R version 2.12.0 (2010-10-15)
Copyright (C) 2010 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: i486-pc-linux-gnu (32-bit)

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Type 'license()' or 'licence()' for distribution details.

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Type 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.

> x <- array(list('C'
+ ,'A'
+ ,'D'
+ ,'B'
+ ,'A'
+ ,'B'
+ ,'D'
+ ,'B'
+ ,'B'
+ ,'B'
+ ,'B'
+ ,'C'
+ ,'C'
+ ,'D'
+ ,'C'
+ ,'A'
+ ,'B'
+ ,'C'
+ ,'B'
+ ,'C'
+ ,'B'
+ ,'A'
+ ,'A'
+ ,'A'
+ ,'C'
+ ,'A'
+ ,'D'
+ ,'B'
+ ,'C'
+ ,'B'
+ ,'A'
+ ,'D'
+ ,'D'
+ ,'B'
+ ,'C'
+ ,'B'
+ ,'A'
+ ,'C'
+ ,'A'
+ ,'A'
+ ,'C'
+ ,'B'
+ ,'A'
+ ,'A'
+ ,'B'
+ ,'A'
+ ,'D'
+ ,'B'
+ ,'C'
+ ,'B'
+ ,'A'
+ ,'B'
+ ,'A'
+ ,'C'
+ ,'B'
+ ,'B'
+ ,'A'
+ ,'B'
+ ,'B'
+ ,'C'
+ ,'D'
+ ,'C'
+ ,'A'
+ ,'A'
+ ,'A'
+ ,'D'
+ ,'B'
+ ,'C'
+ ,'A'
+ ,'B'
+ ,'D'
+ ,'C'
+ ,'D'
+ ,'C'
+ ,'B'
+ ,'D'
+ ,'A'
+ ,'A'
+ ,'B'
+ ,'C'
+ ,'A'
+ ,'A'
+ ,'B'
+ ,'B'
+ ,'A'
+ ,'B'
+ ,'A'
+ ,'D'
+ ,'D'
+ ,'B'
+ ,'C'
+ ,'B'
+ ,'B'
+ ,'A'
+ ,'D'
+ ,'C'
+ ,'B'
+ ,'B'
+ ,'A'
+ ,'C'
+ ,'D'
+ ,'D'
+ ,'B'
+ ,'B'
+ ,'B'
+ ,'B'
+ ,'D'
+ ,'D'
+ ,'A'
+ ,'A'
+ ,'B'
+ ,'B'
+ ,'B'
+ ,'B'
+ ,'B'
+ ,'C'
+ ,'D'
+ ,'D'
+ ,'B'
+ ,'B'
+ ,'B'
+ ,'B'
+ ,'B'
+ ,'C'
+ ,'B'
+ ,'C'
+ ,'D'
+ ,'B'
+ ,'C'
+ ,'D'
+ ,'D'
+ ,'D'
+ ,'C'
+ ,'B'
+ ,'B'
+ ,'B'
+ ,'D'
+ ,'C'
+ ,'C'
+ ,'B'
+ ,'B'
+ ,'C'
+ ,'D'
+ ,'C'
+ ,'A'
+ ,'B'
+ ,'A'
+ ,'A'
+ ,'A'
+ ,'C'
+ ,'B'
+ ,'B'
+ ,'B'
+ ,'C'
+ ,'B'
+ ,'B'
+ ,'D'
+ ,'B'
+ ,'B'
+ ,'C'
+ ,'B'
+ ,'A'
+ ,'C'
+ ,'B'
+ ,'B'
+ ,'B'
+ ,'A'
+ ,'A'
+ ,'D'
+ ,'D'
+ ,'A'
+ ,'C'
+ ,'C'
+ ,'D'
+ ,'D'
+ ,'B'
+ ,'A'
+ ,'A'
+ ,'B'
+ ,'C'
+ ,'B'
+ ,'B'
+ ,'D'
+ ,'C'
+ ,'D'
+ ,'D'
+ ,'A'
+ ,'C'
+ ,'C'
+ ,'A'
+ ,'A'
+ ,'A'
+ ,'B'
+ ,'B'
+ ,'A'
+ ,'A'
+ ,'B'
+ ,'C'
+ ,'B'
+ ,'B'
+ ,'A'
+ ,'A'
+ ,'B'
+ ,'C'
+ ,'A'
+ ,'A'
+ ,'A'
+ ,'A'
+ ,'C'
+ ,'A'
+ ,'C'
+ ,'D'
+ ,'D'
+ ,'C'
+ ,'B'
+ ,'A'
+ ,'A'
+ ,'A'
+ ,'B'
+ ,'C'
+ ,'B'
+ ,'C'
+ ,'A'
+ ,'A'
+ ,'D'
+ ,'A'
+ ,'A'
+ ,'A'
+ ,'D'
+ ,'A'
+ ,'B'
+ ,'D'
+ ,'A'
+ ,'B'
+ ,'D'
+ ,'C'
+ ,'A'
+ ,'B'
+ ,'D'
+ ,'D'
+ ,'D'
+ ,'D'
+ ,'B'
+ ,'C'
+ ,'B'
+ ,'A'
+ ,'D'
+ ,'C'
+ ,'D'
