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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: Thu, 06 Nov 2008 09:18:16 -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/06/t1225988342246h8itp5151x2f.htm/, Retrieved Thu, 06 Nov 2008 16:19:10 +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/06/t1225988342246h8itp5151x2f.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 «
96.8 96.9 96.7 95.4 96.8 91.2 98.0 88.0 101.2 87.0 97.1 97.9 96.7 101.5 96.3 104.9 100.9 106.8 101.9 107.1 110.9 103.9 114.3 101.7 115.2 104.8 103.1 105.7 100.1 106.1 94.1 102.5 90.1 97.4 89.5 95.8 104.3 91.6 96.5 91.3 99.3 102.6 97.7 99.2 97.6 101.1 101.7 100.8 102.2 100.7 104.0 102.8 104.6 105.3 104.6 99.0 105.4 95.9 111.1 94.7 105.4 110.9 102.7 114.9 101.8 107.1 113.5 104.0 124.5 102.5 110.7 116.3 107.9 142.2 105.3 117.1 124.0 113.8 159.7 110.3 118.7 128.8 113.8 165.2 109.8 126.5 133.5 123.1 198.6 117.3 127.5 132.6 125.1 207.8 118.8 134.6 128.4 137.6 219.6 131.3 131.8 127.3 134.0 239.6 125.9 135.9 126.7 140.3 235.3 133.1 142.7 123.3 152.1 218.5 147.0 141.7 123.2 150.6 213.8 145.8 153.4 124.4 167.3 205.5 164.4 145.0 128.2 153.2 198.4 149.8 137.7 128.7 142.0 198.5 137.7 148.3 135.7 154.4 190.2 151.7 152.2 139.0 158.5 180.7 156.8 169.4 145.4 180.9 193.6 180.0 168.6 142.4 181.3 192.8 180.4 161.1 137.7 172.4 195.5 170.4 174.1 137.0 192.0 197.2 191.6 179.0 137.1 199.3 196.9 199.5 190.6 139.3 215.4 178.9 218.2 190.0 139.6 214.3 172.4 217.5 181.6 140.4 201.5 156.4 205.0 174.8 142.3 190.5 143.7 194.0 180.5 148.3 196.0 153.6 199.3 196.8 157.7 215.7 168.8 219.3 193.8 161.6 209.4 185.8 211.1 197.0 161.7 214.1 199.9 215.2 216.3 171.8 237.8 205.4 240.2 221.4 185.1 239.0 197.5 242.2 217.9 176.7 237.8 199.6 240.7 229.7 184.4 251.5 200.5 255.4 227.4 183.0 248.8 193.7 253.0 204.2 180.9 215.4 179.6 218.2 196.6 187.0 201.2 169.1 203.7 198.8 189.9 203.1 169.8 205.6 207.5 193.8 214.2 195.5 215.6 190.7 194.5 188.9 194.8 188.5 201.6 198.7 203.0 204.5 202.9 210.5 204.7 213.3 203.8 214.0 223.5 213.2 228.5 204.8 230.3 223.8 214.7 228.2 204.9 230.0 231.2 211.0 240.9 240.0 241.0 244.0 213.2 258.8 248.3 259.6 234.7 206.3 248.5 258.4 247.8 250.2 210.8 269.2 254.9 270.3
 
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'George Udny Yule' @ 72.249.76.132
R Framework
error message
The field 'Names of X columns' contains a hard return which cannot be interpreted.
Please, resubmit your request without hard returns in the 'Names of X columns'.


Summary of Dendrogram
LabelHeight
11.59059737205869
23.20936130717624
33.25576411921994
43.52562051276084
54.57820925690386
65.175905717843
75.68066897468951
86.12438931013497
96.20886463051015
106.66333249958307
117.48999332442961
127.77560287051749
138.15720540381325
149.62808392152875
1510.1975487250613
1610.2796543061681
1710.8430912916896
1811.2778544058699
1911.5844723660597
2011.8080481028831
2111.8241278748160
2214.1446102809515
2314.7342365347412
2415.7467456955397
2517.6184562320312
2617.8964328711026
2719.3359556887245
2819.9546986947936
2920.2349701761538
3020.3263432145169
3121.1839258603736
3221.4366382779137
3321.8380402051100
3425.589034711971
3528.5424536737741
3628.836328276247
3730.1824864808308
3830.9606046745631
3940.0243536815488
4040.4537529569372
4145.4252851537586
4246.5804363084871
4347.327049623301
4453.7458605364445
4561.6678346389096
4665.5590180930103
4766.4327692151587
4868.8183658341696
4996.987783624418
5098.8066877593632
51111.577760566497
52127.412914111299
53171.899732406559
54213.521190000939
55214.456311085589
56302.315502706050
57764.749376729712
581221.40936314200
593413.92226502828
 
Charts produced by software:
http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Nov/06/t1225988342246h8itp5151x2f/12us41225988293.png (open in new window)
http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Nov/06/t1225988342246h8itp5151x2f/12us41225988293.ps (open in new window)


http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Nov/06/t1225988342246h8itp5151x2f/2zq8x1225988293.png (open in new window)
http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Nov/06/t1225988342246h8itp5151x2f/2zq8x1225988293.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')
}
 




Copyright

Creative Commons License

This work is licensed under a Creative Commons Attribution-Noncommercial-Share Alike 3.0 License.

Software written by Ed van Stee & Patrick Wessa


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