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) 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('A' + ,'UK' + ,'A' + ,'UK' + ,'A' + ,'UK' + ,'A' + ,'UK' + ,'A' + ,'UK' + ,'A' + ,'UK' + ,'A' + ,'UK' + ,'A' + ,'UK' + ,'A' + ,'UK' + ,'A' + ,'UK' + ,'A' + ,'UK' + ,'A' + ,'UK' + ,'A' + ,'UK' + ,'A' + ,'UK' + ,'A' + ,'UK' + ,'A' + ,'UK' + ,'A' + ,'UK' + ,'A' + ,'UK' + ,'A' + ,'UK' + ,'A' + ,'UK' + ,'A' + ,'UK' + ,'A' + ,'UK' + ,'A' + ,'UK' + ,'A' + ,'UK' + ,'A' + ,'UK' + ,'A' + ,'UK' + ,'A' + ,'UK' + ,'A' + ,'UK' + ,'A' + ,'UK' + ,'A' + ,'UK' + ,'A' + ,'UK' + ,'A' + ,'UK' + ,'A' + ,'UK' + ,'A' + ,'UK' + ,'A' + ,'UK' + ,'A' + ,'UK' + ,'A' + ,'UK' + ,'A' + ,'UK' + ,'B' + ,'UK' + ,'B' + ,'UK' + ,'B' + ,'UK' + ,'B' + ,'UK' + ,'B' + ,'UK' + ,'B' + ,'UK' + ,'B' + ,'UK' + ,'B' + ,'UK' + ,'B' + ,'UK' + ,'B' + ,'UK' + ,'B' + ,'UK' + ,'B' + ,'UK' + ,'B' + ,'UK' + ,'B' + ,'UK' + ,'B' + ,'UK' + ,'B' + ,'UK' + ,'B' + ,'UK' + ,'B' + ,'UK' + ,'B' + ,'UK' + ,'B' + ,'UK' + ,'B' + ,'UK' + ,'B' + ,'UK' + ,'B' + ,'UK' + ,'B' + ,'UK' + ,'B' + ,'UK' + ,'B' + ,'UK' + ,'B' + ,'UK' + ,'B' + ,'UK' + ,'B' + ,'UK' + ,'B' + ,'UK' + ,'B' + ,'UK' + ,'B' + ,'UK' + ,'B' + ,'UK' + ,'B' + ,'UK' + ,'C' + ,'UK' + ,'C' + ,'UK' + ,'C' + ,'UK' + ,'C' + ,'UK' + ,'C' + ,'UK' + ,'C' + ,'UK' + ,'C' + ,'UK' + ,'C' + ,'UK' + ,'C' + ,'UK' + ,'C' + ,'UK' + ,'C' + ,'UK' + ,'C' + ,'UK' + ,'C' + ,'UK' + ,'C' + ,'UK' + ,'C' + ,'UK' + ,'C' + ,'UK' + ,'C' + ,'UK' + ,'C' + ,'UK' + ,'C' + ,'UK' + ,'C' + ,'UK' + ,'C' + ,'UK' + ,'C' + ,'UK' + ,'C' + ,'UK' + ,'C' + ,'UK' + ,'C' + ,'UK' + ,'C' + ,'UK' + ,'D' + ,'UK' + ,'D' + ,'UK' + ,'D' + ,'UK' + ,'D' + ,'UK' + ,'D' + ,'UK' + ,'D' + ,'UK' + ,'D' + ,'UK' + ,'D' + ,'UK' + ,'D' + ,'UK' + ,'D' + ,'UK' + ,'D' + ,'UK' + ,'D' + ,'UK' + ,'D' + ,'UK' + ,'D' + ,'UK' + ,'D' + ,'UK' + ,'D' + ,'UK' + ,'A' + ,'B' + ,'A' + ,'B' + ,'A' + ,'B' + ,'A' + ,'B' + ,'A' + ,'B' + ,'A' + ,'B' + ,'A' + ,'B' + ,'A' + ,'B' + ,'A' + ,'B' + ,'A' + ,'B' + ,'A' + ,'B' + ,'A' + ,'B' + ,'A' + ,'B' + ,'A' + ,'B' + ,'A' + ,'B' + ,'A' + ,'B' + ,'A' + ,'B' + ,'A' + ,'B' + ,'A' + ,'B' + ,'A' + ,'B' + ,'A' + ,'B' + ,'A' + ,'B' + ,'A' + ,'B' + ,'A' + ,'B' + ,'A' + ,'B' + ,'A' + ,'B' + ,'A' + ,'B' + ,'A' + ,'B' + ,'A' + ,'B' + ,'A' + ,'B' + ,'A' + ,'B' + ,'A' + ,'B' + ,'A' + ,'B' + ,'A' + ,'B' + ,'A' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'B' + ,'C' + ,'B' + ,'C' + ,'B' + ,'C' + ,'B' + ,'C' + ,'B' + ,'C' + ,'B' + ,'C' + ,'B' + ,'C' + ,'B' + ,'C' + ,'B' + ,'C' + ,'B' + ,'C' + ,'B' + ,'C' + ,'B' + ,'C' + ,'B' + ,'C' + ,'B' + ,'C' + ,'B' + ,'C' + ,'B' + ,'C' + ,'B' + ,'C' + ,'B' + ,'C' + ,'B' + ,'C' + ,'B' + ,'C' + ,'B' + ,'C' + ,'B' + ,'C' + ,'B' + ,'C' + ,'B' + ,'C' + ,'B' + ,'C' + ,'B' + ,'C' + ,'B' + ,'C' + ,'B' + ,'C' + ,'B' + ,'C' + ,'B' + ,'C' + ,'B' + ,'C' + ,'B' + ,'C' + ,'B' + ,'C' + ,'B' + ,'C' + ,'B' + ,'C' + ,'B' + ,'C' + ,'B' + ,'C' + ,'B' + ,'C' + ,'B' + ,'C' + ,'B' + ,'C' + ,'B' + ,'C' + ,'B' + ,'C' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B' + ,'D' + ,'B') + ,dim=c(2 + ,282) + ,dimnames=list(c('Uren' + ,'Land') + ,1:282)) > y <- array(NA,dim=c(2,282),dimnames=list(c('Uren','Land'),1:282)) > 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) > par20 = '' > par19 = '' > par18 = '' > par17 = '' > par16 = '' > par15 = '' > par14 = '' > par13 = '' > par12 = '' > par11 = '' > par10 = '' > par9 = '' > par8 = '' > par7 = '' > par6 = '' > par5 = '' > par4 = '' > par3 = 'Pearson Chi-Squared' > 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,] "A" "UK" [2,] "A" "UK" [3,] "A" "UK" [4,] "A" "UK" [5,] "A" "UK" [6,] "A" "UK" [7,] "A" "UK" [8,] "A" "UK" [9,] "A" "UK" [10,] "A" "UK" [11,] "A" "UK" [12,] "A" "UK" [13,] "A" "UK" [14,] "A" "UK" [15,] "A" "UK" [16,] "A" "UK" [17,] "A" "UK" [18,] "A" "UK" [19,] "A" "UK" [20,] "A" "UK" [21,] "A" "UK" [22,] "A" "UK" [23,] "A" "UK" [24,] "A" "UK" [25,] "A" "UK" [26,] "A" "UK" [27,] "A" "UK" [28,] "A" "UK" [29,] "A" "UK" [30,] "A" "UK" [31,] "A" "UK" [32,] "A" "UK" [33,] "A" "UK" [34,] "A" "UK" [35,] "A" "UK" [36,] "A" "UK" [37,] "A" "UK" [38,] "A" "UK" [39,] "B" "UK" [40,] "B" "UK" [41,] "B" "UK" [42,] "B" "UK" [43,] "B" "UK" [44,] "B" "UK" [45,] "B" "UK" [46,] "B" "UK" [47,] "B" "UK" [48,] "B" "UK" [49,] "B" "UK" [50,] "B" "UK" [51,] "B" "UK" [52,] "B" "UK" [53,] "B" "UK" [54,] "B" "UK" [55,] "B" "UK" [56,] "B" "UK" [57,] "B" "UK" [58,] "B" "UK" [59,] "B" "UK" [60,] "B" "UK" [61,] "B" "UK" [62,] "B" "UK" [63,] "B" "UK" [64,] "B" "UK" [65,] "B" "UK" [66,] "B" "UK" [67,] "B" "UK" [68,] "B" "UK" [69,] "B" "UK" [70,] "B" "UK" [71,] "B" "UK" [72,] "B" "UK" [73,] "C" "UK" [74,] "C" "UK" [75,] "C" "UK" [76,] "C" "UK" [77,] "C" "UK" [78,] "C" "UK" [79,] "C" "UK" [80,] "C" "UK" [81,] "C" "UK" [82,] "C" "UK" [83,] "C" "UK" [84,] "C" "UK" [85,] "C" "UK" [86,] "C" "UK" [87,] "C" "UK" [88,] "C" "UK" [89,] "C" "UK" [90,] "C" "UK" [91,] "C" "UK" [92,] "C" "UK" [93,] "C" "UK" [94,] "C" "UK" [95,] "C" "UK" [96,] "C" "UK" [97,] "C" "UK" [98,] "C" "UK" [99,] "D" "UK" [100,] "D" "UK" [101,] "D" "UK" [102,] "D" "UK" [103,] "D" "UK" [104,] "D" "UK" [105,] "D" "UK" [106,] "D" "UK" [107,] "D" "UK" [108,] "D" "UK" [109,] "D" "UK" [110,] "D" "UK" [111,] "D" "UK" [112,] "D" "UK" [113,] "D" "UK" [114,] "D" "UK" [115,] "A" "B" [116,] "A" "B" [117,] "A" "B" [118,] "A" "B" [119,] "A" "B" [120,] "A" "B" [121,] "A" "B" [122,] "A" "B" [123,] "A" "B" [124,] "A" "B" [125,] "A" "B" [126,] "A" "B" [127,] "A" "B" [128,] "A" "B" [129,] "A" "B" [130,] "A" "B" [131,] "A" "B" [132,] "A" "B" [133,] "A" "B" [134,] "A" "B" [135,] "A" "B" [136,] "A" "B" [137,] "A" "B" [138,] "A" "B" [139,] "A" "B" [140,] "A" "B" [141,] "A" "B" [142,] "A" "B" [143,] "A" "B" [144,] "A" "B" [145,] "A" "B" [146,] "A" "B" [147,] "A" "B" [148,] "A" "B" [149,] "A" "B" [150,] "B" "B" [151,] "B" "B" [152,] "B" "B" [153,] "B" "B" [154,] "B" "B" [155,] "B" "B" [156,] "B" "B" [157,] "B" "B" [158