R version 2.13.0 (2011-04-13)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: i486-pc-linux-gnu (32-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> x <- array(list(41
+ ,38
+ ,39
+ ,32
+ ,30
+ ,35
+ ,31
+ ,33
+ ,34
+ ,37
+ ,35
+ ,29
+ ,39
+ ,31
+ ,34
+ ,36
+ ,36
+ ,35
+ ,37
+ ,38
+ ,38
+ ,31
+ ,36
+ ,34
+ ,38
+ ,35
+ ,39
+ ,38
+ ,33
+ ,37
+ ,32
+ ,33
+ ,36
+ ,32
+ ,38
+ ,38
+ ,39
+ ,38
+ ,32
+ ,32
+ ,32
+ ,33
+ ,31
+ ,31
+ ,39
+ ,38
+ ,37
+ ,39
+ ,39
+ ,32
+ ,41
+ ,32
+ ,36
+ ,35
+ ,33
+ ,37
+ ,33
+ ,33
+ ,34
+ ,33
+ ,31
+ ,28
+ ,27
+ ,32
+ ,37
+ ,31
+ ,34
+ ,37
+ ,34
+ ,30
+ ,32
+ ,33
+ ,29
+ ,31
+ ,36
+ ,33
+ ,29
+ ,31
+ ,35
+ ,33
+ ,37
+ ,32
+ ,34
+ ,33
+ ,38
+ ,32
+ ,35
+ ,33
+ ,38
+ ,28
+ ,37
+ ,35
+ ,38
+ ,39
+ ,33
+ ,34
+ ,36
+ ,38
+ ,38
+ ,32
+ ,32
+ ,38
+ ,32
+ ,30
+ ,32
+ ,33
+ ,34
+ ,38
+ ,32
+ ,32
+ ,37
+ ,32
+ ,39
+ ,34
+ ,29
+ ,34
+ ,37
+ ,36
+ ,35
+ ,34
+ ,30
+ ,28
+ ,38
+ ,34
+ ,34
+ ,35
+ ,31
+ ,35
+ ,34
+ ,31
+ ,35
+ ,37
+ ,36
+ ,35
+ ,30
+ ,27
+ ,39
+ ,40
+ ,35
+ ,37
+ ,38
+ ,36
+ ,31
+ ,38
+ ,34
+ ,39
+ ,38
+ ,41
+ ,34
+ ,27
+ ,39
+ ,30
+ ,37
+ ,37
+ ,34
+ ,31
+ ,28
+ ,31
+ ,37
+ ,27
+ ,33
+ ,36
+ ,37
+ ,38
+ ,35
+ ,37
+ ,37
+ ,33
+ ,32
+ ,34
+ ,33
+ ,31
+ ,38
+ ,39
+ ,33
+ ,34
+ ,29
+ ,32
+ ,33
+ ,33
+ ,31
+ ,36
+ ,36
+ ,32
+ ,35
+ ,41
+ ,32
+ ,28
+ ,29
+ ,30
+ ,39
+ ,36
+ ,37
+ ,35
+ ,35
+ ,31
+ ,37
+ ,34
+ ,32
+ ,36
+ ,38
+ ,36
+ ,37
+ ,35
+ ,36
+ ,37
+ ,32
+ ,28
+ ,33
+ ,39
+ ,40
+ ,32
+ ,38
+ ,35
+ ,41
+ ,39
+ ,36
+ ,35
+ ,43
+ ,42
+ ,30
+ ,34
+ ,31
+ ,33
+ ,32
+ ,41
+ ,32
+ ,33
+ ,37
+ ,34
+ ,37
+ ,32
+ ,33
+ ,40
+ ,34
+ ,40
+ ,33
+ ,35
+ ,38
+ ,36
+ ,33
+ ,37
+ ,31
+ ,27
+ ,38
+ ,39
+ ,37
+ ,38
+ ,33
+ ,31
+ ,31
+ ,33
+ ,39
+ ,32
+ ,44
+ ,39
+ ,33
+ ,36
+ ,35
+ ,33
+ ,32
+ ,33
+ ,28
+ ,32
+ ,40
+ ,37
+ ,27
+ ,30
+ ,37
+ ,38
+ ,32
+ ,29
+ ,28
+ ,22
+ ,34
+ ,35
+ ,30
+ ,35
+ ,35
+ ,34
+ ,31
+ ,35
+ ,32
+ ,34
+ ,30
+ ,34
+ ,30
+ ,35
+ ,31
+ ,23
+ ,40
+ ,31
+ ,32
+ ,27
+ ,36
+ ,36
+ ,32
+ ,31
+ ,35
+ ,32
+ ,38
+ ,39
+ ,42
+ ,37
+ ,34
+ ,38
+ ,35
+ ,39
+ ,35
+ ,34
+ ,33
+ ,31
+ ,36
+ ,32
+ ,32
+ ,37
+ ,33
+ ,36
+ ,34
+ ,32
+ ,32
+ ,35
+ ,34
+ ,36)
+ ,dim=c(2
+ ,162)
+ ,dimnames=list(c('Connected'
+ ,'Separate')
+ ,1:162))
>  y <- array(NA,dim=c(2,162),dimnames=list(c('Connected','Separate'),1:162))
>  for (i in 1:dim(x)[1])
+  {
+  	for (j in 1:dim(x)[2])
+  	{
+  		y[i,j] <- as.numeric(x[i,j])
+  	}
+  }
> 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,]   41   38
  [2,]   39   32
