[Soiltexture-commits] r8 - / pkg/soiltexture/inst/doc pkg/soiltexture/inst/doc/INOUT
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Apr 20 14:34:16 CEST 2010
Author: jmoeys
Date: 2010-04-20 14:34:15 +0200 (Tue, 20 Apr 2010)
New Revision: 8
Added:
SoilTexture_changelog.txt
Sweave_wrapper.R
pkg/soiltexture/inst/doc/INOUT/
pkg/soiltexture/inst/doc/INOUT/CC-By-SA-nonported-88x31.PNG
pkg/soiltexture/inst/doc/INOUT/build.txt
pkg/soiltexture/inst/doc/INOUT/julienmoeysmailaddress-322-24.png
pkg/soiltexture/inst/doc/soiltexture_vignette.R
pkg/soiltexture/inst/doc/soiltexture_vignette.Rnw
pkg/soiltexture/inst/doc/soiltexture_vignette.bib
pkg/soiltexture/inst/doc/soiltexture_vignette.bib.bak
pkg/soiltexture/inst/doc/soiltexture_vignette.pdf
pkg/soiltexture/inst/doc/soiltexture_vignette.pdf.zip
pkg/soiltexture/inst/doc/soiltexture_vignette.tex
soiltexture_vignette_compile.R
Removed:
pkg/soiltexture/inst/doc/TEXTURE_WIZARD_VIGNETTES.pdf
Log:
Added: SoilTexture_changelog.txt
===================================================================
--- SoilTexture_changelog.txt (rev 0)
+++ SoilTexture_changelog.txt 2010-04-20 12:34:15 UTC (rev 8)
@@ -0,0 +1,99 @@
+The Soil Texture Wizard
+change log. From 2009/10/09. Most recent changes first / on top.
+Julien MOEYS
+
+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().
+
+
Added: Sweave_wrapper.R
===================================================================
--- Sweave_wrapper.R (rev 0)
+++ Sweave_wrapper.R 2010-04-20 12:34:15 UTC (rev 8)
@@ -0,0 +1,238 @@
+texi2dvi.wrapper <- function
+### This function is a wrapper to tools:texi2dvi that also deletes
+### the images when the pdf file was created
+
+( #
+ file.name.root,
+### Root of the sweave (and tex) file name (without extention)
+ work.wd,
+### Path of the working directory
+ inout.dir,
+### Path of the subdirectory in which the images are outputted
+ tex.ext = ".tex"
+### Tex file extesion. Any other value than ".tex" may not work
+){ #
+ old.dir <- getwd()
+ #
+ setwd( work.wd )
+ #
+ testfile2 <- paste(
+ file.name.root,
+ tex.ext,
+ sep = ""
+ ) #
+ #
+ msg <- tools::texi2dvi(
+ file = testfile2,
+ pdf = TRUE,
+ clean = TRUE,
+ texinputs = work.wd
+ ) #
+ #
+ cat( "\n\n\n" )
+ cat( paste( "tools::texi2dvi message ", msg, "\n\n\n" ) )
+ #
+ ## Clean the inout directory
+ if( all( is.null(msg) ) )
+ { #
+ inout.wd <- file.path( work.wd, inout.dir )
+ #
+ files.lst <- list.files(
+ path = inout.wd,
+ full.names = TRUE
+ ) #
+ #
+ files.nbc <- nchar( files.lst )
+ #
+ files.ext <- substr(
+ x = files.lst,
+ start = files.nbc - 2,
+ stop = files.nbc
+ ) #
+ #
+ file.name.root2 <- file.path( inout.wd, file.name.root )
+ #
+ files.pre <- substr(
+ x = files.lst,
+ start = 1,
+ stop = nchar( file.name.root2 )
+ ) #
+ #
+ sel.del <- (files.ext %in% c("pdf","eps")) &
+ (files.pre == file.name.root2 )
+ #
+ rm.res <- file.remove( files.lst[ sel.del ] )
+ #
+ cat( "\n\n\n" )
+ cat( paste( "Number of images deleted:", sum( rm.res ), "\n" ) )
+ cat( paste( "Number of images not deleted:", sum( !rm.res ), "\n\n\n" ) )
+ #
+ return( TRUE )
+ }else{
+ cat( "No images deleted. Something went wrong\n\n\n" )
+ #
+ return( FALSE )
