[Soiltexture-commits] r103 - / pkg/ternaryplot prepare
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Mar 28 17:50:32 CET 2014
Author: jmoeys
Date: 2014-03-28 17:50:31 +0100 (Fri, 28 Mar 2014)
New Revision: 103
Added:
prepare/plotParameters-plot.xls
prepare/plotParameters-ternary.xls
soiltexture_1_RCMDBUILD.bat
soiltexture_2_RCMDcheck_noexamples.bat
soiltexture_2_RCMDcheck_notests_novignette.bat
soiltexture_3_RCMDINSTALL_build.BAT
Removed:
1_RCMDBUILD.bat
1_RCMDBUILD.sh
2_RCMDcheck_noexamples.bat
2_RCMDcheck_noexamples.sh
2_RCMDcheck_notests_novignette.bat
2_RCMDcheck_notests_novignette.sh
3_RCMDINSTALL_build.BAT
3_RCMDINSTALL_build.sh
ternaryplot_1_RCMDbuild_novignette.bat
ternaryplot_2_RCMDcheck_notests_noexamples_novignettes.bat
ternaryplot_vignette_compile.R
Modified:
packageUtilities.R
pkg/ternaryplot/REVISION
ternaryplot_1_RCMDbuild.bat
ternaryplot_Document.R
ternaryplot_ToDoList.TXT
Log:
Finlise conversion of ternaryplot from S4 to S3
Deleted: 1_RCMDBUILD.bat
===================================================================
--- 1_RCMDBUILD.bat 2014-03-28 16:47:09 UTC (rev 102)
+++ 1_RCMDBUILD.bat 2014-03-28 16:50:31 UTC (rev 103)
@@ -1,7 +0,0 @@
-set pkgname=soiltexture
-
-cd /D "%rPackagesDir%\%pkgname%\pkg"
-
-R CMD build --compact-vignettes="gs+qpdf" --md5 %pkgname%
-
-pause
Deleted: 1_RCMDBUILD.sh
===================================================================
--- 1_RCMDBUILD.sh 2014-03-28 16:47:09 UTC (rev 102)
+++ 1_RCMDBUILD.sh 2014-03-28 16:50:31 UTC (rev 103)
@@ -1,6 +0,0 @@
-# cd "/home/jules/Documents/_WORK/R_PACKAGES/soiltexture/pkg/"
-cd "/home/jmoeys/Documents/_WORK/R_PACKAGES/soiltexture/pkg/"
-R CMD build --compact-vignettes soiltexture
-echo "press any key to continue"; read line
-
-
Deleted: 2_RCMDcheck_noexamples.bat
===================================================================
--- 2_RCMDcheck_noexamples.bat 2014-03-28 16:47:09 UTC (rev 102)
+++ 2_RCMDcheck_noexamples.bat 2014-03-28 16:50:31 UTC (rev 103)
@@ -1,9 +0,0 @@
-set pkgname=soiltexture
-
-cd /D "%rPackagesDir%\%pkgname%\pkg"
-
-R CMD check --no-examples --as-cran %pkgname%_1.2.13.tar.gz
-
- at REM --as-cran
-
-pause
Deleted: 2_RCMDcheck_noexamples.sh
===================================================================
--- 2_RCMDcheck_noexamples.sh 2014-03-28 16:47:09 UTC (rev 102)
+++ 2_RCMDcheck_noexamples.sh 2014-03-28 16:50:31 UTC (rev 103)
@@ -1,6 +0,0 @@
-# cd "/home/jules/Documents/_WORK/R_PACKAGES/soiltexture/pkg/"
-cd "/home/jmoeys/Documents/_WORK/R_PACKAGES/soiltexture/pkg/"
-R CMD check --no-tests --as-cran soiltexture
-echo "press any key to continue"; read line
-
-
Deleted: 2_RCMDcheck_notests_novignette.bat
===================================================================
--- 2_RCMDcheck_notests_novignette.bat 2014-03-28 16:47:09 UTC (rev 102)
+++ 2_RCMDcheck_notests_novignette.bat 2014-03-28 16:50:31 UTC (rev 103)
@@ -1,9 +0,0 @@
-set pkgname=soiltexture
-
-cd /D "%rPackagesDir%\%pkgname%\pkg"
-
-R CMD check --no-tests --no-examples --no-vignettes %pkgname%
-
-REM --as-cran
-
-pause
Deleted: 2_RCMDcheck_notests_novignette.sh
===================================================================
--- 2_RCMDcheck_notests_novignette.sh 2014-03-28 16:47:09 UTC (rev 102)
+++ 2_RCMDcheck_notests_novignette.sh 2014-03-28 16:50:31 UTC (rev 103)
@@ -1,5 +0,0 @@