  [3,]   30   35
  [4,]   31   33
  [5,]   34   37
  [6,]   35   29
  [7,]   39   31
  [8,]   34   36
  [9,]   36   35
 [10,]   37   38
 [11,]   38   31
 [12,]   36   34
 [13,]   38   35
 [14,]   39   38
 [15,]   33   37
 [16,]   32   33
 [17,]   36   32
 [18,]   38   38
 [19,]   39   38
 [20,]   32   32
 [21,]   32   33
 [22,]   31   31
 [23,]   39   38
 [24,]   37   39
 [25,]   39   32
 [26,]   41   32
 [27,]   36   35
 [28,]   33   37
 [29,]   33   33
 [30,]   34   33
 [31,]   31   28
 [32,]   27   32
 [33,]   37   31
 [34,]   34   37
 [35,]   34   30
 [36,]   32   33
 [37,]   29   31
 [38,]   36   33
 [39,]   29   31
 [40,]   35   33
 [41,]   37   32
 [42,]   34   33
 [43,]   38   32
 [44,]   35   33
 [45,]   38   28
 [46,]   37   35
 [47,]   38   39
 [48,]   33   34
 [49,]   36   38
 [50,]   38   32
 [51,]   32   38
 [52,]   32   30
 [53,]   32   33
 [54,]   34   38
 [55,]   32   32
 [56,]   37   32
 [57,]   39   34
 [58,]   29   34
 [59,]   37   36
 [60,]   35   34
 [61,]   30   28
 [62,]   38   34
 [63,]   34   35
 [64,]   31   35
 [65,]   34   31
 [66,]   35   37
 [67,]   36   35
 [68,]   30   27
 [69,]   39   40
 [70,]   35   37
 [71,]   38   36
 [72,]   31   38
 [73,]   34   39
 [74,]   38   41
 [75,]   34   27
 [76,]   39   30
 [77,]   37   37
 [78,]   34   31
 [79,]   28   31
 [80,]   37   27
 [81,]   33   36
 [82,]   37   38
 [83,]   35   37
 [84,]   37   33
 [85,]   32   34
 [86,]   33   31
 [87,]   38   39
 [88,]   33   34
 [89,]   29   32
 [90,]   33   33
 [91,]   31   36
 [92,]   36   32
 [93,]   35   41
 [94,]   32   28
 [95,]   29   30
 [96,]   39   36
 [97,]   37   35
 [98,]   35   31
 [99,]   37   34
[100,]   32   36
[101,]   38   36
[102,]   37   35
[103,]   36   37
[104,]   32   28
[105,]   33   39
[106,]   40   32
[107,]   38   35
[108,]   41   39
[109,]   36   35
[110,]   43   42
[111,]   30   34
[112,]   31   33
[113,]   32   41
[114,]   32   33
[115,]   37   34
[116,]   37   32
[117,]   33   40
[118,]   34   40
[119,]   33   35
[120,]   38   36
[121,]   33   37
[122,]   31   27
[123,]   38   39
[124,]   37   38
[125,]   33   31
[126,]   31   33
[127,]   39   32
[128,]   44   39
[129,]   33   36
[130,]   35   33
[131,]   32   33
[132,]   28   32
[133,]   40   37
[134,]   27   30
[135,]   37   38
[136,]   32   29
[137,]   28   22
[138,]   34   35
[139,]   30   35
[140,]   35   34
[141,]   31   35
[142,]   32   34
[143,]   30   34
[144,]   30   35
[145,]   31   23
[146,]   40   31
[147,]   32   27
