R version 2.15.2 (2012-10-26) -- "Trick or Treat"
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: i686-pc-linux-gnu (32-bit)

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> x <- array(list('Treatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'Treatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'Treatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'Treatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Good'
+ ,'Treatment'
+ ,'Good'
+ ,'Treatment'
+ ,'Bad'
+ ,'Treatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Good'
+ ,'Treatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Good'
+ ,'Treatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'Treatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'Treatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Good'
+ ,'Treatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Good'
+ ,'Treatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'Treatment'
+ ,'Bad'
+ ,'Treatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'Treatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Good'
+ ,'Treatment'
+ ,'Good'
+ ,'Treatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'Treatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'Treatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Good'
+ ,'Treatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Good'
+ ,'Treatment'
+ ,'Good'
+ ,'Treatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Bad'
+ ,NA
+ ,'Good'
+ ,NA
+ ,'Good'
+ ,NA
+ ,'Bad'
+ ,NA
+ ,'Good'
+ ,NA
+ ,'Bad'
+ ,NA
+ ,'Bad'
+ ,NA
+ ,'Bad'
+ ,NA
+ ,'Bad'
+ ,NA
+ ,'Bad'
+ ,NA
+ ,'Good'
+ ,NA
+ ,'Bad'
+ ,NA
+ ,'Bad'
+ ,NA
+ ,'Bad'
+ ,NA
+ ,'Good'
+ ,NA
+ ,'Good'
+ ,NA
+ ,'Bad'
+ ,NA
+ ,'Bad'
+ ,NA
+ ,'Bad'
+ ,NA
+ ,'Bad'
+ ,NA
+ ,'Bad'
+ ,NA
+ ,'Bad'
+ ,NA
+ ,'Bad'
+ ,NA
+ ,'Bad'
+ ,NA
+ ,'Bad'
+ ,NA
+ ,'Bad'
+ ,NA
+ ,'Bad'
+ ,NA
+ ,'Bad'
+ ,NA
+ ,'Bad'
+ ,NA
+ ,'Bad'
+ ,NA
+ ,'Bad'
+ ,NA
+ ,'Good'
+ ,NA
+ ,'Bad'
+ ,NA
+ ,'Bad'
+ ,NA
+ ,'Good'
+ ,NA
+ ,'Bad'
+ ,NA
+ ,'Bad'
+ ,NA
+ ,'Bad'
+ ,NA
+ ,'Good'
+ ,NA
+ ,'Good'
+ ,NA
+ ,'Bad'
+ ,NA
+ ,'Bad'
+ ,NA
+ ,'Good'
+ ,NA
+ ,'Bad'
+ ,NA
+ ,'Good'
+ ,NA
+ ,'Bad'
+ ,NA
+ ,'Good'
+ ,NA
+ ,'Bad'
+ ,NA
+ ,'Bad'
+ ,NA
+ ,'Bad'
+ ,NA
+ ,'Bad'
+ ,NA
+ ,'Good'
+ ,NA
+ ,'Good'
+ ,NA
+ ,'Bad'
+ ,NA
+ ,'Bad'
+ ,NA
+ ,'Good'
+ ,NA
+ ,'Good'
+ ,NA
+ ,'Bad'
+ ,NA
+ ,'Good'
+ ,NA
+ ,'Bad'
+ ,NA
+ ,'Good'
+ ,NA
+ ,'Bad'
+ ,NA
+ ,'Bad'
+ ,NA
+ ,'Bad'
+ ,NA
+ ,'Good'
+ ,NA
+ ,'Good'
+ ,NA
+ ,'Bad'
+ ,NA
+ ,'Bad'
+ ,NA
+ ,'Bad')
+ ,dim=c(2
+ ,154)
+ ,dimnames=list(c('T40'
+ ,'Outcome')
+ ,1:154))
>  y <- array(NA,dim=c(2,154),dimnames=list(c('T40','Outcome'),1:154))
>  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 = 'Exact Pearson Chi-Squared by Simulation'
> par2 = '2'
> par1 = '1'
> main = 'Association Plot'
> par3 <- 'Exact Pearson Chi-Squared by Simulation'
> par2 <- '2'
> par1 <- '1'
> #'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,] "Treatment"   "Good"
  [2,] "NoTreatment" "Bad" 
  [3,] "NoTreatment" "Bad" 
  [4,] "NoTreatment" "Bad" 
  [5,] "NoTreatment" "Bad" 
  [6,] "NoTreatment" "Good"
  [7,] "NoTreatment" "Bad" 
  [8,] "Treatment"   "Bad" 
  [9,] "NoTreatment" "Good"
 [10,] "NoTreatment" "Bad" 
 [11,] "Treatment"   "Bad" 
 [12,] "NoTreatment" "Bad" 
 [13,] "NoTreatment" "Bad" 
 [14,] "Treatment"   "Bad" 
 [15,] "NoTreatment" "Good"
 [16,] "Treatment"   "Good"
 [17,] "Treatment"   "Bad" 
 [18,] "Treatment"   "Bad" 
 [19,] "NoTreatment" "Good"
 [20,] "Treatment"   "Good"
 [21,] "NoTreatment" "Bad" 
 [22,] "NoTreatment" "Good"
 [23,] "NoTreatment" "Good"
 [24,] "NoTreatment" "Good"
 [25,] "Treatment"   "Good"
 [26,] "NoTreatment" "Bad" 