+ ,'C'
+ ,'A'
+ ,'B'
+ ,'D'
+ ,'D'
+ ,'C'
+ ,'B'
+ ,'B'
+ ,'B'
+ ,'C'
+ ,'B'
+ ,'B'
+ ,'A'
+ ,'B'
+ ,'B'
+ ,'C'
+ ,'D'
+ ,'D'
+ ,'D'
+ ,'B'
+ ,'B'
+ ,'A'
+ ,'A'
+ ,'B'
+ ,'C'
+ ,'B'
+ ,'B'
+ ,'B'
+ ,'B'
+ ,'B'
+ ,'A'
+ ,'D'
+ ,'B'
+ ,'A'
+ ,'A'
+ ,'A'
+ ,'A'
+ ,'D'
+ ,'D'
+ ,'A'
+ ,'A'
+ ,'C'
+ ,'C'
+ ,'A'
+ ,'B'
+ ,'C'
+ ,'C'
+ ,'B'
+ ,'B'
+ ,'B'
+ ,'A'
+ ,'C'
+ ,'B'
+ ,'A'
+ ,'B'
+ ,'A'
+ ,'C'
+ ,'B'
+ ,'C'
+ ,'A'
+ ,'A'
+ ,'B'
+ ,'C'
+ ,'C'
+ ,'B'
+ ,'A'
+ ,'A'
+ ,'A'
+ ,'A')
+ ,dim=c(2
+ ,159)
+ ,dimnames=list(c('PE'
+ ,'PC
')
+ ,1:159))
>  y <- array(NA,dim=c(2,159),dimnames=list(c('PE','PC
'),1:159))
>  for (i in 1:dim(x)[1])
+  {
+  	for (j in 1:dim(x)[2])
+  	{
+  		y[i,j] <- as.numeric(x[i,j])
+  	}
+  }
There were 50 or more warnings (use warnings() to see the first 50)
> par3 = 'Pearson Chi-Squared'
> par2 = '2'
> par1 = '1'
> main = 'Association Plot'
> #'GNU S' R Code compiled by R2WASP v. 1.0.44 ()
> #Author: Dr. Ian E. Holliday
> #To cite this work: Ian E. Holliday, 2009, YOUR SOFTWARE TITLE (vNUMBER) in Free Statistics Software (v$_version), Office for Research Development and Education, URL http://www.wessa.net/rwasp_YOURPAGE.wasp/
> #Source of accompanying publication: 
> #Technical description: 
> library(vcd)
Loading required package: MASS
Loading required package: grid
Loading required package: colorspace
> cat1 <- as.numeric(par1) #
> cat2<- as.numeric(par2) #
> simulate.p.value=FALSE
> if (par3 == 'Exact Pearson Chi-Squared by Simulation') simulate.p.value=TRUE
> x <- t(x)
> (z <- array(unlist(x),dim=c(length(x[,1]),length(x[1,]))))
       [,1] [,2]
  [1,] "C"  "A" 
  [2,] "D"  "B" 
  [3,] "A"  "B" 
  [4,] "D"  "B" 
  [5,] "B"  "B" 
  [6,] "B"  "C" 
  [7,] "C"  "D" 
  [8,] "C"  "A" 
  [9,] "B"  "C" 
 [10,] "B"  "C" 
 [11,] "B"  "A" 
 [12,] "A"  "A" 
 [13,] "C"  "A" 
 [14,] "D"  "B" 
 [15,] "C"  "B" 
 [16,] "A"  "D" 
 [17,] "D"  "B" 
 [18,] "C"  "B" 
 [19,] "A"  "C" 
 [20,] "A"  "A" 
 [21,] "C"  "B" 
 [22,] "A"  "A" 
 [23,] "B"  "A" 
 [24,] "D"  "B" 
 [25,] "C"  "B" 
 [26,] "A"  "B" 
 [27,] "A"  "C" 
 [28,] "B"  "B" 
 [29,] "A"  "B" 
 [30,] "B"  "C" 
