R : Copyright 2005, The R Foundation for Statistical Computing
Version 2.1.1  (2005-06-20), ISBN 3-900051-07-0

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> ### * <HEADER>
> ###
> attach(NULL, name = "CheckExEnv")
> assign(".CheckExEnv", as.environment(2), pos = length(search())) # base
> ## add some hooks to label plot pages for base and grid graphics
> setHook("plot.new", ".newplot.hook")
> setHook("persp", ".newplot.hook")
> setHook("grid.newpage", ".gridplot.hook")
> 
> assign("cleanEx",
+        function(env = .GlobalEnv) {
+ 	   rm(list = ls(envir = env, all.names = TRUE), envir = env)
+            RNGkind("default", "default")
+ 	   set.seed(1)
+    	   options(warn = 1)
+ 	   delayedAssign("T", stop("T used instead of TRUE"),
+ 		  assign.env = .CheckExEnv)
+ 	   delayedAssign("F", stop("F used instead of FALSE"),
+ 		  assign.env = .CheckExEnv)
+ 	   sch <- search()
+ 	   newitems <- sch[! sch %in% .oldSearch]
+ 	   for(item in rev(newitems))
+                eval(substitute(detach(item), list(item=item)))
+ 	   missitems <- .oldSearch[! .oldSearch %in% sch]
+ 	   if(length(missitems))
+ 	       warning("items ", paste(missitems, collapse=", "),
+ 		       " have been removed from the search path")
+        },
+        env = .CheckExEnv)
> assign("..nameEx", "__{must remake R-ex/*.R}__", env = .CheckExEnv) # for now
> assign("ptime", proc.time(), env = .CheckExEnv)
> grDevices::postscript("xgobi-Examples.ps")
> assign("par.postscript", graphics::par(no.readonly = TRUE), env = .CheckExEnv)
> options(contrasts = c(unordered = "contr.treatment", ordered = "contr.poly"))
> options(warn = 1)    
> library('xgobi')
> 
> assign(".oldSearch", search(), env = .CheckExEnv)
> assign(".oldNS", loadedNamespaces(), env = .CheckExEnv)
> cleanEx(); ..nameEx <- "PaulKAI"
> 
> ### * PaulKAI
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: PaulKAI
> ### Title: Occurences of ``kai'' in 10 Epistels of Apostel Paul
> ### Aliases: PaulKAI
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(PaulKAI)
> rownames(PaulKAI) # the ten epistles researched:
 [1] "Rom" "Co1" "Co2" "Gal" "Phi" "Col" "Th1" "Ti1" "Ti2" "Heb"
> ##>  [1] "Rom" "Co1" "Co2" "Gal" "Phi" "Col" "Th1" "Ti1" "Ti2" "Heb"
> PaulKAI # the 10 x 4 count table
      0   1  2 3+
Rom 386 141 34 17
Co1 424 152 35 16
Co2 192  86 28 13
Gal 128  48  5  6
Phi  42  29 19 12
Col  23  32 17  9
Th1  34  23  8 16
Ti1  49  38  9 10
Ti2  45  28 11  4
Heb 155  94 37 24
> mosaicplot(PaulKAI)
> quadplot(PaulKAI)
xgobi -title 'mat3' -std mmx /tmp/RtmpiVHdhY/xgobi-mat310d63af1 & 
sh: line 1: xgobi: command not found
> 
> 
> 
> cleanEx(); ..nameEx <- "morsecodes"
> 
> ### * morsecodes
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: morsecodes
> ### Title: Rothkopf Morse Code Data
> ### Aliases: morsecodes morsecodes.col morsecodes.colors morsecodes.dist
> ###   morsecodes.glyphs morsecodes.linecolors morsecodes.lines
> ###   morsecodes.pos morsecodes.raw morsecodes.row
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(morsecodes)
> ls.str(pat="^morsecode")
morsecodes.col :  chr [1:12] "LEN" "DASH" "POS 1" "POS 2" "POS 3" "POS 4" "POS 5" "SEQ" ...
morsecodes.colors :  chr [1:36] "SkyBlue" "Green" "Green" "Yellow" "HotPink" "Green" "Yellow" ...
morsecodes.dist :  int [1:36, 1:36] 0 167 169 159 180 164 163 163 75 165 ...
morsecodes.glyphs :  num [1:36] 27 27 27 27 27 27 27 27 27 27 ...
morsecodes.linecolors :  chr [1:33] "SkyBlue" "SkyBlue" "Green" "Green" "Green" "Green" "Yellow" ...
morsecodes.lines :  num [1:33, 1:2] 1 1 2 2 3 3 4 4 5 6 ...
morsecodes.pos :  num [1:36, 1:12] 0.25 0.75 0.75 0.5 0 0.75 0.5 0.75 0.25 0.75 ...
morsecodes.raw :  int [1:36, 1:36] 92 5 4 8 6 4 9 3 64 7 ...
morsecodes.row :  chr [1:36, 1:2] "A" "B" "C" "D" "E" "F" "G" "H" "I" "J" "K" "L" "M" "N" ...