-cd "/home/jules/Documents/_WORK/R_PACKAGES/soiltexture/pkg"
-R CMD check --no-tests --no-vignettes --as-cran soiltexture
-echo "press any key to continue"; read line
-
-
Deleted: 3_RCMDINSTALL_build.BAT
===================================================================
--- 3_RCMDINSTALL_build.BAT 2014-03-28 16:47:09 UTC (rev 102)
+++ 3_RCMDINSTALL_build.BAT 2014-03-28 16:50:31 UTC (rev 103)
@@ -1,7 +0,0 @@
-set pkgname=soiltexture
-
-cd /D "%rPackagesDir%\%pkgname%\pkg"
-
-R CMD INSTALL --build --compile-both --compact-docs --byte-compile %pkgname%_1.2.13.tar.gz
-
-pause
Deleted: 3_RCMDINSTALL_build.sh
===================================================================
--- 3_RCMDINSTALL_build.sh 2014-03-28 16:47:09 UTC (rev 102)
+++ 3_RCMDINSTALL_build.sh 2014-03-28 16:50:31 UTC (rev 103)
@@ -1,7 +0,0 @@
-# cd "/home/jules/Documents/_WORK/R_PACKAGES/soiltexture/pkg/"
-cd "/home/jmoeys/Documents/_WORK/R_PACKAGES/soiltexture/pkg/"
-R CMD INSTALL --build --compact-docs --byte-compile soiltexture
-echo "press any key to continue"; read line
-
-
-
Modified: packageUtilities.R
===================================================================
--- packageUtilities.R 2014-03-28 16:47:09 UTC (rev 102)
+++ packageUtilities.R 2014-03-28 16:50:31 UTC (rev 103)
@@ -62,10 +62,14 @@
### Vector of character strings. Names of the packages that needs to be installed
### prior to the package installation. NULL if none
- pkgSuggests=NULL
+ pkgSuggests=NULL,
### Vector of character string. Names of the packages that needs
### to be cited in the "Suggests" field. NULL if none
+ pkgImports=NULL
+### Vector of character string. Names of the packages that needs
+### to be cited in the "Imports" field. NULL if none
+
){
# Read the file DESCRIPTION
desc <- readLines(
@@ -148,16 +152,51 @@
sep = ""
)
- if( any( desc.sel2 ) )
- {
- desc[ desc.sel2 ] <- suggests.txt
+ if( is.null( pkgSuggests ) ){
+ desc <- desc[ !desc.sel2 ]
+
}else{
- desc <- c(
- desc,
- suggests.txt
- )
+ if( any( desc.sel2 ) ){
+ desc[ desc.sel2 ] <- suggests.txt
+ }else{
+ desc <- c(
+ desc,
+ suggests.txt
+ )
+ }
}
+
+
+ # Find where the "Imports:" line is
+ desc.sel2 <- substr(
+ x = desc,
+ start = 1,
+ stop = nchar("Imports:")
+ ) == "Imports:"
+
+ imports.txt <- paste(
+ "Imports: ",
+ paste( pkgImports, collapse = ", " ),
+ sep = ""
+ )
+ if( is.null( pkgImports ) ){
+ desc <- desc[ !desc.sel2 ]
+
+ }else{
+ if( any( desc.sel2 ) )
+ {
+ desc[ desc.sel2 ] <- imports.txt
+ }else{
+ desc <- c(
+ desc,
+ imports.txt
+ )
+ }
+ }
+
+
+
# Write again the description file:
desc <- writeLines(
con = file.path(
Modified: pkg/ternaryplot/REVISION
===================================================================
--- pkg/ternaryplot/REVISION 2014-03-28 16:47:09 UTC (rev 102)
+++ pkg/ternaryplot/REVISION 2014-03-28 16:50:31 UTC (rev 103)
@@ -1 +1 @@
-95:101M
+95:102M
Added: prepare/plotParameters-plot.xls
===================================================================
(Binary files differ)
Property changes on: prepare/plotParameters-plot.xls
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: prepare/plotParameters-ternary.xls
===================================================================
(Binary files differ)
Property changes on: prepare/plotParameters-ternary.xls