,] "B" "B" [159,] "B" "B" [160,] "B" "B" [161,] "B" "B" [162,] "B" "B" [163,] "B" "B" [164,] "B" "B" [165,] "B" "B" [166,] "B" "B" [167,] "B" "B" [168,] "B" "B" [169,] "B" "B" [170,] "B" "B" [171,] "B" "B" [172,] "B" "B" [173,] "B" "B" [174,] "B" "B" [175,] "B" "B" [176,] "B" "B" [177,] "B" "B" [178,] "B" "B" [179,] "B" "B" [180,] "B" "B" [181,] "B" "B" [182,] "B" "B" [183,] "B" "B" [184,] "B" "B" [185,] "B" "B" [186,] "B" "B" [187,] "C" "B" [188,] "C" "B" [189,] "C" "B" [190,] "C" "B" [191,] "C" "B" [192,] "C" "B" [193,] "C" "B" [194,] "C" "B" [195,] "C" "B" [196,] "C" "B" [197,] "C" "B" [198,] "C" "B" [199,] "C" "B" [200,] "C" "B" [201,] "C" "B" [202,] "C" "B" [203,] "C" "B" [204,] "C" "B" [205,] "C" "B" [206,] "C" "B" [207,] "C" "B" [208,] "C" "B" [209,] "C" "B" [210,] "C" "B" [211,] "C" "B" [212,] "C" "B" [213,] "C" "B" [214,] "C" "B" [215,] "C" "B" [216,] "C" "B" [217,] "C" "B" [218,] "C" "B" [219,] "C" "B" [220,] "C" "B" [221,] "C" "B" [222,] "C" "B" [223,] "C" "B" [224,] "C" "B" [225,] "C" "B" [226,] "C" "B" [227,] "C" "B" [228,] "C" "B" [229,] "D" "B" [230,] "D" "B" [231,] "D" "B" [232,] "D" "B" [233,] "D" "B" [234,] "D" "B" [235,] "D" "B" [236,] "D" "B" [237,] "D" "B" [238,] "D" "B" [239,] "D" "B" [240,] "D" "B" [241,] "D" "B" [242,] "D" "B" [243,] "D" "B" [244,] "D" "B" [245,] "D" "B" [246,] "D" "B" [247,] "D" "B" [248,] "D" "B" [249,] "D" "B" [250,] "D" "B" [251,] "D" "B" [252,] "D" "B" [253,] "D" "B" [254,] "D" "B" [255,] "D" "B" [256,] "D" "B" [257,] "D" "B" [258,] "D" "B" [259,] "D" "B" [260,] "D" "B" [261,] "D" "B" [262,] "D" "B" [263,] "D" "B" [264,] "D" "B" [265,] "D" "B" [266,] "D" "B" [267,] "D" "B" [268,] "D" "B" [269,] "D" "B" [270,] "D" "B" [271,] "D" "B" [272,] "D" "B" [273,] "D" "B" [274,] "D" "B" [275,] "D" "B" [276,] "D" "B" [277,] "D" "B" [278,] "D" "B" [279,] "D" "B" [280,] "D" "B" [281,] "D" "B" [282,] "D" "B" > (table1 <- table(z[,cat1],z[,cat2])) B UK A 35 38 B 37 34 C 42 26 D 54 16 > (V1<-dimnames(y)[[1]][cat1]) [1] "Uren" > (V2<-dimnames(y)[[1]][cat2]) [1] "Land" > postscript(file="/var/wessaorg/rcomp/tmp/1imln1358261919.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/2r8om1358261919.tab") > (cst<-chisq.test(table1, simulate.p.value=simulate.p.value) ) Pearson's Chi-squared test data: table1 X-squared = 14.8473, df = 3, p-value = 0.001952 > 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$expected[nr, nc], digits=2), 1, FALSE) + } + a<-table.row.end(a) + } + a<-table.end(a) + table.save(a,file="/var/wessaorg/rcomp/tmp/3w07p1358261919.tab") + } > a<-table.start() > a<-table.row.start(a) > a<-table.element(a,'Statistical Results',2,TRUE) > a<-table.row.end(a) > a<-table.row.start(a) > a<-table.element(a, cst$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/4fdbt1358261919.tab") > > try(system("convert tmp/1imln1358261919.ps tmp/1imln1358261919.png",intern=TRUE)) character(0) > > > proc.time() user system elapsed 1.573 0.142 1.769