 [31,] "D"  "C" 
 [32,] "A"  "A" 
 [33,] "A"  "D" 
 [34,] "B"  "C" 
 [35,] "A"  "B" 
 [36,] "D"  "C" 
 [37,] "D"  "C" 
 [38,] "B"  "D" 
 [39,] "A"  "A" 
 [40,] "B"  "C" 
 [41,] "A"  "A" 
 [42,] "B"  "B" 
 [43,] "A"  "B" 
 [44,] "A"  "D" 
 [45,] "D"  "B" 
 [46,] "C"  "B" 
 [47,] "B"  "A" 
 [48,] "D"  "C" 
 [49,] "B"  "B" 
 [50,] "A"  "C" 
 [51,] "D"  "D" 
 [52,] "B"  "B" 
 [53,] "B"  "B" 
 [54,] "D"  "D" 
 [55,] "A"  "A" 
 [56,] "B"  "B" 
 [57,] "B"  "B" 
 [58,] "B"  "C" 
 [59,] "D"  "D" 
 [60,] "B"  "B" 
 [61,] "B"  "B" 
 [62,] "B"  "C" 
 [63,] "B"  "C" 
 [64,] "D"  "B" 
 [65,] "C"  "D" 
 [66,] "D"  "D" 
 [67,] "C"  "B" 
 [68,] "B"  "B" 
 [69,] "D"  "C" 
 [70,] "C"  "B" 
 [71,] "B"  "C" 
 [72,] "D"  "C" 
 [73,] "A"  "B" 
 [74,] "A"  "A" 
 [75,] "A"  "C" 
 [76,] "B"  "B" 
 [77,] "B"  "C" 
 [78,] "B"  "B" 
 [79,] "D"  "B" 
 [80,] "B"  "C" 
 [81,] "B"  "A" 
 [82,] "C"  "B" 
 [83,] "B"  "B" 
 [84,] "A"  "A" 
 [85,] "D"  "D" 
 [86,] "A"  "C" 
 [87,] "C"  "D" 
 [88,] "D"  "B" 
 [89,] "A"  "A" 
 [90,] "B"  "C" 
 [91,] "B"  "B" 
 [92,] "D"  "C" 
 [93,] "D"  "D" 
 [94,] "A"  "C" 
 [95,] "C"  "A" 
 [96,] "A"  "A" 
 [97,] "B"  "B" 
 [98,] "A"  "A" 
 [99,] "B"  "C" 
[100,] "B"  "B" 
[101,] "A"  "A" 
[102,] "B"  "C" 
[103,] "A"  "A" 
[104,] "A"  "A" 
[105,] "C"  "A" 
[106,] "C"  "D" 
[107,] "D"  "C" 
[108,] "B"  "A" 
[109,] "A"  "A" 
[110,] "B"  "C" 
[111,] "B"  "C" 
[112,] "A"  "A" 
[113,] "D"  "A" 
[114,] "A"  "A" 
[115,] "D"  "A" 
[116,] "B"  "D" 
[117,] "A"  "B" 
[118,] "D"  "C" 
[119,] "A"  "B" 
[120,] "D"  "D" 
[121,] "D"  "D" 
[122,] "B"  "C" 
[123,] "B"  "A" 
[124,] "D"  "C" 
[125,] "D"  "C" 
[126,] "A"  "B" 
[127,] "D"  "D" 
[128,] "C"  "B" 
[129,] "B"  "B" 
[130,] "C"  "B" 
[131,] "B"  "A" 
[132,] "B"  "B" 
[133,] "C"  "D" 
[134,] "D"  "D" 
[135,] "B"  "B" 
[136,] "A"  "A" 
[137,] "B"  "C" 
[138,] "B"  "B" 
[139,] "B"  "B" 
[140,] "B"  "A" 
[141,] "D"  "B" 
[142,] "A"  "A" 
[143,] "A"  "A" 
[144,] "D"  "D" 
[145,] "A"  "A" 
[146,] "C"  "C" 
[147,] "A"  "B" 
[148,] "C"  "C" 
[149,] "B"  "B" 
[150,] "B"  "A" 
[151,] "C"  "B" 
[152,] "A"  "B" 
[153,] "A"  "C" 
[154,] "B"  "C" 
[155,] "A"  "A" 