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Copied: soiltexture_1_RCMDBUILD.bat (from rev 98, 1_RCMDBUILD.bat)
===================================================================
--- soiltexture_1_RCMDBUILD.bat (rev 0)
+++ soiltexture_1_RCMDBUILD.bat 2014-03-28 16:50:31 UTC (rev 103)
@@ -0,0 +1,7 @@
+set pkgname=soiltexture
+
+cd /D "%rPackagesDir%\%pkgname%\pkg"
+
+R CMD build --compact-vignettes="gs+qpdf" --md5 %pkgname%
+
+pause
Copied: soiltexture_2_RCMDcheck_noexamples.bat (from rev 97, 2_RCMDcheck_noexamples.bat)
===================================================================
--- soiltexture_2_RCMDcheck_noexamples.bat (rev 0)
+++ soiltexture_2_RCMDcheck_noexamples.bat 2014-03-28 16:50:31 UTC (rev 103)
@@ -0,0 +1,9 @@
+set pkgname=soiltexture
+
+cd /D "%rPackagesDir%\%pkgname%\pkg"
+
+R CMD check --no-examples --as-cran %pkgname%_1.2.13.tar.gz
+
+ at REM --as-cran
+
+pause
Copied: soiltexture_2_RCMDcheck_notests_novignette.bat (from rev 95, 2_RCMDcheck_notests_novignette.bat)
===================================================================
--- soiltexture_2_RCMDcheck_notests_novignette.bat (rev 0)
+++ soiltexture_2_RCMDcheck_notests_novignette.bat 2014-03-28 16:50:31 UTC (rev 103)
@@ -0,0 +1,9 @@
+set pkgname=soiltexture
+
+cd /D "%rPackagesDir%\%pkgname%\pkg"
+
+R CMD check --no-tests --no-examples --no-vignettes %pkgname%
+
+REM --as-cran
+
+pause
Copied: soiltexture_3_RCMDINSTALL_build.BAT (from rev 97, 3_RCMDINSTALL_build.BAT)
===================================================================
--- soiltexture_3_RCMDINSTALL_build.BAT (rev 0)
+++ soiltexture_3_RCMDINSTALL_build.BAT 2014-03-28 16:50:31 UTC (rev 103)
@@ -0,0 +1,7 @@
+set pkgname=soiltexture
+
+cd /D "%rPackagesDir%\%pkgname%\pkg"
+
+R CMD INSTALL --build --compile-both --compact-docs --byte-compile %pkgname%_1.2.13.tar.gz
+
+pause
Modified: ternaryplot_1_RCMDbuild.bat
===================================================================
--- ternaryplot_1_RCMDbuild.bat 2014-03-28 16:47:09 UTC (rev 102)
+++ ternaryplot_1_RCMDbuild.bat 2014-03-28 16:50:31 UTC (rev 103)
@@ -2,6 +2,8 @@
cd /D "%rPackagesDir%\soiltexture\pkg"
+svnversion > %pkgname%\REVISION
+
R CMD build --compact-vignettes="gs+qpdf" %pkgname%
pause
Deleted: ternaryplot_1_RCMDbuild_novignette.bat
===================================================================
--- ternaryplot_1_RCMDbuild_novignette.bat 2014-03-28 16:47:09 UTC (rev 102)
+++ ternaryplot_1_RCMDbuild_novignette.bat 2014-03-28 16:50:31 UTC (rev 103)
@@ -1,7 +0,0 @@
-set pkgname=ternaryplot
-
-cd /D "%rPackagesDir%\%pkgname%\pkg"
-
-R CMD build --no-vignettes --compact-vignette="gs" %pkgname%
-
-pause
Deleted: ternaryplot_2_RCMDcheck_notests_noexamples_novignettes.bat
===================================================================
--- ternaryplot_2_RCMDcheck_notests_noexamples_novignettes.bat 2014-03-28 16:47:09 UTC (rev 102)
+++ ternaryplot_2_RCMDcheck_notests_noexamples_novignettes.bat 2014-03-28 16:50:31 UTC (rev 103)
@@ -1,9 +0,0 @@
-set pkgname=ternaryplot
-
-cd /D "%rPackagesDir%\%pkgname%\pkg"
-
-R CMD check --no-tests --no-examples --no-vignettes %pkgname%
-
- at REM --as-cran
-
-pause
Modified: ternaryplot_Document.R
===================================================================
--- ternaryplot_Document.R 2014-03-28 16:47:09 UTC (rev 102)
+++ ternaryplot_Document.R 2014-03-28 16:50:31 UTC (rev 103)
