R version 3.0.2 (2013-09-25) -- "Frisbee Sailing" Copyright (C) 2013 The R Foundation for Statistical Computing 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. 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xlab = 'cases' > main = 'Dendrogram' > par4 <- 'FALSE' > par3 <- 'FALSE' > par2 <- '5' > par1 <- 'median' > #'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) > d <- as.dendrogram(hc) > str(d) --[dendrogram w/ 2 branches and 90 members at h = 118] |--[dendrogram w/ 2 branches and 15 members at h = 52.7] | |--[dendrogram w/ 2 branches and 2 members at h = 7] | | |--leaf "24" | | `--leaf "81" | `--[dendrogram w/ 2 branches and 13 members at h = 31.6] | |--[dendrogram w/ 2 branches and 3 members at h = 8.5] | | |--leaf "82" | | `--[dendrogram w/ 2 branches and 2 members at h = 6] | | |--leaf "23" | | `--leaf "60" | `--[dendrogram w/ 2 branches and 10 members at h = 22] | |--[dendrogram w/ 2 branches and 6 members at h = 5.87] | | |--[dendrogram w/ 2 branches and 3 members at h = 2.96] | | | |--leaf "55" | | | `--[dendrogram w/ 2 branches and 2 members at h = 0.172] | | | |--leaf "14" | | | `--leaf "20" | | `--[dendrogram w/ 2 branches and 3 members at h = 4.5] | | |--leaf "59" | | `--[dendrogram w/ 2 branches and 2 members at h = 2.01] | | |--leaf "29" | | `--leaf "86" | `--[dendrogram w/ 2 branches and 4 members at h = 10] | |--[dendrogram w/ 2 branches and 2 members at h = 5] | | |--leaf "26" | | `--leaf "28" | `--[dendrogram w/ 2 branches and 2 members at h = 7] | |--leaf "22" | `--leaf "25" `--[dendrogram w/ 2 branches and 75 members at h = 53.7] |--[dendrogram w/ 2 branches and 37 members at h = 24.6] | |--[dendrogram w/ 2 branches and 13 members at h = 5.77] | | |--[dendrogram w/ 2 branches and 5 members at h = 1.49] | | | |--[dendrogram w/ 2 branches and 3 members at h = 0.975] | | | | |--leaf "4" | | | | `--[dendrogram w/ 2 branches and 2 members at h = 0.127] | | | | |--leaf "42" | | | | `--leaf "52" | | | `--[dendrogram w/ 2 branches and 2 members at h = 1.01] | | | |--leaf "9" | | | `--leaf "38" | | `--[dendrogram w/ 2 branches and 8 members at h = 3.61] | | |--[dendrogram w/ 2 branches and 3 members at h = 1.95] | | | |--leaf "8" | | | `--[dendrogram w/ 2 branches and 2 members at h = 0.209] | | | |--leaf "6" | | | `--leaf "51" | | `--[dendrogram w/ 2 branches and 5 members at h = 2.48] | | |--[dendrogram w/ 2 branches and 3 members at h = 0.989] | | | |--leaf "36" | | | `--[dendrogram w/ 2 branches and 2 members at h = 0.217] | | | |--leaf "3" | | | `--leaf "77" | | `--[dendrogram w/ 2 branches and 2 members at h = 1.04] | | |--leaf "71" | | `--leaf "72" | `--[dendrogram w/ 2 branches and 24 members at h = 15] | |--[dendrogram w/ 2 branches and 7 members at h = 6.97] | | |--leaf "44" | | `--[dendrogram w/ 2 branches and 6 members at h = 3.86] | | |--leaf "45" | | `--[dendrogram w/ 2 branches and 5 members at h = 1.5] | | |--[dendrogram w/ 2 branches and 2 members at h = 1.03] | | | |--leaf "61" | | | `--leaf "75" | | `--[dendrogram w/ 2 branches and 3 members at h = 1.05] | | |--leaf "39" | | `--[dendrogram w/ 2 branches and 2 members at h = 0.212] | | |--leaf "43" | | `--leaf "68" | `--[dendrogram w/ 2 branches and 17 members at h = 10.1] | |--[dendrogram w/ 2 branches and 9 members at h = 4.34] | | |--[dendrogram w/ 2 branches and 4 members at h = 1.26] | | | |--leaf "40" | | | `--[dendrogram w/ 2 branches and 3 members at h = 0.982] | | | |--leaf "69" | | | `--[dendrogram w/ 2 branches and 2 members at h = 0.179] | | | |--leaf "32" | | | `--leaf "89" | | `--[dendrogram w/ 2 branches and 5 members at h = 2.16] | | |--[dendrogram w/ 2 branches and 2 members at h = 0.319] | | | |--leaf "33" | | | `--leaf "65" | | `--[dendrogram w/ 2 branches and 3 members at h = 0.938] | | |--leaf "35" | | `--[dendrogram w/ 2 branches and 2 members at h = 0.359] | | |--leaf "37" | | `--leaf "73" | `--[dendrogram w/ 2 branches and 8 members at h = 6.23] | |--[dendrogram w/ 2 branches and 3 members at h = 1.26] | | |--leaf "64" | | `--[dendrogram w/ 2 branches and 2 members at h = 1.04] | | |--leaf "41" | | `--leaf "66" | `--[dendrogram w/ 2 branches and 5 members at h = 3.73] | |--[dendrogram w/ 2 branches and 2 members at h = 1] | | |--leaf "67" | | `--leaf "78" | `--[dendrogram w/ 2 branches and 3 members at h = 1.99] | |--leaf "79" | `--[dendrogram w/ 2 branches and 2 members at h = 0.282] | |--leaf "31" | `--leaf "34" `--[dendrogram w/ 2 branches and 38 members at h = 30.6] |--[dendrogram w/ 2 branches and 13 members at h = 15.2] | |--[dendrogram w/ 2 branches and 3 members at h = 7.5] | | |--leaf "12" | | `--[dendrogram w/ 2 branches and 2 members at h = 6] | | |--leaf "21" | | `--leaf "48" | `--[dendrogram w/ 2 branches and 10 members at h = 8.45] | |--[dendrogram w/ 2 branches and 3 members at h = 4.25] | | |--leaf "30" | | `--[dendrogram w/ 2 branches and 2 members at h = 1.03] | | |--leaf "18" | | `--leaf "84" | `--[dendrogram w/ 2 branches and 7 members at h = 5.55] | |--[dendrogram w/ 2 branches and 2 members at h = 1.01] | | |--leaf "1" | | `--leaf "19" | `--[dendrogram w/ 2 branches and 5 members at h = 1.26] | |--leaf "7" | `--[dendrogram w/ 2 branches and 4 members at h = 0.966] | |--leaf "57" | `--[dendrogram w/ 2 branches and 3 members at h = 0.104] | |--leaf "11" | `--[dendrogram w/ 2 branches and 2 members at h = 0.0938] | |--leaf "13" | `--leaf "27" `--[dendrogram w/ 2 branches and 25 members at h = 18.5] |--[dendrogram w/ 2 branches and 13 members at h = 8.14] | |--leaf "46" | `--[dendrogram w/ 2 branches and 12 members at h = 4.3] | |--[dendrogram w/ 2 branches and 5 members at h = 2.23] | | |--leaf "50" | | `--[dendrogram w/ 2 branches and 4 members at h = 0.939] | | |--[dendrogram w/ 2 branches and 2 members at h = 0.141] | | | |--leaf "49" | | | `--leaf "70" | | `--[dendrogram w/ 2 branches and 2 members at h = 0.144] | | |--leaf "16" | | `--leaf "87" | `--[dendrogram w/ 2 branches and 7 members at h = 2.96] | |--[dendrogram w/ 2 branches and 2 members at h = 0.248] | | |--leaf "58" | | `--leaf "83" | `--[dendrogram w/ 2 branches and 5 members at h = 2.06] | |--[dendrogram w/ 2 branches and 2 members at h = 1.04] | | |--leaf "2" | | `--leaf "76" | `--[dendrogram w/ 2 branches and 3 members at h = 1.26] | |--leaf "15" | `--[dendrogram w/ 2 branches and 2 members at h = 1] | |--leaf "54" | `--leaf "56" `--[dendrogram w/ 2 branches and 12 members at h = 11.6] |--[dendrogram w/ 2 branches and 4 members at h = 6.25] | |--[dendrogram w/ 2 branches and 2 members at h = 1.01] | | |--leaf "10" | | `--leaf "80" | `--[dendrogram w/ 2 branches and 2 members at h = 4] | |--leaf "17" | `--leaf "88" `--[dendrogram w/ 2 branches and 8 members at h = 6.64] |--[dendrogram w/ 2 branches and 5 members at h = 3.31] | |--leaf "62" | `--[dendrogram w/ 2 branches and 4 members at h = 1.24] | |--leaf "63" | `--[dendrogram w/ 2 branches and 3 members at h = 0.939] | |--leaf "47" | `--[dendrogram w/ 2 branches and 2 members at h = 0.363] | |--leaf "5" | `--leaf "90" `--[dendrogram w/ 2 branches and 3 members at h = 4.25] |--leaf "53" `--[dendrogram w/ 2 branches and 2 members at h = 1.01] |--leaf "74" `--leaf "85" > mysub <- paste('Method: ',par1) > postscript(file="/var/wessaorg/rcomp/tmp/1z5ne1383225443.ps",horizontal=F,onefile=F,pagecentre=F,paper="special",width=16.666666666667,height=11.111111111111) > 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/2mlt21383225443.ps",horizontal=F,onefile=F,pagecentre=F,paper="special",width=16.666666666667,height=11.111111111111) + 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) + } --[dendrogram w/ 2 branches and 5 members at h = 111] |--[dendrogram w/ 2 branches and 3 members at h = 59.4] | |--leaf 3 | `--[dendrogram w/ 2 branches and 2 members at h = 44.8] | |--leaf 4 | `--leaf 5 `--[dendrogram w/ 2 branches and 2 members at h = 69.9] |--leaf 1 `--leaf 2 > > #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$height[i]) + a<-table.row.end(a) + } > a<-table.end(a) > table.save(a,file="/var/wessaorg/rcomp/tmp/3849p1383225443.tab") > if (par2 != 'ALL'){ + a<-table.start() + a<-table.row.start(a) + a<-table.element(a,'Summary of Cut Dendrogram',2,TRUE) + a<-table.row.end(a) + a<-table.row.start(a) + a<-table.element(a,'Label',header=TRUE) + a<-table.element(a,'Height',header=TRUE) + a<-table.row.end(a) + num <- par2-1 + for (i in 1:num) + { + a<-table.row.start(a) + a<-table.element(a,i) + a<-table.element(a,hc1$height[i]) + a<-table.row.end(a) + } + a<-table.end(a) + table.save(a,file="/var/wessaorg/rcomp/tmp/4g6z51383225444.tab") + } > > try(system("convert tmp/1z5ne1383225443.ps tmp/1z5ne1383225443.png",intern=TRUE)) character(0) > try(system("convert tmp/2mlt21383225443.ps tmp/2mlt21383225443.png",intern=TRUE)) character(0) > > > proc.time() user system elapsed 3.071 1.028 4.078