+ } #
+ #
+ setwd( old.dir )
+ #
+### The function returns several messages about the Stangle, Sweave,
+### tools::texi2dvi and image deleting processes. It also returns
+### TRUE if the images were deleted, and FALSE if not
+} #
+
+
+
+Sweave.wrapper <- function
+### Sweave.wrapper is a function that performs different
+### operations otherwise done step by step with Stangle, Sweave and
+### tools::texi2dvi, and that do a bit of cleaning in the folder
+### after that (delete images)
+
+( #
+ file.name.root,
+### Root of the sweave (and tex) file name (without extention)
+ work.wd,
+### Path of the working directory
+ inout.dir,
+### Path of the subdirectory in which the images are outputted
+ sweave.ext = ".Rnw",
+### Sweave file extesion. Any other value than ".Rnw" may not work
+ tex.ext = ".tex"
+### Tex file extesion. Any other value than ".tex" may not work
+){ #
+ old.dir <- getwd()
+ #
+ setwd( work.wd )
+ #
+ testfile <- paste(
+ file.name.root,
+ sweave.ext,
+ sep = ""
+ ) #
+ #
+ cat( paste( "Ready to process ", testfile, "\n\n\n" ) )
+ #
+ ## enforce par(ask=FALSE)
+ options(device.ask.default=FALSE)
+ #
+ # Extract the R code from the Sweave file
+ Stangle( testfile )
+ #
+ ## create a LaTeX file
+ Sweave( testfile )
+ #
+ setwd( work.wd )
+ #
+ res <- texi2dvi.wrapper(
+ file.name.root = file.name.root,
+ work.wd = work.wd,
+ inout.dir = inout.dir,
+ tex.ext = tex.ext
+ ) #
+ #
+ setwd( old.dir )
+ #
+ return( res )
+### The function returns several messages about the Stangle, Sweave,
+### tools::texi2dvi and image deleting processes. It also returns
+### TRUE if the images were deleted, and FALSE if not
+} #
+
+
+
+MC.search.path <- function
+### Search if a given file is present along the system PATH
+### Function created after Vladimir Eremeev, who created it after
+### Brian Ripley.
+### <http://finzi.psych.upenn.edu/R/Rhelp02/archive/101078.html> or
+### <http://finzi.psych.upenn.edu/R/Rhelp02/archive/92829.html>
+
+( #
+ file.name = "7z.exe",
+### Name of the 7zip command line file.
+ s.path = Sys.getenv("PATH"),
+### Value of windwos PATH variable. Default is set to Sys.getenv("PATH")
+ p.sep = .Platform$path.sep
+### Platform specific folder separator in pathes. Default set to .Platform$path.sep
+){ #
+ s.path <- strsplit(
+ x = s.path,
+ split = p.sep
+ )[[1]]
+ #
+ tmp <- lapply(
+ X = s.path,
+ FUN = function(X){
+ fp <- file.path(X, file.name)
+ #
+ file.exists( fp )
+ } #
+ ) #
+ #
+ return( any( unlist( tmp ) ) )
+### Returns TRUE if 7zip command line executable was found in along the PATH
+} #
+
+
+
+zipMe <- function
+### ZipMe is an R wrapper for 7zip command line executable. It is
+### used to compress files in ZIP archives format
+
+( #
+ file.name,
+### Name of the file to be zipped.
+ file.dir,
+### Directory of the file to be zipped.
+ zip.name = "7z.exe",
+### Name of the 7zip command line file.
+ intern = TRUE,
+### See ?system .
+ ignore.stderr = FALSE,
+### See ?system .
+ wait = TRUE,
+### See ?system .
+ input = NULL,
+### See ?system .
+ show.output.on.console = TRUE,
+### See ?system .
+ minimized = TRUE,
+### See ?system .
+ invisible = TRUE
+### See ?system .
