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('E',1,'F',0,'F',1,'H',1,'H',1,'H',1,'E',1,'F',1,'E',1,'F',0,'H',0,'E',0,'F',1,'H',0,'E',0,'H',0,'E',1,'F',1,'H',0,'F',0,'H',0,'H',1,'H',0,'E',0,'F',0,'E',0,'E',0,'F',1,'F',0,'H',0,'E',1,'E',1,'H',1,'E',1,'F',1,'E',1,'F',0,'H',0,'E',0,'F',0,'F',0,'F',0,'F',0,'H',1,'E',0,'E',0,'H',0,'E',1,'F',1,'F',0,'H',0,'E',1,'F',1,'E',1,'H',1,'H',1,'H',1,'E',1,'H',0,'E',0,'H',1,'F',1,'H',1,'F',0,'E',1,'E',1,'F',0,'H',1,'F',0,'E',1,'E',1,'H',0,'H',1,'F',1,'H',1,'E',0,'F',1,'E',0,'E',0,'E',0,'F',1,'E',1,'F',1,'H',1,'H',1,'H',1,'F',0,'H',1,'H',1,'F',1,'F',1,'H',0,'F',1,'H',1,'E',0,'F',1,'E',0,'H',1,'F',1,'F',1,'H',1,'E',1,'F',0,'H',1,'E',1,'F',0,'H',0,'H',1,'F',1,'F',1,'H',1,'E',0,'H',1,'E',1,'E',0,'F',1,'F',1),dim=c(2,117),dimnames=list(c('treat','gender'),1:117))
>  y <- array(NA,dim=c(2,117),dimnames=list(c('treat','gender'),1:117))
>  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'
> 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,] "E"  "1" 
  [2,] "F"  "0" 
  [3,] "F"  "1" 
  [4,] "H"  "1" 
  [5,] "H"  "1" 
  [6,] "H"  "1" 
  [7,] "E"  "1" 
  [8,] "F"  "1" 
  [9,] "E"  "1" 
 [10,] "F"  "0" 
 [11,] "H"  "0" 
 [12,] "E"  "0" 
 [13,] "F"  "1" 
 [14,] "H"  "0" 
 [15,] "E"  "0" 
 [16,] "H"  "0" 
 [17,] "E"  "1" 
 [18,] "F"  "1" 
 [19,] "H"  "0" 
 [20,] "F"  "0" 
 [21,] "H"  "0" 
 [22,] "H"  "1" 
 [23,] "H"  "0" 
 [24,] "E"  "0" 
 [25,] "F"  "0" 
 [26,] "E"  "0" 
 [27,] "E"  "0" 
 [28,] "F"  "1" 
 [29,] "F"  "0" 
 [30,] "H"  "0" 
 [31,] "E"  "1" 
 [32,] "E"  "1" 
 [33,] "H"  "1" 
 [34,] "E"  "1" 
 [35,] "F"  "1" 
 [36,] "E"  "1" 
 [37,] "F"  "0" 
 [38,] "H"  "0" 
 [39,] "E"  "0" 
 [40,] "F"  "0" 
 [41,] "F"  "0" 
 [42,] "F"  "0" 
 [43,] "F"  "0" 
 [44,] "H"  "1" 
 [45,] "E"  "0" 
 [46,] "E"  "0" 
 [47,] "H"  "0" 
 [48,] "E"  "1" 
 [49,] "F"  "1" 
 [50,] "F"  "0" 
 [51,] "H"  "0" 
 [52,] "E"  "1" 
 [53,] "F"  "1" 
 [54,] "E"  "1" 
 [55,] "H"  "1" 
 [56,] "H"  "1" 
 [57,] "H"  "1" 
 [58,] "E"  "1" 
 [59,] "H"  "0" 
 [60,] "E"  "0" 
 [61,] "H"  "1" 
 [62,] "F"  "1" 
 [63,] "H"  "1" 
 [64,] "F"  "0" 
 [65,] "E"  "1" 
 [66,] "E"  "1" 
 [67,] "F"  "0" 
 [68,] "H"  "1" 
 [69,] "F"  "0" 
 [70,] "E"  "1" 
 [71,] "E"  "1" 
 [72,] "H"  "0" 
 [73,] "H"  "1" 
 [74,] "F"  "1" 
 [75,] "H"  "1" 
 [76,] "E"  "0" 
 [77,] "F"  "1" 
 [78,] "E"  "0" 
 [79,] "E"  "0" 
 [80,] "E"  "0" 
 [81,] "F"  "1" 
 [82,] "E"  "1" 
 [83,] "F"  "1" 
 [84,] "H"  "1" 
 [85,] "H"  "1" 
 [86,] "H"  "1" 
 [87,] "F"  "0" 
 [88,] "H"  "1" 
 [89,] "H"  "1" 
 [90,] "F"  "1" 
 [91,] "F"  "1" 
 [92,] "H"  "0" 
 [93,] "F"  "1" 
 [94,] "H"  "1" 
 [95,] "E"  "0" 
 [96,] "F"  "1" 
 [97,] "E"  "0" 
 [98,] "H"  "1" 
 [99,] "F"  "1" 
[100,] "F"  "1" 
[101,] "H"  "1" 
[102,] "E"  "1" 
[103,] "F"  "0" 
[104,] "H"  "1" 
[105,] "E"  "1" 
[106,] "F"  "0" 
[107,] "H"  "0" 
[108,] "H"  "1" 
[109,] "F"  "1" 
[110,] "F"  "1" 
[111,] "H"  "1" 
[112,] "E"  "0" 
[113,] "H"  "1" 
[114,] "E"  "1" 
[115,] "E"  "0" 
[116,] "F"  "1" 
[117,] "F"  "1" 
> (table1 <- table(z[,cat1],z[,cat2]))
   
     0  1
  E 17 20
  F 17 23
  H 14 26
> (V1<-dimnames(y)[[1]][cat1])
[1] "treat"
> (V2<-dimnames(y)[[1]][cat2])
[1] "gender"
> postscript(file="/var/fisher/rcomp/tmp/1uj2s1356024493.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/2um341356024493.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 = 1.0064, df = NA, p-value = 0.6277

> if (par3 == 'McNemar Chi-Squared') {
+ (cst <- mcnemar.test(table1))
+ }
> if (par3 != 'McNemar Chi-Squared') {
+ 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$expected[nr, nc], digits=2), 1, FALSE)
+ }
+ a<-table.row.end(a)
+ }
+ a<-table.end(a)
+ table.save(a,file="/var/fisher/rcomp/tmp/33vpe1356024493.tab") 
+ }
> a<-table.start()
> a<-table.row.start(a)
> a<-table.element(a,'Statistical Results',2,TRUE)
> a<-table.row.end(a)
> a<-table.row.start(a)
> a<-table.element(a, cst$method, 2,TRUE)
> a<-table.row.end(a)
> a<-table.row.start(a)
> a<-table.element(a, 'Chi Square Statistic', 1, TRUE)
> a<-table.element(a, round(cst$statistic, digits=2), 1,FALSE)
> a<-table.row.end(a)
> if(!simulate.p.value){
+ a<-table.row.start(a)
+ a<-table.element(a, 'Degrees of Freedom', 1, TRUE)
+ a<-table.element(a, cst$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/4f06m1356024493.tab") 
> 
> try(system("convert tmp/1uj2s1356024493.ps tmp/1uj2s1356024493.png",intern=TRUE))
character(0)
> 
> 
> proc.time()
   user  system elapsed 
  1.426   0.299   1.746