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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You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> x <- array(list('Good'
+ ,'Treatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'Treatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'Treatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'Treatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Good'
+ ,'Treatment'
+ ,'Bad'
+ ,'Treatment'
+ ,'Bad'
+ ,'Treatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Good'
+ ,'Treatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Good'
+ ,'Treatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Good'
+ ,'Treatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'Treatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'Treatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'Treatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'Treatment'
+ ,'Bad'
+ ,'Treatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Good'
+ ,'Treatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Good'
+ ,'Treatment'
+ ,'Good'
+ ,'Treatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Good'
+ ,'Treatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'Treatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Good'
+ ,'Treatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Good'
+ ,'Treatment'
+ ,'Bad'
+ ,'Treatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'Good'
+ ,'NoTreatment'
+ ,'Bad'
+ ,'NoTreatment'
+ ,'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'
+ ,NA)
+ ,dim=c(2
+ ,154)
+ ,dimnames=list(c('outcome'
+ ,'t40')
+ ,1:154))
>  y <- array(NA,dim=c(2,154),dimnames=list(c('outcome','t40'),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 = 'Pearson Chi-Squared'
> par2 = '2'
> par1 = '1'
> main = 'Association Plot'
> par3 <- 'Pearson Chi-Squared'
> 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,] "Good" "Treatment"  
  [2,] "Bad"  "NoTreatment"
  [3,] "Bad"  "NoTreatment"
  [4,] "Bad"  "NoTreatment"
  [5,] "Bad"  "NoTreatment"
  [6,] "Good" "NoTreatment"
  [7,] "Bad"  "NoTreatment"
  [8,] "Bad"  "Treatment"  
  [9,] "Good" "NoTreatment"
 [10,] "Bad"  "NoTreatment"
 [11,] "Bad"  "Treatment"  
 [12,] "Bad"  "NoTreatment"
 [13,] "Bad"  "NoTreatment"
 [14,] "Bad"  "Treatment"  
 [15,] "Good" "NoTreatment"
 [16,] "Good" "Treatment"  
 [17,] "Bad"  "Treatment"  
 [18,] "Bad"  "Treatment"  
 [19,] "Good" "NoTreatment"
 [20,] "Good" "Treatment"  
 [21,] "Bad"  "NoTreatment"
 [22,] "Good" "NoTreatment"
 [23,] "Good" "NoTreatment"
 [24,] "Good" "NoTreatment"
 [25,] "Good" "Treatment"  
 [26,] "Bad"  "NoTreatment"
 [27,] "Good" "NoTreatment"
 [28,] "Bad"  "NoTreatment"
 [29,] "Good" "NoTreatment"
 [30,] "Bad"  "NoTreatment"
 [31,] "Bad"  "NoTreatment"
 [32,] "Bad"  "NoTreatment"
 [33,] "Bad"  "NoTreatment"
 [34,] "Good" "Treatment"  
 [35,] "Bad"  "NoTreatment"
 [36,] "Bad"  "NoTreatment"
 [37,] "Bad"  "Treatment"  
 [38,] "Good" "NoTreatment"
 [39,] "Good" "NoTreatment"
 [40,] "Bad"  "Treatment"  
 [41,] "Good" "NoTreatment"
 [42,] "Good" "NoTreatment"
 [43,] "Good" "NoTreatment"
 [44,] "Bad"  "Treatment"  
 [45,] "Bad"  "NoTreatment"
 [46,] "Good" "NoTreatment"
 [47,] "Bad"  "NoTreatment"
 [48,] "Good" "NoTreatment"
 [49,] "Good" "NoTreatment"
 [50,] "Bad"  "NoTreatment"
 [51,] "Bad"  "Treatment"  
 [52,] "Bad"  "Treatment"  
 [53,] "Good" "NoTreatment"
 [54,] "Bad"  "NoTreatment"
 [55,] "Bad"  "NoTreatment"
 [56,] "Good" "Treatment"  
 [57,] "Good" "NoTreatment"
 [58,] "Good" "NoTreatment"
 [59,] "Good" "NoTreatment"
 [60,] "Good" "Treatment"  
 [61,] "Good" "Treatment"  
 [62,] "Bad"  "NoTreatment"
 [63,] "Bad"  "NoTreatment"
 [64,] "Good" "Treatment"  
 [65,] "Bad"  "NoTreatment"
 [66,] "Bad"  "NoTreatment"
 [67,] "Bad"  "Treatment"  
 [68,] "Bad"  "NoTreatment"
 [69,] "Good" "NoTreatment"
 [70,] "Bad"  "NoTreatment"
 [71,] "Bad"  "NoTreatment"
 [72,] "Good" "NoTreatment"
 [73,] "Good" "NoTreatment"
 [74,] "Bad"  "NoTreatment"
 [75,] "Good" "NoTreatment"
 [76,] "Good" "Treatment"  
 [77,] "Good" "NoTreatment"
 [78,] "Good" "NoTreatment"
 [79,] "Good" "Treatment"  
 [80,] "Bad"  "Treatment"  
 [81,] "Bad"  "NoTreatment"
 [82,] "Good" "NoTreatment"
 [83,] "Bad"  "NoTreatment"
 [84,] "Bad"  "NoTreatment"
 [85,] "Good" "NoTreatment"
 [86,] "Bad"  "NoTreatment"
 [87,] "Good" NA           
 [88,] "Good" NA           
 [89,] "Bad"  NA           
 [90,] "Good" NA           
 [91,] "Bad"  NA           
 [92,] "Bad"  NA           
 [93,] "Bad"  NA           
 [94,] "Bad"  NA           
 [95,] "Bad"  NA           
 [96,] "Good" NA           
 [97,] "Bad"  NA           
 [98,] "Bad"  NA           
 [99,] "Bad"  NA           
[100,] "Good" NA           
[101,] "Good" NA           
[102,] "Bad"  NA           
[103,] "Bad"  NA           
[104,] "Bad"  NA           
[105,] "Bad"  NA           
[106,] "Bad"  NA           
[107,] "Bad"  NA           
[108,] "Bad"  NA           
[109,] "Bad"  NA           
[110,] "Bad"  NA           
[111,] "Bad"  NA           
[112,] "Bad"  NA           
[113,] "Bad"  NA           
[114,] "Bad"  NA           
[115,] "Bad"  NA           
[116,] "Bad"  NA           
[117,] "Good" NA           
[118,] "Bad"  NA           
[119,] "Bad"  NA           
[120,] "Good" NA           
[121,] "Bad"  NA           
[122,] "Bad"  NA           
[123,] "Bad"  NA           
[124,] "Good" NA           
[125,] "Good" NA           
[126,] "Bad"  NA           
[127,] "Bad"  NA           
[128,] "Good" NA           
[129,] "Bad"  NA           
[130,] "Good" NA           
[131,] "Bad"  NA           
[132,] "Good" NA           
[133,] "Bad"  NA           
[134,] "Bad"  NA           
[135,] "Bad"  NA           
[136,] "Bad"  NA           
[137,] "Good" NA           
[138,] "Good" NA           
[139,] "Bad"  NA           
[140,] "Bad"  NA           
[141,] "Good" NA           
[142,] "Good" NA           
[143,] "Bad"  NA           
[144,] "Good" NA           
[145,] "Bad"  NA           
[146,] "Good" NA           
[147,] "Bad"  NA           
[148,] "Bad"  NA           
[149,] "Bad"  NA           
[150,] "Good" NA           
[151,] "Good" NA           
[152,] "Bad"  NA           
[153,] "Bad"  NA           
[154,] "Bad"  NA           
> (table1 <- table(z[,cat1],z[,cat2]))
      