+){ #
+ old.dir <- getwd()
+ #
+ setwd( file.dir )
+ #
+ z7 <- MC.search.path( file.name = zip.name )
+ #
+ if( z7 )
+ { #
+ z7.cmd <- paste(
+ sep = "",
+ "7z a -tzip -mx=1 ",
+ file.name, ".zip ",
+ file.name
+ ) #
+ #
+ sys.msg <- system(
+ command = z7.cmd,
+ intern = intern,
+ ignore.stderr = ignore.stderr,
+ wait = wait,
+ input = input,
+ show.output.on.console = show.output.on.console,
+ minimized = minimized,
+ invisible = invisible
+ ) #
+ #
+ cat( sys.msg )
+ }else{
+ message("7zip not found. Files were not zipped")
+ } #
+ #
+ setwd( old.dir )
+} #
+
Added: pkg/soiltexture/inst/doc/INOUT/CC-By-SA-nonported-88x31.PNG
===================================================================
(Binary files differ)
Property changes on: pkg/soiltexture/inst/doc/INOUT/CC-By-SA-nonported-88x31.PNG
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Added: pkg/soiltexture/inst/doc/INOUT/build.txt
===================================================================
--- pkg/soiltexture/inst/doc/INOUT/build.txt (rev 0)
+++ pkg/soiltexture/inst/doc/INOUT/build.txt 2010-04-20 12:34:15 UTC (rev 8)
@@ -0,0 +1 @@
+37
Added: pkg/soiltexture/inst/doc/INOUT/julienmoeysmailaddress-322-24.png
===================================================================
(Binary files differ)
Property changes on: pkg/soiltexture/inst/doc/INOUT/julienmoeysmailaddress-322-24.png
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Deleted: pkg/soiltexture/inst/doc/TEXTURE_WIZARD_VIGNETTES.pdf
===================================================================
--- pkg/soiltexture/inst/doc/TEXTURE_WIZARD_VIGNETTES.pdf 2010-04-16 13:33:36 UTC (rev 7)
+++ pkg/soiltexture/inst/doc/TEXTURE_WIZARD_VIGNETTES.pdf 2010-04-20 12:34:15 UTC (rev 8)
@@ -1,43691 +0,0 @@
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-<< /S /GoTo /D (section.1) >>
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-(Why creating 'The soil texture wizard'?)
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-endobj
-15 0 obj
-(About R)
-endobj
-16 0 obj
-<< /S /GoTo /D (subsection.1.3) >>
-endobj
-19 0 obj
-(About the author)
-endobj
-20 0 obj
-<< /S /GoTo /D (subsection.1.4) >>
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-(Credits and License)
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-(Introduction: About soil texture, texture triangles and texture classifications)
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-(What are soil granulometry and soil texture\(s\)?)
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-35 0 obj
-(What are soil texture triangle and classes)
-endobj
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-<< /S /GoTo /D (section.3) >>
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-39 0 obj
-(Importing the function and preparing the work directory)
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-<< /S /GoTo /D (section.4) >>
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-(Plotting soil texture triangles and classification systems)
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-<< /S /GoTo /D (subsection.4.1) >>
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-endobj
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-<< /S /GoTo /D (subsection.4.2) >>
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-(The USDA soil texture classification)
-endobj
-52 0 obj
-<< /S /GoTo /D (subsection.4.3) >>
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-55 0 obj
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-endobj
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-<< /S /GoTo /D (subsection.4.4) >>
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-endobj
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-(UK Soil Survey of England and Wales texture classification)
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-(The Belgian soil texture classification)
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-(Overplotting two soil texture classification systems)
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-(Case 2: Overplotting two soil texture classification systems with different geometries)
-endobj
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-<< /S /GoTo /D (section.6) >>
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-(Plotting soil texture data)
-endobj
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-<< /S /GoTo /D (subsection.6.1) >>
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-(Simple plot of soil texture data)
-endobj
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-<< /S /GoTo /D (subsection.6.2) >>
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-(Bubble plot of soil texture data and a 3rd variable)
-endobj
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-<< /S /GoTo /D (subsection.6.3) >>
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-(Heatmap and / or contour plot of soil texture data and a 4th variable)
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-(Two-dimensional kernel \(probability\) density estimation for texture data)
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-<< /S /GoTo /D (subsection.6.5) >>
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-(Contour plot of texture data Mahalanobis distance)
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-<< /S /GoTo /D (subsection.6.6) >>
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-(Plotting text in a texture triangle)
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-<< /S /GoTo /D (section.7) >>
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-(Control of soil texture data in The Soil Texture Wizard)
-endobj
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-<< /S /GoTo /D (subsection.7.1) >>
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-(Normalizing soil texture data \(sum of the 3 texture classes\))
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[TRUNCATED]
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svnlook diff /svnroot/soiltexture -r 8
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