[148,]   36   36
[149,]   32   31
[150,]   35   32
[151,]   38   39
[152,]   42   37
[153,]   34   38
[154,]   35   39
[155,]   35   34
[156,]   33   31
[157,]   36   32
[158,]   32   37
[159,]   33   36
[160,]   34   32
[161,]   32   35
[162,]   34   36
> (table1 <- table(z[,cat1],z[,cat2]))
    
     22 23 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42
  27  0  0  0  0  0  1  0  1  0  0  0  0  0  0  0  0  0  0
  28  1  0  0  0  0  0  1  1  0  0  0  0  0  0  0  0  0  0
  29  0  0  0  0  0  1  2  1  0  1  0  0  0  0  0  0  0  0
  30  0  0  1  1  0  0  0  0  0  2  3  0  0  0  0  0  0  0
  31  0  1  1  1  0  0  1  0  3  0  2  1  0  1  0  0  0  0
  32  0  0  1  2  1  1  1  2  6  2  1  1  1  1  0  0  1  0
  33  0  0  0  0  0  0  3  0  2  2  1  3  3  0  1  1  0  0
  34  0  0  1  0  0  1  2  1  2  0  2  2  2  2  1  1  0  0
  35  0  0  0  0  1  0  1  1  3  3  0  0  3  0  1  0  1  0
  36  0  0  0  0  0  0  0  3  1  1  4  1  1  1  0  0  0  0
  37  0  0  1  0  0  0  1  3  1  2  3  1  1  4  1  0  0  0
  38  0  0  0  1  0  0  1  2  0  1  2  3  0  1  4  0  1  0
  39  0  0  0  0  0  1  1  3  0  1  0  1  0  3  0  1  0  0
  40  0  0  0  0  0  0  1  1  0  0  0  0  1  0  0  0  0  0
  41  0  0  0  0  0  0  0  1  0  0  0  0  0  1  1  0  0  0
  42  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0
  43  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  1
  44  0  0  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0  0
> (V1<-dimnames(y)[[1]][cat1])
[1] "Connected"
> (V2<-dimnames(y)[[1]][cat2])
[1] "Separate"
> postscript(file="/var/wessaorg/rcomp/tmp/1f9l31321433107.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/2aef81321433107.tab") 
> (cst<-chisq.test(table1, simulate.p.value=simulate.p.value) )

	Pearson's Chi-squared test

data:  table1 
X-squared = 447.1938, df = 289, p-value = 6.509e-09

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$expected[nr, nc], digits=2), 1, FALSE)
+ }
+ a<-table.row.end(a)
+ }
+ a<-table.end(a)
+ table.save(a,file="/var/wessaorg/rcomp/tmp/3dmz71321433107.tab") 
+ }
> a<-table.start()
> a<-table.row.start(a)
> a<-table.element(a,'Statistical Results',2,TRUE)
> a<-table.row.end(a)
> a<-table.row.start(a)
> a<-table.element(a, cst$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/4xu6f1321433107.tab") 
> 
> try(system("convert tmp/1f9l31321433107.ps tmp/1f9l31321433107.png",intern=TRUE))
character(0)
> 
> 
> proc.time()
   user  system elapsed 
  3.112   0.153   3.415