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

> x <- array(list(1
+ ,'4T'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4T'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4T'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4T'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4T'
+ ,2
+ ,'4T'
+ ,1
+ ,'4T'
+ ,1
+ ,'4NT'
+ ,2
+ ,'4T'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4T'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4T'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4T'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4T'
+ ,2
+ ,'4NT'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4T'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4T'
+ ,2
+ ,'4T'
+ ,1
+ ,'4NT'
+ ,2
+ ,'4NT'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4T'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4NT'
+ ,2
+ ,'4T'
+ ,1
+ ,'4T'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4T'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4NT'
+ ,2
+ ,'4T'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4T'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4NT'
+ ,2
+ ,'4T'
+ ,1
+ ,'4T'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4NT'
+ ,2
+ ,'4NT'
+ ,1
+ ,'4NT'
+ ,1
+ ,'4NT'
+ ,1
+ ,'2NT'
+ ,1
+ ,'2T'
+ ,1
+ ,'2NT'
+ ,1
+ ,'2NT'
+ ,1
+ ,'2NT'
+ ,1
+ ,'2T'
+ ,1
+ ,'2NT'
+ ,1
+ ,'2NT'
+ ,1
+ ,'2T'
+ ,1
+ ,'2NT'
+ ,1
+ ,'2T'
+ ,1
+ ,'2NT'
+ ,1
+ ,'2NT'
+ ,1
+ ,'2NT'
+ ,1
+ ,'2NT'
+ ,1
+ ,'2NT'
+ ,1
+ ,'2NT'
+ ,1
+ ,'2NT'
+ ,1
+ ,'2T'
+ ,1
+ ,'2NT'
+ ,1
+ ,'2NT'
+ ,1
+ ,'2T'
+ ,1
+ ,'2NT'
+ ,1
+ ,'2NT'
+ ,1
+ ,'2T'
+ ,1
+ ,'2T'
+ ,1
+ ,'2NT'
+ ,1
+ ,'2T'
+ ,1
+ ,'2NT'
+ ,1
+ ,'2NT'
+ ,1
+ ,'2NT'
+ ,1
+ ,'2NT'
+ ,1
+ ,'2NT'
+ ,1
+ ,'2NT'
+ ,1
+ ,'2NT'
+ ,1
+ ,'2NT'
+ ,1
+ ,'2T'
+ ,1
+ ,'2NT'
+ ,1
+ ,'2NT'
+ ,1
+ ,'2T'
+ ,1
+ ,'2NT'
+ ,1
+ ,'2NT'
+ ,1
+ ,'2NT'
+ ,1
+ ,'2NT'
+ ,1
+ ,'2NT'
+ ,1
+ ,'2NT'
+ ,1
+ ,'2NT'
+ ,1
+ ,'2NT'
+ ,1
+ ,'2NT'
+ ,1
+ ,'2NT'
+ ,1
+ ,'2NT'
+ ,1
+ ,'2T'
+ ,1
+ ,'2T'
+ ,1
+ ,'2NT'
+ ,2
+ ,'2NT'
+ ,1
+ ,'2T'
+ ,1
+ ,'2NT'
+ ,1
+ ,'2NT'
+ ,1
+ ,'2NT'
+ ,1
+ ,'2T'
+ ,1
+ ,'2T'
+ ,1
+ ,'2T'
+ ,1
+ ,'2NT'
+ ,1
+ ,'2NT'
+ ,1
+ ,'2NT'
+ ,2
+ ,'2NT'
+ ,2
+ ,'2NT'
+ ,1
+ ,'2NT')
+ ,dim=c(2
+ ,154)
+ ,dimnames=list(c('x'
+ ,'y')
+ ,1:154))
>  y <- array(NA,dim=c(2,154),dimnames=list(c('x','y'),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'
> 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,] "1"  "4T" 
  [2,] "1"  "4NT"
  [3,] "1"  "4NT"
  [4,] "1"  "4NT"
  [5,] "1"  "4NT"
  [6,] "1"  "4NT"
  [7,] "1"  "4NT"
  [8,] "1"  "4T" 
  [9,] "1"  "4NT"
 [10,] "1"  "4NT"
 [11,] "1"  "4T" 
 [12,] "1"  "4NT"
 [13,] "1"  "4NT"
 [14,] "1"  "4T" 
 [15,] "1"  "4NT"
 [16,] "1"  "4T" 
 [17,] "2"  "4T" 
 [18,] "1"  "4T" 
 [19,] "1"  "4NT"
 [20,] "2"  "4T" 
 [21,] "1"  "4NT"
 [22,] "1"  "4NT"
 [23,] "1"  "4NT"
 [24,] "1"  "4NT"
 [25,] "1"  "4T" 
 [26,] "1"  "4NT"
 [27,] "1"  "4NT"
 [28,] "1"  "4NT"
 [29,] "1"  "4NT"
 [30,] "1"  "4NT"
 [31,] "1"  "4NT"
 [32,] "1"  "4NT"
 [33,] "1"  "4NT"
 [34,] "1"  "4T" 
 [35,] "1"  "4NT"
 [36,] "1"  "4NT"
 [37,] "1"  "4T" 
 [38,] "1"  "4NT"
