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) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. 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('B' + ,'HI' + ,'C' + ,'LO' + ,'A' + ,'HI' + ,'B' + ,'LO' + ,'A' + ,'HI' + ,'B' + ,'LO' + ,'A' + ,'LO' + ,'C' + ,'HI' + ,'D' + ,'HI' + ,'B' + ,'HI' + ,'D' + ,'LO' + ,'D' + ,'HI' + ,'A' + ,'HI' + ,'A' + ,'HI' + ,'D' + ,'HI' + ,'A' + ,'LO' + ,'A' + ,'LO' + ,'C' + ,'HI' + ,'D' + ,'HI' + ,'B' + ,'LO' + ,'D' + ,'LO' + ,'A' + ,'LO' + ,'B' + ,'HI' + ,'A' + ,'HI' + ,'C' + ,'LO' + ,'D' + ,'LO' + ,'C' + ,'HI' + ,'A' + ,'HI' + ,'A' + ,'LO' + ,'B' + ,'LO' + ,'D' + ,'LO' + ,'A' + ,'LO' + ,'D' + ,'LO' + ,'C' + ,'HI' + ,'B' + ,'LO' + ,'D' + ,'LO' + ,'A' + ,'LO' + ,'B' + ,'LO' + ,'D' + ,'LO' + ,'D' + ,'LO' + ,'D' + ,'LO' + ,'A' + ,'LO' + ,'D' + ,'LO' + ,'A' + ,'LO' + ,'C' + ,'LO' + ,'B' + ,'HI' + ,'D' + ,'HI' + ,'C' + ,'HI' + ,'A' + ,'HI' + ,'C' + ,'LO' + ,'D' + ,'HI' + ,'A' + ,'LO' + ,'A' + ,'LO' + ,'A' + ,'HI' + ,'C' + ,'LO' + ,'B' + ,'LO' + ,'B' + ,'HI' + ,'D' + ,'HI' + ,'D' + ,'HI' + ,'A' + ,'HI' + ,'A' + ,'LO' + ,'B' + ,'HI' + ,'B' + ,'HI' + ,'A' + ,'HI' + ,'B' + ,'LO' + ,'C' + ,'HI' + ,'A' + ,'HI' + ,'B' + ,'LO' + ,'B' + ,'HI' + ,'A' + ,'HI' + ,'B' + ,'HI' + ,'A' + ,'HI' + ,'B' + ,'HI' + ,'D' + ,'HI' + ,'C' + ,'LO' + ,'A' + ,'LO' + ,'B' + ,'HI' + ,'A' + ,'LO' + ,'B' + ,'LO' + ,'D' + ,'LO' + ,'C' + ,'HI' + ,'D' + ,'HI' + ,'D' + ,'HI' + ,'B' + ,'LO' + ,'B' + ,'HI' + ,'B' + ,'LO' + ,'B' + ,'HI' + ,'B' + ,'HI' + ,'A' + ,'LO' + ,'A' + ,'LO' + ,'B' + ,'HI' + ,'A' + ,'LO' + ,'B' + ,'HI' + ,'A' + ,'LO' + ,'D' + ,'LO' + ,'C' + ,'HI' + ,'A' + ,'HI' + ,'C' + ,'LO' + ,'C' + ,'HI' + ,'D' + ,'HI' + ,'D' + ,'HI' + ,'A' + ,'HI' + ,'B' + ,'HI' + ,'C' + ,'LO' + ,'A' + ,'HI' + ,'A' + ,'LO' + ,'C' + ,'HI' + ,'A' + ,'HI' + ,'A' + ,'HI' + ,'A' + ,'HI' + ,'A' + ,'HI' + ,'A' + ,'LO' + ,'C' + ,'HI' + ,'A' + ,'LO' + ,'B' + ,'HI' + ,'D' + ,'LO' + ,'A' + ,'HI' + ,'B' + ,'HI' + ,'D' + ,'HI' + ,'A' + ,'HI' + ,'A' + ,'HI' + ,'A' + ,'LO' + ,'C' + ,'HI' + ,'D' + ,'HI' + ,'C' + ,'LO' + ,'C' + ,'LO' + ,'D' + ,'LO' + ,'D' + ,'HI' + ,'C' + ,'HI' + ,'B' + ,'LO' + ,'C' + ,'LO' + ,'A' + ,'LO' + ,'D' + ,'HI' + ,'A' + ,'LO' + ,'B' + ,'HI' + ,'A' + ,'LO' + ,'A' + ,'LO' + ,'A' + ,'HI' + ,'A' + ,'HI' + ,'C' + ,'HI' + ,'B' + ,'HI' + ,'D' + ,'HI' + ,'A' + ,'HI' + ,'B' + ,'HI' + ,'B' + ,'LO' + ,'C' + ,'LO' + ,'B' + ,'LO' + ,'B' + ,'HI' + ,'C' + ,'LO' + ,'A' + ,'LO' + ,'B' + ,'HI' + ,'A' + ,'HI' + ,'D' + ,'HI' + ,'B' + ,'HI' + ,'A' + ,'HI' + ,'A' + ,'LO' + ,'A' + ,'LO' + ,'A' + ,'HI' + ,'C' + ,'HI' + ,'D' + ,'LO' + ,'A' + ,'HI' + ,'A' + ,'HI') + ,dim=c(2 + ,162) + ,dimnames=list(c('Depression' + ,'Separate') + ,1:162)) > y <- array(NA,dim=c(2,162),dimnames=list(c('Depression','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]) + } + } There were 50 or more warnings (use warnings() to see the first 50) > 