 [27,] "NoTreatment" "Good"
 [28,] "NoTreatment" "Bad" 
 [29,] "NoTreatment" "Good"
 [30,] "NoTreatment" "Bad" 
 [31,] "NoTreatment" "Bad" 
 [32,] "NoTreatment" "Bad" 
 [33,] "NoTreatment" "Bad" 
 [34,] "Treatment"   "Good"
 [35,] "NoTreatment" "Bad" 
 [36,] "NoTreatment" "Bad" 
 [37,] "Treatment"   "Bad" 
 [38,] "NoTreatment" "Good"
 [39,] "NoTreatment" "Good"
 [40,] "Treatment"   "Bad" 
 [41,] "NoTreatment" "Good"
 [42,] "NoTreatment" "Good"
 [43,] "NoTreatment" "Good"
 [44,] "Treatment"   "Bad" 
 [45,] "NoTreatment" "Bad" 
 [46,] "NoTreatment" "Good"
 [47,] "NoTreatment" "Bad" 
 [48,] "NoTreatment" "Good"
 [49,] "NoTreatment" "Good"
 [50,] "NoTreatment" "Bad" 
 [51,] "Treatment"   "Bad" 
 [52,] "Treatment"   "Bad" 
 [53,] "NoTreatment" "Good"
 [54,] "NoTreatment" "Bad" 
 [55,] "NoTreatment" "Bad" 
 [56,] "Treatment"   "Good"
 [57,] "NoTreatment" "Good"
 [58,] "NoTreatment" "Good"
 [59,] "NoTreatment" "Good"
 [60,] "Treatment"   "Good"
 [61,] "Treatment"   "Good"
 [62,] "NoTreatment" "Bad" 
 [63,] "NoTreatment" "Bad" 
 [64,] "Treatment"   "Good"
 [65,] "NoTreatment" "Bad" 
 [66,] "NoTreatment" "Bad" 
 [67,] "Treatment"   "Bad" 
 [68,] "NoTreatment" "Bad" 
 [69,] "NoTreatment" "Good"
 [70,] "NoTreatment" "Bad" 
 [71,] "NoTreatment" "Bad" 
 [72,] "NoTreatment" "Good"
 [73,] "NoTreatment" "Good"
 [74,] "NoTreatment" "Bad" 
 [75,] "NoTreatment" "Good"
 [76,] "Treatment"   "Good"
 [77,] "NoTreatment" "Good"
 [78,] "NoTreatment" "Good"
 [79,] "Treatment"   "Good"
 [80,] "Treatment"   "Bad" 
 [81,] "NoTreatment" "Bad" 
 [82,] "NoTreatment" "Good"
 [83,] "NoTreatment" "Bad" 
 [84,] "NoTreatment" "Bad" 
 [85,] "NoTreatment" "Good"
 [86,] "NoTreatment" "Bad" 
 [87,] NA            "Good"
 [88,] NA            "Good"
 [89,] NA            "Bad" 
 [90,] NA            "Good"
 [91,] NA            "Bad" 
 [92,] NA            "Bad" 
 [93,] NA            "Bad" 
 [94,] NA            "Bad" 
 [95,] NA            "Bad" 
 [96,] NA            "Good"
 [97,] NA            "Bad" 
 [98,] NA            "Bad" 
 [99,] NA            "Bad" 
[100,] NA            "Good"
[101,] NA            "Good"
[102,] NA            "Bad" 
[103,] NA            "Bad" 
[104,] NA            "Bad" 
[105,] NA            "Bad" 
[106,] NA            "Bad" 
[107,] NA            "Bad" 
[108,] NA            "Bad" 
[109,] NA            "Bad" 
[110,] NA            "Bad" 
[111,] NA            "Bad" 
[112,] NA            "Bad" 
[113,] NA            "Bad" 
[114,] NA            "Bad" 
[115,] NA            "Bad" 
[116,] NA            "Bad" 
[117,] NA            "Good"
[118,] NA            "Bad" 
[119,] NA            "Bad" 
[120,] NA            "Good"
[121,] NA            "Bad" 
[122,] NA            "Bad" 
[123,] NA            "Bad" 
[124,] NA            "Good"
[125,] NA            "Good"
[126,] NA            "Bad" 
[127,] NA            "Bad" 
[128,] NA            "Good"
[129,] NA            "Bad" 
[130,] NA            "Good"
[131,] NA            "Bad" 
[132,] NA            "Good"
[133,] NA            "Bad" 
[134,] NA            "Bad" 
[135,] NA            "Bad" 
[136,] NA            "Bad" 
[137,] NA            "Good"
[138,] NA            "Good"
[139,] NA            "Bad" 
[140,] NA            "Bad" 
[141,] NA            "Good"
[142,] NA            "Good"
[143,] NA            "Bad" 
[144,] NA            "Good"
[145,] NA            "Bad" 
[146,] NA            "Good"
[147,] NA            "Bad" 
[148,] NA            "Bad" 
[149,] NA            "Bad" 
[150,] NA            "Good"
[151,] NA            "Good"
[152,] NA            "Bad" 
[153,] NA            "Bad" 
[154,] NA            "Bad" 
> (table1 <- table(z[,cat1],z[,cat2]))
             
