)
-
-}
-
\arguments{
\item{class.sys}{
Modified: pkg/soiltexture/man/TT.col2hsv.Rd
===================================================================
--- pkg/soiltexture/man/TT.col2hsv.Rd 2012-03-08 10:35:18 UTC (rev 79)
+++ pkg/soiltexture/man/TT.col2hsv.Rd 2012-09-12 16:14:49 UTC (rev 80)
@@ -6,12 +6,8 @@
\description{Convert any colors to hsv. Wrapper around rgb2hsv() and col2rgb(). }
-\usage{
+\usage{TT.col2hsv(col)}
-TT.col2hsv(col)
-
-}
-
\arguments{
\item{col}{
Modified: pkg/soiltexture/man/TT.contour.Rd
===================================================================
--- pkg/soiltexture/man/TT.contour.Rd 2012-03-08 10:35:18 UTC (rev 79)
+++ pkg/soiltexture/man/TT.contour.Rd 2012-09-12 16:14:49 UTC (rev 80)
@@ -12,82 +12,22 @@
TT.kde2d(), before or after plot.}
-\usage{
+\usage{TT.contour(geo, x, add = FALSE, tri.sum.tst = NULL, tri.pos.tst = NULL,
-TT.contour(geo,
+ text.tol = NULL, unit.ps = NULL, unit.tx = NULL, b.lim = NULL,
-x,
+ l.lim = NULL, main = NULL, new.mar = NULL, bg = NULL, fg = NULL,
-add = FALSE,
+ col = NULL, cex.main = NULL, lang = NULL, nlevels = 10, levels = NA,
-tri.sum.tst = NULL,
+ labels = NULL, xlim = NA, ylim = NA, zlim = NA, labcex = 1,
-tri.pos.tst = NULL,
+ drawlabels = TRUE, method = "flattest", axes = TRUE, frame.plot = NA,
-text.tol = NULL,
+ lty = NA, lwd = NA, blr.clock = NULL, tlr.an = NULL, blr.tx = NULL,
-unit.ps = NULL,
+ text.sum = NULL, base.css.ps.lim = NULL, ...)}
-unit.tx = NULL,
-
-b.lim = NULL,
-
-l.lim = NULL,
-
-main = NULL,
-
-new.mar = NULL,
-
-bg = NULL,
-
-fg = NULL,
-
-col = NULL,
-
-cex.main = NULL,
-
-lang = NULL,
-
-nlevels = 10,
-
-levels = NA,
-
-labels = NULL,
-
-xlim = NA,
-
-ylim = NA,
-
-zlim = NA,
-
-labcex = 1,
-
-drawlabels = TRUE,
-
-method = "flattest",
-
-axes = TRUE,
-
-frame.plot = NA,
-
-lty = NA,
-
-lwd = NA,
-
-blr.clock = NULL,
-
-tlr.an = NULL,
-
-blr.tx = NULL,
-
-text.sum = NULL,
-
-base.css.ps.lim = NULL,
-
-...)
-
-}
-
\arguments{
\item{geo}{
Modified: pkg/soiltexture/man/TT.css2xy.Rd
===================================================================
--- pkg/soiltexture/man/TT.css2xy.Rd 2012-03-08 10:35:18 UTC (rev 79)
+++ pkg/soiltexture/man/TT.css2xy.Rd 2012-09-12 16:14:49 UTC (rev 80)
@@ -8,28 +8,10 @@
function is the 'heart' of most soiltexture plot functions.}
-\usage{
+\usage{TT.css2xy(tri.data, geo, css.names = NULL, text.tol = NULL, tri.sum.tst = NULL,
-TT.css2xy(tri.data,
+ tri.pos.tst = NULL, set.par = FALSE, text.sum = NULL, blr.clock = NULL)}
-geo,
-
-css.names = NULL,
-
-text.tol = NULL,
-
-tri.sum.tst = NULL,
-
-tri.pos.tst = NULL,
-
-set.par = FALSE,
-
-text.sum = NULL,
-
-blr.clock = NULL)
-
-}
-
\arguments{
\item{tri.data}{
Modified: pkg/soiltexture/man/TT.data.test.Rd
===================================================================
--- pkg/soiltexture/man/TT.data.test.Rd 2012-03-08 10:35:18 UTC (rev 79)
+++ pkg/soiltexture/man/TT.data.test.Rd 2012-09-12 16:14:49 UTC (rev 80)
@@ -18,22 +18,10 @@
(ignored).}
-\usage{
+\usage{TT.data.test(tri.data, css.names = NULL, text.sum = NULL, text.tol = NULL,
-TT.data.test(tri.data,
+ tri.sum.tst = NULL, tri.pos.tst = NULL)}
-css.names = NULL,
-
-text.sum = NULL,
-
-text.tol = NULL,
-
-tri.sum.tst = NULL,
-
-tri.pos.tst = NULL)
-
-}
-
\arguments{
\item{tri.data}{
Modified: pkg/soiltexture/man/TT.data.test.X.Rd
===================================================================
--- pkg/soiltexture/man/TT.data.test.X.Rd 2012-03-08 10:35:18 UTC (rev 79)
+++ pkg/soiltexture/man/TT.data.test.X.Rd 2012-09-12 16:14:49 UTC (rev 80)
@@ -18,20 +18,10 @@
'tri.data' should only contains texture data, and nothing else.}
-\usage{
+\usage{TT.data.test.X(tri.data, text.sum = NULL, text.tol = NULL, tri.sum.tst = NULL,
-TT.data.test.X(tri.data,
+ tri.pos.tst = NULL)}
-text.sum = NULL,
-
-text.tol = NULL,
-
-tri.sum.tst = NULL,
-
-tri.pos.tst = NULL)
-
-}
-
\arguments{
\item{tri.data}{
Modified: pkg/soiltexture/man/TT.dataset.Rd
===================================================================
