R version 3.2.3 (2015-12-10) -- "Wooden Christmas-Tree" Copyright (C) 2015 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-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(1 + ,4 + ,1 + ,-3 + ,1 + ,3 + ,-1 + ,4 + ,-2 + ,-3 + ,-4 + ,-1 + ,2 + ,2 + ,-1 + ,-1 + ,-1 + ,-1 + ,1 + ,1 + ,0 + ,3 + ,1 + ,2 + ,-2 + ,-1 + ,0 + ,3 + ,2 + ,-2 + ,3 + ,1 + ,0 + ,-3 + ,4 + ,3 + ,4 + ,3 + ,-4 + ,-2 + ,1 + ,-1 + ,3 + ,0 + ,1 + ,-2 + ,-1 + ,2 + ,-3 + ,-2 + ,-2 + ,2 + ,-2 + ,1 + ,1 + ,-2 + ,3 + ,-1 + ,1 + ,3 + ,3 + ,2 + ,-1 + ,3 + ,-1 + ,1 + ,3 + ,3 + ,2 + ,-1 + ,0 + ,2 + ,0 + ,-4 + ,3 + ,2 + ,2 + ,2 + ,4 + ,2 + ,2 + ,-1 + ,1 + ,-3 + ,3 + ,3 + ,-1 + ,0 + ,-1 + ,2 + ,3 + ,2 + ,2 + ,1 + ,4 + ,-3 + ,-1 + ,-2 + ,3 + ,2 + ,-1 + ,-3 + ,-1 + ,4 + ,0 + ,0 + ,4 + ,3 + ,1 + ,-3 + ,-1 + ,2 + ,3 + ,2 + ,2 + ,3 + ,-2 + ,0 + ,0 + ,-1 + ,2 + ,2 + ,3 + ,-1 + ,2 + ,-2 + ,3 + ,4 + ,2 + ,-4 + ,-3 + ,1 + ,-3 + ,0 + ,3 + ,-1 + ,4 + ,-1 + ,-2 + ,-4 + ,0 + ,4 + ,-1 + ,0 + ,2 + ,3 + ,1 + ,-2 + ,0 + ,-1 + ,1 + ,0 + ,2 + ,0 + ,2 + ,3 + ,-3 + ,-4 + ,1 + ,-1 + ,1 + ,-1 + ,1 + ,-2 + ,1 + ,3 + ,3 + ,1 + ,1 + ,4 + ,3 + ,2 + ,-4 + ,2 + ,0 + ,1 + ,1 + ,-1 + ,-4 + ,-1 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,-2 + ,-1 + ,-2 + ,2 + ,-1 + ,-2 + ,0 + ,0 + ,0 + ,1 + ,1 + ,-1 + ,2 + ,4 + ,2 + ,2 + ,0 + ,2 + ,1 + ,0 + ,-2 + ,-1 + ,4 + ,0 + ,-1 + ,3 + ,2 + ,4 + ,0 + ,-2 + ,1 + ,4 + ,-1 + ,-4 + ,3 + ,2 + ,-2 + ,4 + ,3 + ,2 + ,-1 + ,0 + ,-2 + ,0 + ,4 + ,-1 + ,1 + ,-2 + ,2 + ,3 + ,-1 + ,2 + ,2 + ,1 + ,-3 + ,-2 + ,2 + ,1) + ,dim=c(7 + ,142) + ,dimnames=list(c('V1' + ,'V2' + ,'V3' + ,'V4' + ,'V5' + ,'V6' + ,'V7') + ,1:142)) > y <- array(NA,dim=c(7,142),dimnames=list(c('V1','V2','V3','V4','V5','V6','V7'),1:142)) > for (i in 1:dim(x)[1]) + { + for (j in 1:dim(x)[2]) + { + y[i,j] <- as.numeric(x[i,j]) + } + } > par4 = 'FALSE' > par3 = 'FALSE' > par2 = 'ALL' > par1 = 'ward' > ylab = 'height' > xlab = 'cases' > main = 'Dendrogram' > par4 <- 'FALSE' > par3 <- 'FALSE' > par2 <- 'ALL' > par1 <- 'ward' > #'GNU S' R Code compiled by R2WASP v. 1.2.291 () > #Author: root > #To cite this work: Wessa, P., (2012), Hierarchical Clustering (v1.0.3) in Free Statistics Software (v$_version), Office for Research Development and Education, URL http://www.wessa.net/rwasp_hierarchicalclustering.wasp/ > #Source of accompanying publication: Office for Research, Development, and Education > # > par3 <- as.logical(par3) > par4 <- as.logical(par4) > if (par3 == 'TRUE'){ + dum = xlab + xlab = ylab + ylab = dum + } > x <- t(y) > hc <- hclust(dist(x),method=par1) The "ward" method has been renamed to "ward.D"; note new "ward.D2" > d <- as.dendrogram(hc) > str(d) --[dendrogram w/ 2 branches and 142 members at h = 110] |--[dendrogram w/ 2 branches and 73 members at h = 50.1] | |--[dendrogram