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Hierarchical Clustering

*The author of this computation has been verified*
R Software Module: rwasp_hierarchicalclustering.wasp (opens new window with default values)
Title produced by software: Hierarchical Clustering
Date of computation: Mon, 10 Nov 2008 08:35:47 -0700
 
Cite this page as follows:
Statistical Computations at FreeStatistics.org, Office for Research Development and Education, URL http://www.freestatistics.org/blog/date/2008/Nov/10/t1226331375r17fz7g9ru9kq9e.htm/, Retrieved Mon, 10 Nov 2008 15:36:15 +0000
 
BibTeX entries for LaTeX users:
@Manual{KEY,
    author = {{YOUR NAME}},
    publisher = {Office for Research Development and Education},
    title = {Statistical Computations at FreeStatistics.org, URL http://www.freestatistics.org/blog/date/2008/Nov/10/t1226331375r17fz7g9ru9kq9e.htm/},
    year = {2008},
}
@Manual{R,
    title = {R: A Language and Environment for Statistical Computing},
    author = {{R Development Core Team}},
    organization = {R Foundation for Statistical Computing},
    address = {Vienna, Austria},
    year = {2008},
    note = {{ISBN} 3-900051-07-0},
    url = {http://www.R-project.org},
}
 
Family? (F = Feedback message, R = changed R code, M = changed R Module, P = changed Parameters, D = changed Data)
 
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Original text written by user:
 
IsPrivate?
No (this computation is public)
 
User-defined keywords:
 
Dataseries X:
» Textbox « » Textfile « » CSV «
105.15 118.63 118.76 107.06 105.24 121.83 119.28 109.98 105.57 119.97 119.89 112.64 105.62 124.98 120.38 112.89 106.17 129.99 121.39 112.9 106.27 126.6 121.86 112.9 106.41 121.71 122.21 112.91 106.94 119.28 122.61 112.99 107.16 122.63 123.7 113.01 107.32 116.74 125.53 113 107.32 114.23 126.03 113.07 107.35 113.23 126.17 113.07 107.55 112.75 126.39 113.21 107.87 113.54 127.55 114.13 108.37 115.3 128.86 114.59 108.38 121.05 129.59 114.88 107.92 119.51 130.4 115.3 108.03 116.78 130.52 115.33 108.14 117.17 130.55 115.36 108.3 117.5 130.67 115.41 108.64 119.65 131.13 115.43 108.66 120.97 132.15 115.43 109.04 117.18 132.69 115.43 109.03 116.87 132.8 115.43 109.03 119.46 132.96 115.56 109.54 122.52 133.05 115.88 109.75 124.1 133.23 116.02 109.83 118.39 135.32 116.09 109.65 113.1 136.22 116.28 109.82 113.94 136.33 116.28 109.95 114.58 136.53 116.28 110.12 118.79 136.6 116.25 110.15 120.44 136.77 116.07 110.21 118.37 137.49 116.08 109.99 118.44 138.06 116.07 110.14 117.93 138.46 115.92 110.14 117.76 138.34 116.07 110.81 118.29 139.06 117.22 110.97 121.11 139.95 117.75 110.99 124.86 140.41 117.78 109.73 131.17 141.39 117.78 109.81 130.16 141.87 117.81 110.02 131.76 141.91 117.81 110.18 134.7 141.99 117.74 110.21 135.32 142.26 117.75 110.25 140.23 142.38 117.76 110.36 136.31 143.17 117.76 110.51 131.62 143.28 117.75 110.6 128.9 143.8 117.8 110.95 133.89 144.16 118.09 111.18 138.21 145.36 118.95 111.19 146.12 146.83 119.03 111.69 144.69 147.56 118.9 111.7 149.18 148.04 118.9 111.83 156.6 148.69 118.9 111.77 158.87 148.93 118.87 111.73 164.85 149.21 118.88 112.01 162.89 149.86 119.36 111.86 153.31 150.64 119.39 112.04 150.91 150.69 119.47
 
Output produced by software:

Enter (or paste) a matrix (table) containing all data (time) series. Every column represents a different variable and must be delimited by a space or Tab. Every row represents a period in time (or category) and must be delimited by hard returns. The easiest way to enter data is to copy and paste a block of spreadsheet cells. Please, do not use commas or spaces to seperate groups of digits!


Summary of computational transaction
Raw Inputview raw input (R code)
Raw Outputview raw output of R engine
Computing time3 seconds
R Server'Herman Ole Andreas Wold' @ 193.190.124.10:1001


Summary of Dendrogram
LabelHeight
10.256515106767611
20.329089653438094
30.389101529166864
40.581721582889963
50.615060972587264
60.676978581640509
70.683008052661166
80.78752777728788
90.838749068553885
101.04297650980259
111.07935165724614
121.38133992919919
131.54159008818817
141.54677082982581
151.61012421881046
161.61421807696481
171.68662384662378
181.7578395831247
191.90761631362285
202.00432033367922
212.03246156175215
222.05246193630966
232.13843400646362
242.14785939949523
252.16834037918404
262.28363744933386
272.28853665035104
282.4085887984461
292.49329099785805
302.53136326907065
312.70064807037128
323.14227624501730
333.47680888171898
343.77828003197222
353.84316276001942
363.89617761402122
373.9040747943655
384.02925551435995
394.09793850612721
404.36404628756387
414.51559519886361
424.90451832497341
435.33867961203892
446.63045247324797
457.32215815180196
467.38052843636552
478.0225307727674
488.1787590745785
498.32397140792784
5011.0345185667523
5111.4025304209197
5213.0809976683738
5314.0341797052767
5414.8643802427145
5515.8131938582944
5623.3980084622602
5729.2442883312280
5844.4264448273773
5957.3130325493251
 
Charts produced by software:
http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Nov/10/t1226331375r17fz7g9ru9kq9e/1ou4d1226331342.png (open in new window)
http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Nov/10/t1226331375r17fz7g9ru9kq9e/1ou4d1226331342.ps (open in new window)


http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Nov/10/t1226331375r17fz7g9ru9kq9e/2pb3e1226331342.png (open in new window)
http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Nov/10/t1226331375r17fz7g9ru9kq9e/2pb3e1226331342.ps (open in new window)


 
Parameters (Session):
par1 = complete ; par2 = ALL ; par3 = FALSE ; par4 = FALSE ;
 
Parameters (R input):
par1 = complete ; par2 = ALL ; par3 = FALSE ; par4 = FALSE ;
 
R code (references can be found in the software module):
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)
mysub <- paste('Method: ',par1)
bitmap(file='test1.png')
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()
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)
bitmap(file='test2.png')
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)
}
load(file='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='mytable1.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='mytable2.tab')
}
 




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Software written by Ed van Stee & Patrick Wessa


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