--- pkg/soiltexture/man/TT.dataset.Rd 2012-03-08 10:35:18 UTC (rev 79)
+++ pkg/soiltexture/man/TT.dataset.Rd 2012-09-12 16:14:49 UTC (rev 80)
@@ -8,18 +8,8 @@
where Z is a virtual 4th variable correlated to the texture.}
-\usage{
+\usage{TT.dataset(n, seed.val = NULL, css.names = NULL, text.sum = NULL)}
-TT.dataset(n,
-
-seed.val = NULL,
-
-css.names = NULL,
-
-text.sum = NULL)
-
-}
-
\arguments{
\item{n}{
Modified: pkg/soiltexture/man/TT.deg2rad.Rd
===================================================================
--- pkg/soiltexture/man/TT.deg2rad.Rd 2012-03-08 10:35:18 UTC (rev 79)
+++ pkg/soiltexture/man/TT.deg2rad.Rd 2012-09-12 16:14:49 UTC (rev 80)
@@ -6,12 +6,8 @@
\description{Function to convert angle in degree to angle in radian.}
-\usage{
+\usage{TT.deg2rad(A)}
-TT.deg2rad(A)
-
-}
-
\arguments{
\item{A}{Angle in Degrees}
Modified: pkg/soiltexture/man/TT.dia2phi.Rd
===================================================================
--- pkg/soiltexture/man/TT.dia2phi.Rd 2012-03-08 10:35:18 UTC (rev 79)
+++ pkg/soiltexture/man/TT.dia2phi.Rd 2012-09-12 16:14:49 UTC (rev 80)
@@ -8,12 +8,8 @@
phi = -log2(dia). See also TT.phi2dia().}
-\usage{
+\usage{TT.dia2phi(dia)}
-TT.dia2phi(dia)
-
-}
-
\arguments{
\item{dia}{Particle size diameter in micro-meters (will be converted in milli-meters)}
Modified: pkg/soiltexture/man/TT.edges.Rd
===================================================================
--- pkg/soiltexture/man/TT.edges.Rd 2012-03-08 10:35:18 UTC (rev 79)
+++ pkg/soiltexture/man/TT.edges.Rd 2012-09-12 16:14:49 UTC (rev 80)
@@ -10,32 +10,12 @@
called before (usually inside TT.plot()).}
-\usage{
+\usage{TT.edges(geo, text.tol = NULL, text.sum = NULL, blr.clock = NULL,
-TT.edges(geo,
+ col.axis = NULL, plot.axis = TRUE, frame.bg.col = NULL, lwd.axis = NULL,
-text.tol = NULL,
+ tri.sum.tst = NULL, tri.pos.tst = NULL, bg = NULL)}
-text.sum = NULL,
-
-blr.clock = NULL,
-
-col.axis = NULL,
-
-plot.axis = TRUE,
-
-frame.bg.col = NULL,
-
-lwd.axis = NULL,
-
-tri.sum.tst = NULL,
-
-tri.pos.tst = NULL,
-
-bg = NULL)
-
-}
-
\arguments{
\item{geo}{
Modified: pkg/soiltexture/man/TT.gen.op.set.Rd
===================================================================
--- pkg/soiltexture/man/TT.gen.op.set.Rd 2012-03-08 10:35:18 UTC (rev 79)
+++ pkg/soiltexture/man/TT.gen.op.set.Rd 2012-09-12 16:14:49 UTC (rev 80)
@@ -6,16 +6,8 @@
\description{Retrieve and set default values from options (that do _not_ superseed par()). }
-\usage{
+\usage{TT.gen.op.set(param, assign.op = TRUE, p.env = parent.frame())}
-TT.gen.op.set(param,
-
-assign.op = TRUE,
-
-p.env = parent.frame())
-
-}
-
\arguments{
\item{param}{
Modified: pkg/soiltexture/man/TT.geo.get.Rd
===================================================================
--- pkg/soiltexture/man/TT.geo.get.Rd 2012-03-08 10:35:18 UTC (rev 79)
+++ pkg/soiltexture/man/TT.geo.get.Rd 2012-09-12 16:14:49 UTC (rev 80)
@@ -6,22 +6,10 @@
\description{Retrieve and return the geometrical parameters from a list of parameter values (NULL or not).}
-\usage{
+\usage{TT.geo.get(class.sys = NULL, blr.clock = NULL, tlr.an = NULL,
-TT.geo.get(class.sys = NULL,
+ blr.tx = NULL, text.sum = NULL, base.css.ps.lim = NULL)}
-blr.clock = NULL,
-
-tlr.an = NULL,
-
-blr.tx = NULL,
-
-text.sum = NULL,
-
-base.css.ps.lim = NULL)
-
-}
-
\arguments{
\item{class.sys}{
Modified: pkg/soiltexture/man/TT.geo.set.Rd
===================================================================
--- pkg/soiltexture/man/TT.geo.set.Rd 2012-03-08 10:35:18 UTC (rev 79)
+++ pkg/soiltexture/man/TT.geo.set.Rd 2012-09-12 16:14:49 UTC (rev 80)
@@ -6,14 +6,8 @@
\description{Takes "geo" values and assign them individually in the parent function. }
-\usage{
+\usage{TT.geo.set(geo, p.env = parent.frame())}
-TT.geo.set(geo,
-
-p.env = parent.frame())
-
-}
-
\arguments{
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/soiltexture -r 80
More information about the Soiltexture-commits
mailing list