 [39,] "1"  "4NT"
 [40,] "1"  "4T" 
 [41,] "2"  "4NT"
 [42,] "1"  "4NT"
 [43,] "1"  "4NT"
 [44,] "1"  "4T" 
 [45,] "1"  "4NT"
 [46,] "1"  "4NT"
 [47,] "1"  "4NT"
 [48,] "1"  "4NT"
 [49,] "1"  "4NT"
 [50,] "1"  "4NT"
 [51,] "1"  "4T" 
 [52,] "2"  "4T" 
 [53,] "1"  "4NT"
 [54,] "2"  "4NT"
 [55,] "1"  "4NT"
 [56,] "1"  "4T" 
 [57,] "1"  "4NT"
 [58,] "1"  "4NT"
 [59,] "1"  "4NT"
 [60,] "2"  "4T" 
 [61,] "1"  "4T" 
 [62,] "1"  "4NT"
 [63,] "1"  "4NT"
 [64,] "1"  "4T" 
 [65,] "1"  "4NT"
 [66,] "1"  "4NT"
 [67,] "2"  "4T" 
 [68,] "1"  "4NT"
 [69,] "1"  "4NT"
 [70,] "1"  "4NT"
 [71,] "1"  "4NT"
 [72,] "1"  "4NT"
 [73,] "1"  "4NT"
 [74,] "1"  "4NT"
 [75,] "1"  "4NT"
 [76,] "1"  "4T" 
 [77,] "1"  "4NT"
 [78,] "1"  "4NT"
 [79,] "2"  "4T" 
 [80,] "1"  "4T" 
 [81,] "1"  "4NT"
 [82,] "1"  "4NT"
 [83,] "1"  "4NT"
 [84,] "2"  "4NT"
 [85,] "1"  "4NT"
 [86,] "1"  "4NT"
 [87,] "1"  "2NT"
 [88,] "1"  "2T" 
 [89,] "1"  "2NT"
 [90,] "1"  "2NT"
 [91,] "1"  "2NT"
 [92,] "1"  "2T" 
 [93,] "1"  "2NT"
 [94,] "1"  "2NT"
 [95,] "1"  "2T" 
 [96,] "1"  "2NT"
 [97,] "1"  "2T" 
 [98,] "1"  "2NT"
 [99,] "1"  "2NT"
[100,] "1"  "2NT"
[101,] "1"  "2NT"
[102,] "1"  "2NT"
[103,] "1"  "2NT"
[104,] "1"  "2NT"
[105,] "1"  "2T" 
[106,] "1"  "2NT"
[107,] "1"  "2NT"
[108,] "1"  "2T" 
[109,] "1"  "2NT"
[110,] "1"  "2NT"
[111,] "1"  "2T" 
[112,] "1"  "2T" 
[113,] "1"  "2NT"
[114,] "1"  "2T" 
[115,] "1"  "2NT"
[116,] "1"  "2NT"
[117,] "1"  "2NT"
[118,] "1"  "2NT"
[119,] "1"  "2NT"
[120,] "1"  "2NT"
[121,] "1"  "2NT"
[122,] "1"  "2NT"
[123,] "1"  "2T" 
[124,] "1"  "2NT"
[125,] "1"  "2NT"
[126,] "1"  "2T" 
[127,] "1"  "2NT"
[128,] "1"  "2NT"
[129,] "1"  "2NT"
[130,] "1"  "2NT"
[131,] "1"  "2NT"
[132,] "1"  "2NT"
[133,] "1"  "2NT"
[134,] "1"  "2NT"
[135,] "1"  "2NT"
[136,] "1"  "2NT"
[137,] "1"  "2NT"
[138,] "1"  "2T" 
[139,] "1"  "2T" 
[140,] "1"  "2NT"
[141,] "2"  "2NT"
[142,] "1"  "2T" 
[143,] "1"  "2NT"
[144,] "1"  "2NT"
[145,] "1"  "2NT"
[146,] "1"  "2T" 
[147,] "1"  "2T" 
[148,] "1"  "2T" 
[149,] "1"  "2NT"
[150,] "1"  "2NT"
[151,] "1"  "2NT"
[152,] "2"  "2NT"
[153,] "2"  "2NT"
[154,] "1"  "2NT"
> (table1 <- table(z[,cat1],z[,cat2]))
   
    2NT 2T 4NT 4T
  1  48 17  60 17
  2   3  0   3  6
> (V1<-dimnames(y)[[1]][cat1])
[1] "x"
> (V2<-dimnames(y)[[1]][cat2])
[1] "y"
> postscript(file="/var/fisher/rcomp/tmp/15tzh1356122987.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/2ei011356122987.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 = 13.2147, df = NA, p-value = 0.004998

> 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$expected[nr, nc], digits=2), 1, FALSE)
+ }
+ a<-table.row.end(a)
+ }
+ a<-table.end(a)
+ table.save(a,file="/var/fisher/rcomp/tmp/3dxav1356122987.tab") 
+ }
> a<-table.start()
> a<-table.row.start(a)
> a<-table.element(a,'Statistical Results',2,TRUE)
> a<-table.row.end(a)
> a<-table.row.start(a)
> a<-table.element(a, cst$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/4v23d1356122987.tab") 
> 
> try(system("convert tmp/15tzh1356122987.ps tmp/15tzh1356122987.png",intern=TRUE))
character(0)
> 
> 
> proc.time()
   user  system elapsed 
  1.446   0.353   1.782