w/ 2 branches and 30 members at h = 20.7] | | |--[dendrogram w/ 2 branches and 7 members at h = 6.16] | | | |--[dendrogram w/ 2 branches and 4 members at h = 3.5] | | | | |--leaf "86" | | | | `--[dendrogram w/ 2 branches and 3 members at h = 3.23] | | | | |--leaf "70" | | | | `--[dendrogram w/ 2 branches and 2 members at h = 2.65] | | | | |--leaf "72" | | | | `--leaf "98" | | | `--[dendrogram w/ 2 branches and 3 members at h = 5.74] | | | |--leaf "25" | | | `--[dendrogram w/ 2 branches and 2 members at h = 3.74] | | | |--leaf "16" | | | `--leaf "137" | | `--[dendrogram w/ 2 branches and 23 members at h = 17.2] | | |--[dendrogram w/ 2 branches and 13 members at h = 9.16] | | | |--[dendrogram w/ 2 branches and 4 members at h = 3.58] | | | | |--leaf "131" | | | | `--[dendrogram w/ 2 branches and 3 members at h = 2.2] | | | | |--leaf "39" | | | | `--[dendrogram w/ 2 branches and 2 members at h = 1.41] | | | | |--leaf "114" | | | | `--leaf "134" | | | `--[dendrogram w/ 2 branches and 9 members at h = 6.06] | | | |--[dendrogram w/ 2 branches and 3 members at h = 3.25] | | | | |--leaf "117" | | | | `--[dendrogram w/ 2 branches and 2 members at h = 2.83] | | | | |--leaf "62" | | | | `--leaf "66" | | | `--[dendrogram w/ 2 branches and 6 members at h = 4.95] | | | |--[dendrogram w/ 2 branches and 2 members at h = 2.65] | | | | |--leaf "47" | | | | `--leaf "84" | | | `--[dendrogram w/ 2 branches and 4 members at h = 3.72] | | | |--leaf "14" | | | `--[dendrogram w/ 2 branches and 3 members at h = 2.59] | | | |--leaf "50" | | | `--[dendrogram w/ 2 branches and 2 members at h = 2] | | | |--leaf "17" | | | `--leaf "118" | | `--[dendrogram w/ 2 branches and 10 members at h = 10.8] | | |--[dendrogram w/ 2 branches and 3 members at h = 3.79] | | | |--leaf "36" | | | `--[dendrogram w/ 2 branches and 2 members at h = 3.32] | | | |--leaf "110" | | | `--leaf "112" | | `--[dendrogram w/ 2 branches and 7 members at h = 7.81] | | |--[dendrogram w/ 2 branches and 5 members at h = 4.91] | | | |--[dendrogram w/ 2 branches and 2 members at h = 2.83] | | | | |--leaf "105" | | | | `--leaf "113" | | | `--[dendrogram w/ 2 branches and 3 members at h = 3.13] | | | |--leaf "53" | | | `--[dendrogram w/ 2 branches and 2 members at h = 2.24] | | | |--leaf "12" | | | `--leaf "74" | | `--[dendrogram w/ 2 branches and 2 members at h = 5.1] | | |--leaf "20" | | `--leaf "95" | `--[dendrogram w/ 2 branches and 43 members at h = 38.3] | |--[dendrogram w/ 2 branches and 16 members at h = 20.3] | | |--[dendrogram w/ 2 branches and 8 members at h = 9.01] | | | |--[dendrogram w/ 2 branches and 3 members at h = 5.25] | | | | |--leaf "8" | | | | `--[dendrogram w/ 2 branches and 2 members at h = 2.83] | | | | |--leaf "3" | | | | `--leaf "22" | | | `--[dendrogram