@@ -15,9 +15,10 @@
pkgDescription(
pkgName = pkgName,
pkgDir = pkgDir,
- pkgVersion = "0.1.2",
- pkgDepends = "methods",
+ pkgVersion = "0.3.0",
+ pkgDepends = c( "sp", "MASS" ),
pkgSuggests = NULL,
+ pkgImports = NULL,
RVersion = NULL
)
Modified: ternaryplot_ToDoList.TXT
===================================================================
--- ternaryplot_ToDoList.TXT 2014-03-28 16:47:09 UTC (rev 102)
+++ ternaryplot_ToDoList.TXT 2014-03-28 16:50:31 UTC (rev 103)
@@ -1,38 +1,146 @@
-Create functions
- blrLabels to set the labels
+aa01-ternaryplot-options.R
- ternaryPlot()
- Add ticks labels
- DONE: Add arrows
- fix axis arrows labels pos and srt
-
- ternaryAxis() that bundles ticks, ticks labels,
- arrows and arrows label
-
- fix axis arrows labels pos and srt
+ tpPar
+ getTpPar
- DONE: ternaryPoints() to plot points on ternary plots
+ .tpParList (environment)
+ tpParList (environment)
- ternaryLines() to plot lines on ternary plots
+aa02-ternaryplot-classes.R
- DONE: ternarySegment() to plot segments on ternary plot
+ ternaryCheck ternaryGeometry ternaryVariables ternarySystem
+ createTernaryGeometry
+ createTernaryVariables
+ createTernarySystem
+
+aa03-ternaryplot-classes-utility.R
+
+ blrNames ternaryVariables ternarySystem
+ blrNames<- ternaryVariables ternarySystem
+ blrLabels ternaryVariables ternarySystem
+ blrLabels<- ternaryVariables ternarySystem
+ blrClock ternaryGeometry ternarySystem
+ blrClock<- ternaryGeometry ternarySystem
+ fracSum ternaryGeometry ternarySystem
+ fracSum<- ternaryGeometry ternarySystem
+ tlrAngles ternaryGeometry ternarySystem
+ tlrAngles<- ternaryGeometry ternarySystem
+ ternaryGeometry ternarySystem
+ ternaryGeometry<- ternarySystem
+ ternaryVariables ternarySystem
+ ternaryVariables<- ternarySystem
+
+aa04-ternarySystems.R
+
+ ternarySystemEnv (environment)
+ getTernarySystem
+ listTernarySystem
- DONE: ternaryArrows() to plot arrows on a ternary plot
+onAttach.R
- ternaryPolygons() to plot polygons on ternary plots
+ .onAttach
+
+ternaryplot.R
- ternaryClass() that plot ternary classes (polygons + labels)
+ ternaryData ternarySystem character missing (includes tests)
- ternaryClassify() that classify according to ternary classes
+ .setTernarySystem
+ ternaryWindow ternarySystem character missing
+ ternaryBox ternarySystem
+ ternaryPoints data.frame matrix >> make function of "ternarySystem character" (+ internal 'data' handling)
+ ternarySegments data.frame matrix >> make function of "ternarySystem character" (+ internal 'data' handling)
+ ternaryArrows data.frame >> make function of "ternarySystem character" (+ internal 'data' handling)
+ .ternaryGridBase ternarySystem
+ .ternaryTicks ternarySystem
+ ternaryGrid ternarySystem
+ ternaryPlot data.frame matrix >> make function of "ternarySystem character" (+ internal 'data' handling)
+ TO DO: type = "p" points, "l" lines, "b" both, "c" counts,
+ "de" density, "di" distance (contour chosen via "...")
+ TO DO: facet = {category}, fCol, fPch, zCol, zCex
+ TO DO: make axes ticks depend on axTicks()
+ TO DO: make arrows and arrows labels distance from the plot a function of margin size using par("plt")
+ and *backward* calculating the label position
+
+ (1) regression between plt and usr (plt -> usr) for plotting points into margin, in X-axis margin (Y coordinates!)