> morsecodes.row # remember what you learned in...
      [,1] [,2]   
 [1,] "A"  ".-"   
 [2,] "B"  "-..." 
 [3,] "C"  "-.-." 
 [4,] "D"  "-.."  
 [5,] "E"  "."    
 [6,] "F"  "..-." 
 [7,] "G"  "--."  
 [8,] "H"  "...." 
 [9,] "I"  ".."   
[10,] "J"  ".---" 
[11,] "K"  "-.-"  
[12,] "L"  ".-.." 
[13,] "M"  "--"   
[14,] "N"  "-."   
[15,] "O"  "---"  
[16,] "P"  ".--." 
[17,] "Q"  "--.-" 
[18,] "R"  ".-."  
[19,] "S"  "..."  
[20,] "T"  "-"    
[21,] "U"  "..-"  
[22,] "V"  "...-" 
[23,] "W"  ".--"  
[24,] "X"  "-..-" 
[25,] "Y"  "-.--" 
[26,] "Z"  "--.." 
[27,] "1"  ".----"
[28,] "2"  "..---"
[29,] "3"  "...--"
[30,] "4"  "....-"
[31,] "5"  "....."
[32,] "6"  "-...."
[33,] "7"  "--..."
[34,] "8"  "---.."
[35,] "9"  "----."
[36,] "0"  "-----"
> ## real row names
> (mc.row <- paste(morsecodes.row[,1], morsecodes.row[,2]))[1:8]
[1] "A .-"   "B -..." "C -.-." "D -.."  "E ."    "F ..-." "G --."  "H ...."
> 
> image(1:36, 1:36, morsecodes.raw, main="`morsecodes' raw confusion rates")
> text(1:36,1:36, morsecodes.row[,1])
> 
> ##--> help(xgvis) for running multidimensional scaling (MDS) and XGobi on these
> 
> 
> 
> cleanEx(); ..nameEx <- "quadplot"
> 
> ### * quadplot
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: quadplot
> ### Title: Tetrahedral Display for Four-Category Proportions using XGobi
> ### Aliases: quadplot
> ### Keywords: dynamic hplot
> 
> ### ** Examples
> 
> data(PaulKAI)
> quadplot(PaulKAI, normalize = TRUE)
xgobi -title 'mat3' -std mmx /tmp/RtmpiVHdhY/xgobi-mat360b7acd9 & 
sh: line 1: xgobi: command not found
> 
> 
> 
> cleanEx(); ..nameEx <- "reggeom"
> 
> ### * reggeom
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: reggeom
> ### Title: Geometry of Regression with Two Regressors
> ### Aliases: reggeom
> ### Keywords: dynamic
> 
> ### ** Examples
> 
> reggeom()
xgobi -title 'Regression Geometry' -std msd /tmp/RtmpiVHdhY/xgobi-RgrsG3ab50c2a & 
sh: line 1: xgobi: command not found
> 
> ## The arguments given in this example are modifications of the default,
> ## some lines dropped, some added, some line colors changed,
> ## in order to emphasize the geometry of backfitting.
> reggeom(
+       lines= cbind(c(1,6,8,1,11,7,1,1,6,6,15,17,8,5,9, 5,6,14,15,16,14,15,5),
+                    c(6,8,2,11,7,3,4,5,4,15,17,5,5,9,7,11,14,15,16,17,4,4,4)),
+       linecolors=c("red", rep("yellow",5), "orchid", "green",
+                    "slateblue", rep("skyblue",3), rep("white",3), "skyblue",
+                    rep("red",4), rep("slateblue", 2), "green"),
+       title="Regression Geometry - Backfitting")
xgobi -title 'Regression Geometry - Backfitting' -std msd /tmp/RtmpiVHdhY/xgobi-RgrGB4431b782 & 
sh: line 1: xgobi: command not found
> 
> 
> 
> cleanEx(); ..nameEx <- "xgobi"
> 
> ### * xgobi
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: xgobi
> ### Title: XGobi: Dynamic Graphics for Data Analysis
> ### Aliases: xgobi xgobi.colors.default
> ### Keywords: dynamic multivariate
> 
> ### ** Examples
> 
> data(laser)
> xgobi(laser)
xgobi -title 'laser' -std mmx /tmp/RtmpiVHdhY/xgobi-laser1c06dac8 & 
sh: line 1: xgobi: command not found
> 
> Xdir <- file.path(dirname(tempfile()), "xgobi")
> ## Don't show:
> if(file.exists(Xdir)) unlink(Xdir, recursive = TRUE)
> ## End Don't show
> dir.create(Xdir)
> xgobi(laser, colors = xgobi.colors.default[c(1,3,5,7,9,10)[as.factor(laser$ Ir)]],
+       glyphs = c(23,8)[1+(laser$lambda > 1576)],
+       keep = TRUE, fprefix="xgobi/L-")
xgobi -title 'laser' -std mmx /tmp/RtmpiVHdhY/xgobi/L-laser56e509fe & 
sh: line 1: xgobi: command not found
> file.info(list.files(Xdir, full=TRUE))[, c(1,3,4)] # >> Files "L-laser..."