w/ 2 branches and 5 members at h = 6.61] | | | |--leaf "106" | | | `--[dendrogram w/ 2 branches and 4 members at h = 4.66] | | | |--leaf "54" | | | `--[dendrogram w/ 2 branches and 3 members at h = 3.74] | | | |--leaf "135" | | | `--[dendrogram w/ 2 branches and 2 members at h = 2.45] | | | |--leaf "55" | | | `--leaf "128" | | `--[dendrogram w/ 2 branches and 8 members at h = 15.3] | | |--[dendrogram w/ 2 branches and 4 members at h = 4.9] | | | |--[dendrogram w/ 2 branches and 2 members at h = 3.46] | | | | |--leaf "64" | | | | `--leaf "80" | | | `--[dendrogram w/ 2 branches and 2 members at h = 4.12] | | | |--leaf "133" | | | `--leaf "138" | | `--[dendrogram w/ 2 branches and 4 members at h = 6.86] | | |--[dendrogram w/ 2 branches and 2 members at h = 2] | | | |--leaf "18" | | | `--leaf "79" | | `--[dendrogram w/ 2 branches and 2 members at h = 3.87] | | |--leaf "88" | | `--leaf "122" | `--[dendrogram w/ 2 branches and 27 members at h = 25.5] | |--[dendrogram w/ 2 branches and 14 members at h = 13.1] | | |--[dendrogram w/ 2 branches and 6 members at h = 8.18] | | | |--[dendrogram w/ 2 branches and 2 members at h = 4.47] | | | | |--leaf "48" | | | | `--leaf "49" | | | `--[dendrogram w/ 2 branches and 4 members at h = 5.89] | | | |--[dendrogram w/ 2 branches and 2 members at h = 0] | | | | |--leaf "9" | | | | `--leaf "10" | | | `--[dendrogram w/ 2 branches and 2 members at h = 3.61] | | | |--leaf "42" | | | `--leaf "125" | | `--[dendrogram w/ 2 branches and 8 members at h = 12.4] | | |--[dendrogram w/ 2 branches and 4 members at h = 3.33] | | | |--[dendrogram w/ 2 branches and 2 members at h = 2.65] | | | | |--leaf "28" | | | | `--leaf "115" | | | `--[dendrogram w/ 2 branches and 2 members at h = 2.65] | | | |--leaf "35" | | | `--leaf "141" | | `--[dendrogram w/ 2 branches and 4 members at h = 4.99] | | |--leaf "94" | | `--[dendrogram w/ 2 branches and 3 members at h = 3.89] | | |--leaf "58" | | `--[dendrogram w/ 2 branches and 2 members at h = 3] | | |--leaf "24" | | `--leaf "136" | `--[dendrogram w/ 2 branches and 13 members at h = 14.7] | |--[dendrogram w/ 2 branches and 4 members at h = 6.23] | | |--[dendrogram w/ 2 branches and 2 members at h = 3.87] | | | |--leaf "5" | | | `--leaf "52" | | `--[dendrogram w/ 2 branches and 2 members at h = 4.36] | | |--leaf "67" | | `--leaf "111" | `--[dendrogram w/ 2 branches and 9 members at h = 13.2] | |--[dendrogram w/ 2 branches and 4 members at h = 5.52] | | |--[dendrogram w/ 2 branches and 2 members at h = 3] | | | |--leaf "75" | | | `--leaf "116" | | `--[dendrogram w/ 2 branches and 2 members at h = 3.46] | | |--leaf "82" | | `--leaf "107" | `--[dendrogram w/ 2 branches and 5 members at h = 6.19] | |--[dendrogram w/ 2 branches and 2 members at h = 2.83] | | |--leaf "100" | | `--leaf "103" | `--[dendrogram w/ 2 branches and 3 members at h = 3.14] | |--leaf "89" | `--[dendrogram w/ 2 branches and 2 members at h = 2.24] | |--leaf "59" | `--leaf "92" `--[dendrogram w/ 2 branches and 69 members at h = 56.8] |--[dendrogram w/ 2 branches and 24 members at h = 18.1] | |--[dendrogram w/ 2 branches and 10 members at h = 9.29] | | |--[dendrogram w/ 2 branches and 3 members at h = 4.08] | | | |--leaf "45" | | | `--[dendrogram w/ 2 branches and 2 members at h = 3] | | | |--leaf "38" | | | `--leaf "139" | | `--[dendrogram w/ 2 branches and 7 members at h = 6.01] | | |--[dendrogram w/ 2 branches and 3 members at h = 3.18] | | | |--leaf "127" | | | `--[dendrogram w/ 2 branches and 2 members at h = 2.45] | | | |--leaf "76" | | | `--leaf "96" | | `--[dendrogram w/ 2 branches and 4 members at h = 4.47] | | |--[dendrogram w/ 2 branches and 2 members at h = 2.83] | | | |--leaf "21" | | | `--leaf "40" | | `--[dendrogram w/ 2 branches and 2 members at h = 3] | | |--leaf "61" | | `--leaf "81" | `--[dendrogram w/ 2 branches and 14 members at h = 10.8] | |--[dendrogram w/ 2 branches and 8 members at h = 7.41] | | |--[dendrogram w/ 2 branches and 4 members at h = 5.03] | | | |--leaf "123" | | | `--[dendrogram w/ 2 branches and 3 members at h = 3.69] | | | |--leaf "23" | | | `--[dendrogram w/ 2 branches and 2 members at h = 2.24] | | | |--leaf "31" | | | `--leaf "124" | | `--[dendrogram w/ 2 branches and 4 members at h = 6.48] | | |--leaf "29" | | `--[dendrogram w/ 2 branches and 3 members at h = 3.4] | | |--leaf "37" | | `--[dendrogram w/ 2 branches and 2 members at h = 2.45] | | |--leaf "11" | | `--leaf "97" | `--[dendrogram w/ 2 branches and 6 members at h = 7.79] | |--[dendrogram w/ 2 branches and 3 members at h = 5.29] | | |--leaf "68" | | `--[dendrogram w/ 2 branches and 2 members at h = 2.24] | | |--leaf "56" | | `--leaf "132" | `--[dendrogram w/ 2 branches and 3 members at h = 5.4] | |--leaf "102" | `--[dendrogram w/ 2 branches and 2 members at h = 3.74] | |--leaf "51" | `--leaf "119" `--[dendrogram w/ 2 branches and 45 members at h = 44.6] |--[dendrogram w/ 2 branches and 22 members at h = 12.9] | |--[dendrogram w/ 2 branches and 7 members at h = 5.25] | | |--[dendrogram w/ 2 branches and 2 members at h = 2] | | | |--leaf "1" | | | `--leaf "69" | | `--[dendrogram w/ 2 branches and 5 members at h = 4.46] | | |--[dendrogram w/ 2 branches and 2 members at h = 1.73] | | | |--leaf "57" | | | `--leaf "108" | | `--[dendrogram w/ 2 branches and 3 members at h = 4.15] | | |--leaf "90" | | `--[dendrogram w/ 2 branches and 2 members at h = 2.83] | | |--leaf "73" | | `--leaf "78" | `--[dendrogram w/ 2 branches and 15 members at h = 11.5] | |--[dendrogram w/ 2 branches and 8 members at h = 6.64] | | |--[dendrogram