[156,] "B"  "C" 
[157,] "C"  "B" 
[158,] "A"  "A" 
[159,] "A"  "A" 
> (table1 <- table(z[,cat1],z[,cat2]))
   
     A  B  C  D
  A 25 11  7  3
  B  9 23 21  2
  C  5 12  2  5
  D  2 10 11 11
> (V1<-dimnames(y)[[1]][cat1])
[1] "PE"
> (V2<-dimnames(y)[[1]][cat2])
[1] "PC\r"
> postscript(file="/var/www/rcomp/tmp/1y39j1292272365.ps",horizontal=F,onefile=F,pagecentre=F,paper="special",width=8.3333333333333,height=5.5555555555556) 
> assoc(ftable(z[,cat1],z[,cat2],row.vars=1,dnn=c(V1,V2)),shade=T)
Warning message:
In grid.Call.graphics("L_text", as.graphicsAnnot(x$label), x$x,  :
  font width unknown for character 0xd
> dev.off()
null device 
          1 
> 
> #Note: the /var/www/rcomp/createtable file can be downloaded at http://www.wessa.net/cretab
> load(file="/var/www/rcomp/createtable")
> 
> a<-table.start()
> a<-table.row.start(a)
> a<-table.element(a,'Tabulation of Results',ncol(table1)+1,TRUE)
> a<-table.row.end(a)
> a<-table.row.start(a)
> a<-table.element(a,paste(V1,' x ', V2),ncol(table1)+1,TRUE)
> a<-table.row.end(a)
> a<-table.row.start(a)
> a<-table.element(a, ' ', 1,TRUE)
> for(nc in 1:ncol(table1)){
+ a<-table.element(a, colnames(table1)[nc], 1, TRUE)
+ }
> a<-table.row.end(a)
> for(nr in 1:nrow(table1) ){
+ a<-table.element(a, rownames(table1)[nr], 1, TRUE)
+ for(nc in 1:ncol(table1) ){
+ a<-table.element(a, table1[nr, nc], 1, FALSE)
+ }
+ a<-table.row.end(a)
+ }
> a<-table.end(a)
> table.save(a,file="/var/www/rcomp/tmp/2j4p71292272365.tab") 
> (cst<-chisq.test(table1, simulate.p.value=simulate.p.value) )

	Pearson's Chi-squared test

data:  table1 
X-squared = 50.5997, df = 9, p-value = 8.307e-08

Warning message:
In chisq.test(table1, simulate.p.value = simulate.p.value) :
  Chi-squared approximation may be incorrect
> if (par3 == 'McNemar Chi-Squared') {
+ (cst <- mcnemar.test(table1))
+ }
> if (par3=='Fisher Exact Test') {
+ (cst <- fisher.test(table1))
+ }
> if ((par3 != 'McNemar Chi-Squared') & (par3 != 'Fisher Exact Test')) {
+ a<-table.start()
+ a<-table.row.start(a)
+ a<-table.element(a,'Tabulation of Expected Results',ncol(table1)+1,TRUE)
