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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 03:51:28 -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/t12263143496j03un7587l49bu.htm/, Retrieved Mon, 10 Nov 2008 10:52:32 +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/t12263143496j03un7587l49bu.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 «
4,43 88,3 4,61 88,6 4,54 91 4,2 91,5 4,08 95,4 3,95 98,7 4,19 99,9 4,23 98,6 3,89 100,3 3,92 100,2 4,14 100,4 4,24 101,4 4,08 103 4,37 109,1 4,43 111,4 4,3 114,1 4,27 121,8 4,06 127,6 3,96 129,9 4,21 128 4,31 123,5 4,35 124 4,25 127,4 4,06 127,6 4 128,4 3,87 131,4 3,71 135,1 3,63 134 3,48 144,5 3,6 147,3 3,66 150,9 3,45 148,7 3,3 141,4 3,14 138,9 3,21 139,8 3,12 145,6 3,14 147,9 3,4 148,5 3,42 151,1 3,29 157,5 3,49 167,5 3,52 172,3 3,81 173,5 4,03 187,5 3,98 205,5 4,1 195,1 3,96 204,5 3,83 204,5 3,72 201,7 3,82 207 3,76 206,6 3,98 210,6 4,14 211,1 4 215 4,13 223,9 4,28 238,2 4,46 238,9 4,63 229,6 4,49 232,2 4,41 222,1 4,5 221,6 4,39 227,3 4,33 221 4,45 213,6 4,17 243,4 4,13 253,8 4,33 265,3 4,47 268,2 4,63 268,5 4,9 266,9
 
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 time1 seconds
R Server'Gwilym Jenkins' @ 72.249.127.135


Summary of Dendrogram
LabelHeight
10
20.1044030650891
30.13
40.206155281280872
50.297321374946373
60.312409987036259
70.34000000000001
80.342918721839033
90.349857113690716
100.367816379310222
110.404474968323139
120.451774279923066
130.501597448159378
140.508035431835221
150.524976189936267
160.59122080450209
170.604648658313239
180.722772439983723
190.756042326857427
200.902718117686806
210.981670674337408
221.10290525431697
231.15741090369842
241.21820981059473
251.23454445039455
261.29759160054122
271.47054411698528
281.50269757436418
291.58712084703855
301.60798009937934
311.69849933765071
322.30078247559391
332.31248783780584
342.43408390931402
352.43752330659312
363.15662684972837
373.53540047824407
383.62295788799493
393.924238009204
404.23236192374821
414.36881770407533
425.13832199667298
435.14292449699659
445.58142180313298
455.93138866297624
466.23274124925701
476.51164336427747
486.55128267730654
496.79423253179157
507.43637705227406
517.6003223615844
528.57031883938793
5311.2138966029096
5415.0221891164245
5518.1185167951723
5618.7133475648716
5720.1693662932021
5827.2706086376061
5940.721749166757
6043.1832114125376
6150.2170352711611
6255.369809249064
6364.8708625508368
64139.135869789165
65151.849447819497
66170.072398849113
67375.184498272536
68538.994605484967
692414.73615853108
 
Charts produced by software:
http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Nov/10/t12263143496j03un7587l49bu/11d2p1226314285.png (open in new window)
http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Nov/10/t12263143496j03un7587l49bu/11d2p1226314285.ps (open in new window)


http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Nov/10/t12263143496j03un7587l49bu/2jbnj1226314285.png (open in new window)
http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Nov/10/t12263143496j03un7587l49bu/2jbnj1226314285.ps (open in new window)


 
Parameters (Session):
par1 = ward ; par2 = ALL ; par3 = FALSE ; par4 = FALSE ;
 
Parameters (R input):
par1 = ward ; 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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