+ (2) convert between axis margin line par( "mgp" )[2] to relative 0-1 coordinates of the margin, using par( "mar" )
+ (= number of lines in the margin). Summary mgp -> 0-1 coords -> plt -> XY (usr)
+ transfMgpTo0_1() transf0_1ToPlt() transfPltToXY()
+ (3) converting from X-Y to ternary coordinates with ternary2xy()
+ that gives the Y-distance between the triangle frame and the axis labels
+ (4) Using that distance to position the other two axis arrows and labels
+ ternaryLims data.frame matrix >> make function of "ternarySystem character" (+ internal 'data' handling)
+ deg2rad
+ ternary2xy data.frame matrix >> make function of "ternarySystem character" (+ internal 'data' handling)
+ ternaryClockSwitch data.frame matrix >> make function of "ternarySystem character" (+ internal 'data' handling)
+ ternaryText data.frame matrix >> make function of "ternarySystem character" (+ internal 'data' handling)
+ .ternaryAxisArrowsBase ternarySystem
+ .ternaryAxisArrows ternarySystem
+
+ TO DO: ternaryLines ternarySystem
+
+ TO DO: ternaryPolygon ternarySystem
+ TO DO: ternaryClasses ternarySystem >> draw ternary classification systems
+ TO DO: ternaryClassify ternarySystem >> Same as ternaryOver
+
+ TO DO: ternaryDensity ternarySystem
+ TO DO: ternaryBin ternarySystem
+ TO DO: ternaryDistance mahalanobis
+ TO DO: ternaryContour ternaryDensity ternaryBin
+
+ TO DO: ternaryNormalise ternarySystem
+
+ TO DO: as.data.frame ternarySystem >> what = "vertices" or "classes"
+
+ TO DO: ternaryTheme( "default" ) Switch between themes
+ TO DO: more graphical parameters from par() can be overwritten with tpPar()
+
+ TO DO: ternary2SpatialPointsDataFrame ternarySystem+data.frame or ternaryData or ternarySystem (includes extra columns)
+ TO DO: ternary2SpatialPolygonsDataFrame ternarySystem or ternaryPolygons (classes)
+
+ TO DO: ternaryOver >> ternary version of sp::over
+ TO DO: ternaryAggregate >> ternary version of sp::aggregate
+
+ TO DO: use ternaryGrid (ternaryPolygons) + ternaryAggregate to calculate summary statistics
+
+
+Examples:
+
+ Ternary Diagrams of Shepard and Pejrup:
+ http://rgm3.lab.nig.ac.jp/RGM/R_rdfile?f=rysgran/man/rysgran.ternary.Rd&d=R_CC
+ http://www.mgs.md.gov/coastal_geology/shepards.html
+
+ QAPF diagram:
+ http://en.wikipedia.org/wiki/QAPF_diagram
+
+ http://en.wikipedia.org/wiki/De_Finetti_diagram
-
-### Classes
-
-class texturePlot
- ternarySystem
- silt-sand limit
-
-NB: particle size transformations shall be done *before* plotting.
+Graphical parameters:
+
+ See plotParameters.xls
+
+ Notes:
+ Number segments in arrows yes tpPar("arrow.seg")
+ Margins no tpPar("mar")
+
+ type =
+ "n" nothing
+ "p" points (ternaryPoints) or text if !is.null(labels) (ternaryText)
+ "l" lines (ternaryLines)
+ "b" both points and lines
+ "d" density (ternaryGrid + ternaryDensity)
+ "c" counts (ternaryGrid + ternaryCounts)
+
+ facet Factor variable for plot facets (sub-plots)
+
+ extra A list of parameters passed to ternaryPoints or ternaryLines
+ fPch Factor variable for point symbols
+ fCol Factor variable for point or line colors
+ fLty Factor variable for line type
+ cCol Continuous variable for point or line colors use cut( x, breaks = 5 )
+ cCex Continuous variable for point expansion use cut( x, breaks = 5 )
+ position Legend position(s) (if several)
+
+
\ No newline at end of file
Deleted: ternaryplot_vignette_compile.R
===================================================================
--- ternaryplot_vignette_compile.R 2014-03-28 16:47:09 UTC (rev 102)
+++ ternaryplot_vignette_compile.R 2014-03-28 16:50:31 UTC (rev 103)
@@ -1,26 +0,0 @@
-rm(list=ls(all=TRUE))
-pkg.name <- "template"
-rootDir <- "C:/_R_PACKAGES"
-
-
-
-setwd( file.path( rootDir, pkg.name, "pkg", pkg.name, "inst/doc" ) )
-
-Stangle( paste( pkg.name, "vignette.Rnw", sep = "_" )
-
-Sweave( paste( pkg.name, "vignette.Rnw", sep = "_" )
-
-msg <- tools::texi2dvi(
- file = paste( pkg.name, "vignette.tex", sep = "_",
- pdf = TRUE,
- clean = TRUE,
- texinputs = getwd()
-) #
-
-file.remove( list.files( getwd(), "\\.tex$", full.names = TRUE ) )
-file.remove( list.files( getwd(), "\\.bib.bak$", full.names = TRUE ) )
-file.remove( list.files( getwd(), "\\.R$", full.names = TRUE ) )
-
-library("tools")
-res <- compactPDF( paths = getwd(), gs_quality = "ebook" ) # paste(sep="",file.name.root,".pdf")
-res
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