+ a<-table.row.end(a)
+ a<-table.row.start(a)
+ a<-table.element(a,paste(V1,' x ', V2),ncol(table1)+1,TRUE)
+ a<-table.row.end(a)
+ a<-table.row.start(a)
+ a<-table.element(a, ' ', 1,TRUE)
+ for(nc in 1:ncol(table1)){
+ a<-table.element(a, colnames(table1)[nc], 1, TRUE)
+ }
+ a<-table.row.end(a)
+ for(nr in 1:nrow(table1) ){
+ a<-table.element(a, rownames(table1)[nr], 1, TRUE)
+ for(nc in 1:ncol(table1) ){
+ a<-table.element(a, round(cst$expected[nr, nc], digits=2), 1, FALSE)
+ }
+ a<-table.row.end(a)
+ }
+ a<-table.end(a)
+ table.save(a,file="/var/www/rcomp/tmp/3n4od1292272365.tab") 
+ }
> a<-table.start()
> a<-table.row.start(a)
> a<-table.element(a,'Statistical Results',2,TRUE)
> a<-table.row.end(a)
> a<-table.row.start(a)
> a<-table.element(a, cst$method, 2,TRUE)
> a<-table.row.end(a)
> a<-table.row.start(a)
> if (par3=='Pearson Chi-Squared') a<-table.element(a, 'Pearson Chi Square Statistic', 1, TRUE)
> if (par3=='Exact Pearson Chi-Squared by Simulation') a<-table.element(a, 'Exact Pearson Chi Square Statistic', 1, TRUE)
> if (par3=='McNemar Chi-Squared') a<-table.element(a, 'McNemar Chi Square Statistic', 1, TRUE)
> if (par3=='Fisher Exact Test') a<-table.element(a, 'Odds Ratio', 1, TRUE)
> if (par3=='Fisher Exact Test') {
+ if ((ncol(table1) == 2) & (nrow(table1) == 2)) {
+ a<-table.element(a, round(cst$estimate, digits=2), 1,FALSE)
+ } else {
+ a<-table.element(a, '--', 1,FALSE)
+ }
+ } else {
+ a<-table.element(a, round(cst$statistic, digits=2), 1,FALSE)
+ }
> a<-table.row.end(a)
> if(!simulate.p.value){
+ if(par3!='Fisher Exact Test') {
+ a<-table.row.start(a)
+ a<-table.element(a, 'Degrees of Freedom', 1, TRUE)
+ a<-table.element(a, cst$parameter, 1,FALSE)
+ a<-table.row.end(a)
+ }
+ }
> a<-table.row.start(a)
> a<-table.element(a, 'P value', 1, TRUE)
> a<-table.element(a, round(cst$p.value, digits=2), 1,FALSE)
> a<-table.row.end(a)
> a<-table.end(a)
> table.save(a,file="/var/www/rcomp/tmp/4jwm31292272365.tab") 
> 
> try(system("convert tmp/1y39j1292272365.ps tmp/1y39j1292272365.png",intern=TRUE))
character(0)
> 
> 
> proc.time()
   user  system elapsed 
   0.94    0.27    1.17