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,] "B" "HI" [2,] "C" "LO" [3,] "A" "HI" [4,] "B" "LO" [5,] "A" "HI" [6,] "B" "LO" [7,] "A" "LO" [8,] "C" "HI" [9,] "D" "HI" [10,] "B" "HI" [11,] "D" "LO" [12,] "D" "HI" [13,] "A" "HI" [14,] "A" "HI" [15,] "D" "HI" [16,] "A" "LO" [17,] "A" "LO" [18,] "C" "HI" [19,] "D" "HI" [20,] "B" "LO" [21,] "D" "LO" [22,] "A" "LO" [23,] "B" "HI" [24,] "A" "HI" [25,] "C" "LO" [26,] "D" "LO" [27,] "C" "HI" [28,] "A" "HI" [29,] "A" "LO" [30,] "B" "LO" [31,] "D" "LO" [32,] "A" "LO" [33,] "D" "LO" [34,] "C" "HI" [35,] "B" "LO" [36,] "D" "LO" [37,] "A" "LO" [38,] "B" "LO" [39,] "D" "LO" [40,] "D" "LO" [41,] "D" "LO" [42,] "A" "LO" [43,] "D" "LO" [44,] "A" "LO" [45,] "C" "LO" [46,] "B" "HI" [47,] "D" "HI" [48,] "C" "HI" [49,] "A" "HI" [50,] "C" "LO" [51,] "D" "HI" [52,] "A" "LO" [53,] "A" "LO" [54,] "A" "HI" [55,] "C" "LO" [56,] "B" "LO" [57,] "B" "HI" [58,] "D" "HI" [59,] "D" "HI" [60,] "A" "HI" [61,] "A" "LO" [62,] "B" "HI" [63,] "B" "HI" [64,] "A" "HI" [65,] "B" "LO" [66,] "C" "HI" [67,] "A" "HI" [68,] "B" "LO" [69,] "B" "HI" [70,] "A" "HI" [71,] "B" "HI" [72,] "A" "HI" [73,] "B" "HI" [74,] "D" "HI" [75,] "C" "LO" [76,] "A" "LO" [77,] "B" "HI" [78,] "A" "LO" [79,] "B" "LO" [80,] "D" "LO" [81,] "C" "HI" [82,] "D" "HI" [83,] "D" "HI" [84,] "B" "LO" [85,] "B" "HI" [86,] "B" "LO" [87,] "B" "HI" [88,] "B" "HI" [89,] "A" "LO" [90,] "A" "LO" [91,] "B" "HI" [92,] "A" "LO" [93,] "B" "HI" [94,] "A" "LO" [95,] "D" "LO" [96,] "C" "HI" [97,] "A" "HI" [98,] "C" "LO" [99,] "C" "HI" [100,] "D" "HI" [101,] "D" "HI" [102,] "A" "HI" [103,] "B" "HI" [104,] "C" "LO" [105,] "A" "HI" [106,] "A" "LO" [107,] "C" "HI" [108,] "A" "HI" [109,] "A" "HI" [110,] "A" "HI" [111,] "A" "HI" [112,] "A" "LO" [113,] "C" "HI" [114,] "A" "LO" [115,] "B" "HI" [116,] "D" "LO" [117,] "A" "HI" [118,] "B" "HI" [119,] "D" "HI" [120,] "A" "HI" [121,] "A" "HI" [122,] "A" "LO" [123,] "C" "HI" [124,] "D" "HI" [125,] "C" "LO" [126,] "C" "LO" [127,] "D" "LO" [128,] "D" "HI" [129,] "C" "HI" [130,] "B" "LO" [131,] "C" "LO" [132,] "A" "LO" [133,] "D" "HI" [134,] "A" "LO" [135,] "B" "HI" [136,] "A" "LO" [137,] "A" "LO" [138,] "A" "HI" [139,] "A" "HI" [140,] "C" "HI" [141,] "B" "HI" [142,] "D" "HI" [143,] "A" "HI" [144,] "B" "HI" [145,] "B" "LO" [146,] "C" "LO" [147,] "B" "LO" [148,] "B" "HI" [149,] "C" "LO" [150,] "A" "LO" [151,] "B" "HI" [152,] "A" "HI" [153,] "D" "HI" [154,] "B" "HI" [155,] "A" "HI" [156,] "A" "LO" [157,] "A" "LO" [158,] "A" "HI" [159,] "C" "HI" [160,] "D" "LO" [161,] "A" "HI" [162,] "A" "HI" > (table1 <- table(z[,cat1],z[,cat2])) HI LO A 31 29 B 25 15 C 15 13 D 19 15 > (V1<-dimnames(y)[[1]][cat1]) [1] "Depression" > (V2<-dimnames(y)[[1]][cat2]) [1] "Separate" > postscript(file="/var/wessaorg/rcomp/tmp/1u9lt1321142824.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/2bzmi1321142824.tab") > (cst<-chisq.test(table1, simulate.p.value=simulate.p.value) ) Pearson's Chi-squared test data: table1 X-squared = 1.1949, df = 3, p-value = 0.7542 > 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/3hsy31321142824.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/4l98d1321142824.tab") > > try(system("convert tmp/1u9lt1321142824.ps tmp/1u9lt1321142824.png",intern=TRUE)) character(0) > > > proc.time() user system elapsed 1.004 0.091 1.101