              Bad Good
  NoTreatment  34   29
  Treatment    12   11
> (V1<-dimnames(y)[[1]][cat1])
[1] "T40"
> (V2<-dimnames(y)[[1]][cat2])
[1] "Outcome"
> postscript(file="/var/wessaorg/rcomp/tmp/1kl621355658615.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)
> dev.off()
null device 
          1 
> 
> #Note: the /var/wessaorg/rcomp/createtable file can be downloaded at http://www.wessa.net/cretab
> load(file="/var/wessaorg/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/wessaorg/rcomp/tmp/245ho1355658615.tab") 
> (cst<-chisq.test(table1, simulate.p.value=simulate.p.value) )

	Pearson's Chi-squared test with simulated p-value (based on 2000
	replicates)

data:  table1 
X-squared = 0.0218, df = NA, p-value = 1

> 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$expected[nr, nc], digits=2), 1, FALSE)
+ }
+ a<-table.row.end(a)
+ }
+ a<-table.end(a)
+ table.save(a,file="/var/wessaorg/rcomp/tmp/3v1111355658615.tab") 
+ }
> a<-table.start()
> a<-table.row.start(a)
> a<-table.element(a,'Statistical Results',2,TRUE)
> a<-table.row.end(a)
> a<-table.row.start(a)
> a<-table.element(a, cst$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/wessaorg/rcomp/tmp/4ns751355658615.tab") 
> 
> try(system("convert tmp/1kl621355658615.ps tmp/1kl621355658615.png",intern=TRUE))
character(0)
> 
> 
> proc.time()
   user  system elapsed 
  1.759   0.267   1.969