w/ 2 branches and 3 members at h = 3.92] | | | |--leaf "104" | | | `--[dendrogram w/ 2 branches and 2 members at h = 3.16] | | | |--leaf "43" | | | `--leaf "142" | | `--[dendrogram w/ 2 branches and 5 members at h = 5.92] | | |--[dendrogram w/ 2 branches and 2 members at h = 2.45] | | | |--leaf "6" | | | `--leaf "19" | | `--[dendrogram w/ 2 branches and 3 members at h = 4.65] | | |--leaf "130" | | `--[dendrogram w/ 2 branches and 2 members at h = 3.61] | | |--leaf "7" | | `--leaf "99" | `--[dendrogram w/ 2 branches and 7 members at h = 7.29] | |--[dendrogram w/ 2 branches and 4 members at h = 3.57] | | |--leaf "65" | | `--[dendrogram w/ 2 branches and 3 members at h = 2.65] | | |--leaf "77" | | `--[dendrogram w/ 2 branches and 2 members at h = 2.24] | | |--leaf "126" | | `--leaf "129" | `--[dendrogram w/ 2 branches and 3 members at h = 5.27] | |--leaf "41" | `--[dendrogram w/ 2 branches and 2 members at h = 3.32] | |--leaf "34" | `--leaf "140" `--[dendrogram w/ 2 branches and 23 members at h = 14.8] |--[dendrogram w/ 2 branches and 9 members at h = 7.31] | |--[dendrogram w/ 2 branches and 5 members at h = 3.83] | | |--[dendrogram w/ 2 branches and 3 members at h = 1.84] | | | |--leaf "44" | | | `--[dendrogram w/ 2 branches and 2 members at h = 1.41] | | | |--leaf "33" | | | `--leaf "85" | | `--[dendrogram w/ 2 branches and 2 members at h = 2.24] | | |--leaf "87" | | `--leaf "91" | `--[dendrogram w/ 2 branches and 4 members at h = 4.07] | |--leaf "120" | `--[dendrogram w/ 2 branches and 3 members at h = 2.83] | |--leaf "32" | `--[dendrogram w/ 2 branches and 2 members at h = 2.83] | |--leaf "13" | `--leaf "30" `--[dendrogram w/ 2 branches and 14 members at h = 10.7] |--[dendrogram w/ 2 branches and 4 members at h = 4.58] | |--[dendrogram w/ 2 branches and 2 members at h = 2.24] | | |--leaf "83" | | `--leaf "93" | `--[dendrogram w/ 2 branches and 2 members at h = 3.74] | |--leaf "15" | `--leaf "71" `--[dendrogram w/ 2 branches and 10 members at h = 7.01] |--[dendrogram w/ 2 branches and 4 members at h = 4.42] | |--leaf "101" | `--[dendrogram w/ 2 branches and 3 members at h = 3.28] | |--leaf "4" | `--[dendrogram w/ 2 branches and 2 members at h = 2] | |--leaf "63" | `--leaf "121" `--[dendrogram w/ 2 branches and 6 members at h = 5.91] |--[dendrogram w/ 2 branches and 2 members at h = 2.65] | |--leaf "46" | `--leaf "60" `--[dendrogram w/ 2 branches and 4 members at h = 5.59] |--[dendrogram w/ 2 branches and 2 members at h = 3] | |--leaf "26" | `--leaf "27" `--[dendrogram w/ 2 branches and 2 members at h = 3.61] |--leaf "2" `--leaf "109" > mysub <- paste('Method: ',par1) > postscript(file="/var/wessaorg/rcomp/tmp/1s5rc1454007139.ps",horizontal=F,onefile=F,pagecentre=F,paper="special",width=8.3333333333333,height=5.5555555555556) > if (par4 == 'TRUE'){ + plot(d,main=main,ylab=ylab,xlab=xlab,horiz=par3, nodePar=list(pch = c(1,NA), cex=0.8, lab.cex = 0.8),type='t',center=T, sub=mysub) + } else { + plot(d,main=main,ylab=ylab,xlab=xlab,horiz=par3, nodePar=list(pch = c(1,NA), cex=0.8, lab.cex = 0.8), sub=mysub) + } > dev.off() null device 1 > if (par2 != 'ALL'){ + if (par3 == 'TRUE'){ + ylab = 'cluster' + } else { + xlab = 'cluster' + } + par2 <- as.numeric(par2) + memb <- cutree(hc, k = par2) + cent <- NULL + for(k in 1:par2){ + cent <- rbind(cent, colMeans(x[memb == k, , drop = FALSE])) + } + hc1 <- hclust(dist(cent),method=par1, members = table(memb)) + de <- as.dendrogram(hc1) + postscript(file="/var/wessaorg/rcomp/tmp/288ct1454007139.ps",horizontal=F,onefile=F,pagecentre=F,paper="special",width=8.3333333333333,height=5.5555555555556) + if (par4 == 'TRUE'){ + plot(de,main=main,ylab=ylab,xlab=xlab,horiz=par3, nodePar=list(pch = c(1,NA), cex=0.8, lab.cex = 0.8),type='t',center=T, sub=mysub) + } else { + plot(de,main=main,ylab=ylab,xlab=xlab,horiz=par3, nodePar=list(pch = c(1,NA), cex=0.8, lab.cex = 0.8), sub=mysub) + } + dev.off() + str(de) + } > > #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,'Summary of Dendrogram',2,TRUE) > a<-table.row.end(a) > a<-table.row.start(a) > a<-table.element(a,'Label',header=TRUE) > a<-table.element(a,'Height',header=TRUE) > a<-table.row.end(a) > num <- length(x[,1])-1 > for (i in 1:num) + { + a<-table.row.start(a) + a<-table.element(a,hc$labels[i]) + a<-table.element(a,hc$height[i]) + a<-table.row.end(a) + } > a<-table.end(a) > table.save(a,file="/var/wessaorg/rcomp/tmp/34d6l1454007139.tab") > if (par2 != 'ALL'){ + a<-table.start() + a<-table.row.start(a) + a<-table.element(a,'Summary of Cut Dendrogram',2,TRUE) + a<-table.row.end(a) + a<-table.row.start(a) + a<-table.element(a,'Label',header=TRUE) + a<-table.element(a,'Height',header=TRUE) + a<-table.row.end(a) + num <- par2-1 + for (i in 1:num) + { + a<-table.row.start(a) + a<-table.element(a,i) + a<-table.element(a,hc1$height[i]) + a<-table.row.end(a) + } + a<-table.end(a) + table.save(a,file="/var/wessaorg/rcomp/tmp/4m5e21454007139.tab") + } > > try(system("convert tmp/1s5rc1454007139.ps tmp/1s5rc1454007139.png",intern=TRUE)) character(0) > try(system("convert tmp/288ct1454007139.ps tmp/288ct1454007139.png",intern=TRUE)) convert.im6: unable to open image `tmp/288ct1454007139.ps': No such file or directory @ error/blob.c/OpenBlob/2638. convert.im6: no images defined `tmp/288ct1454007139.png' @ error/convert.c/ConvertImageCommand/3044. character(0) attr(,"status") [1] 1 Warning message: running command 'convert tmp/288ct1454007139.ps tmp/288ct1454007139.png' had status 1 > > > proc.time() user system elapsed 1.155 0.159 1.310