                                             size mode               mtime
/tmp/RtmpiVHdhY/xgobi/L-laser56e509fe        1196  644 2005-07-13 20:40:29
/tmp/RtmpiVHdhY/xgobi/L-laser56e509fe.col      19  644 2005-07-13 20:40:29
/tmp/RtmpiVHdhY/xgobi/L-laser56e509fe.colors  698  644 2005-07-13 20:40:29
/tmp/RtmpiVHdhY/xgobi/L-laser56e509fe.glyphs  143  644 2005-07-13 20:40:29
/tmp/RtmpiVHdhY/xgobi/L-laser56e509fe.row     183  644 2005-07-13 20:40:29
> ## remove manually when finally unused:
> unlink(Xdir, recursive = TRUE)
> 
> ##>>> see also the morsecodes example in  help(xgvis) <<<
> ##                 ------------------     -----------
> 
> 
> 
> cleanEx(); ..nameEx <- "xgvis"
> 
> ### * xgvis
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: xgvis
> ### Title: XGvis: Interactive Multidimensional Scaling Using XGobi for
> ###   Display
> ### Aliases: xgvis
> ### Keywords: dynamic multivariate
> 
> ### ** Examples
> 
> data(morsecodes) ## from the XGobi/XGvis data, see  ?morsecodes
> mc.row <- paste(morsecodes.row[,1],morsecodes.row[,2])
> 
> xgvis(dmat = morsecodes.dist,
+       pos = morsecodes.pos,
+       rowlab = mc.row,
+       colors = morsecodes.colors,
+       glyphs = morsecodes.glyphs,
+       lines = morsecodes.lines,
+       linecolors = morsecodes.linecolors)
xgvis /tmp/RtmpiVHdhY/xgvis-56f32f43 & 
sh: line 1: xgvis: command not found
> 
> ##>   2) Show lines by hitting "l" with the mouse over the plot.
> ##>   3) Examine morsecode labels by hitting "i" and mousing around on the plot.
> ##>   3b) Press "r" (on the plot) to switch 3D rotation in xgobi.
> ##>   4) Run MDS in 3D by clicking "Run MDS" (in xgvis).
> ##>   5) Speed up the optimization by increasing the "Stepsize" with the slider.
> ##>      The "Stress function" value may go as low as 0.1925 (MM).
> ##>   6) When the optimization calms down, click "Run MDS" to toggle MDS off.
> ##>   7) Rotate the MDS configuration in 3D {by "r" with mouse over plot}.
> ##>   8) Increase the rotation speed with the slider in the top left and
> ##>      control the rotation direction by dragging the mouse on the plot.
> ##>   9) You can check out the initial configuration by
> 
> ## In order to have no color warning :
> Mcolors <- unique(morsecodes.colors)
> (Mcolors <- paste("*brushColor", 0:(length(Mcolors)-1),": ", Mcolors, sep=""))
[1] "*brushColor0: SkyBlue" "*brushColor1: Green"   "*brushColor2: Yellow" 
[4] "*brushColor3: HotPink" "*brushColor4: Red"    
> 
> xgobi(morsecodes.pos, collab = morsecodes.col, rowlab = mc.row,
+       colors = morsecodes.colors,
+       glyphs = morsecodes.glyphs,
+       lines  = morsecodes.lines,
+       linecolors = morsecodes.linecolors,
+       resources= c("*showLines: True", Mcolors))
xgobi -title 'morsecodes.pos' -std mmx /tmp/RtmpiVHdhY/xgobi-mrscd77a4044d & 
sh: line 1: xgobi: command not found
> 
> ##>      This XGobi window will be linked with
> ##>      the XGvis window for glyph-color brushing and labeling.
> 
> 
> 
> ### * <FOOTER>
> ###
> cat("Time elapsed: ", proc.time() - get("ptime", env = .CheckExEnv),"\n")
Time elapsed:  12.96 1.75 22.31 0.02 0.1 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')