       NoTreatment Treatment
  Bad           34        12
  Good          29        11
> (V1<-dimnames(y)[[1]][cat1])
[1] "outcome"
> (V2<-dimnames(y)[[1]][cat2])
[1] "t40"
> postscript(file="/var/fisher/rcomp/tmp/1y2iq1356107293.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/fisher/rcomp/createtable file can be downloaded at http://www.wessa.net/cretab
> load(file="/var/fisher/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/fisher/rcomp/tmp/2q2r31356107293.tab") 
> (cst<-chisq.test(table1, simulate.p.value=simulate.p.value) )

	Pearson's Chi-squared test with Yates' continuity correction

data:  table1 
X-squared = 0, df = 1, 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$expected[nr, nc], digits=2), 1, FALSE)
+ }
+ a<-table.row.end(a)
+ }
+ a<-table.end(a)
+ table.save(a,file="/var/fisher/rcomp/tmp/3g2e21356107293.tab") 
+ }
> a<-table.start()
> a<-table.row.start(a)
> a<-table.element(a,'Statistical Results',2,TRUE)
> a<-table.row.end(a)
> a<-table.row.start(a)
> a<-table.element(a, cst$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/fisher/rcomp/tmp/454581356107294.tab") 
> 
> try(system("convert tmp/1y2iq1356107293.ps tmp/1y2iq1356107293.png",intern=TRUE))
character(0)
> 
> 
> proc.time()
   user  system elapsed 
  1.513   0.346   1.844