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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: Tue, 11 Nov 2008 12:18:42 -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/11/t1226431210e7ujjl2l3gn56ue.htm/, Retrieved Tue, 11 Nov 2008 19:20:10 +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/11/t1226431210e7ujjl2l3gn56ue.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 «
5014 2400 3180 1712 6153 4700 4151 2641 6441 3700 4023 2267 5584 2900 3431 2126 6427 2800 3874 2231 6062 3000 2617 1517 5589 3100 3580 2010 6216 3700 5267 2628 5809 3000 3832 2115 4989 2000 3441 1829 6706 1900 3228 1636 7174 1900 3397 1787 6122 1800 3971 2122 8075 3400 4625 2620 6292 3800 4486 2555 6337 2800 4131 2337 8576 3100 4686 2524 6077 2100 3174 1801 5931 2000 4282 2417 6288 2500 4209 2389 7167 2400 4159 2267 6054 2500 3936 2135 6468 3300 3153 1760 6401 3100 3620 1905 6927 3700 4227 2176 7914 5600 4441 2344 7728 3700 4808 2673 8699 2900 4850 2766 8522 4000 5040 2785 6481 2900 3546 2003 7502 2400 4669 2588 7778 3300 5410 2739 7424 3800 5134 2703 6941 4400 4864 2464 8574 4000 3999 1974 9169 3100 4459 2164 7701 2700 4622 2385 9035 5200 5360 2936 7158 4600 4658 2700 8195 3700 5173 2855 8124 3200 4845 2764 7073 2400 3325 1808 7017 2200 4720 2588 7390 3200 4895 2600 7776 3100 5071 2526 6197 2300 4895 2259 6889 2500 3805 1738 7087 2900 4187 1902 6485 2700 4435 2137 7654 5000 4475 2460 6501 3500 4774 2495 6313 3000 5161 2525 7826 3800 4529 2465 6589 2800 3284 1828 6729 2400 4303 2273 5684 2700 4610 2377 8105 2800 4691 2344 6391 2700 4200 2071 5901 2600 3471 1611 6758 3100 3132 1671
 
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 time2 seconds
R Server'Sir Ronald Aylmer Fisher' @ 193.190.124.24


Summary of Dendrogram
LabelHeight
1247.951608181919
2261.566435155583
3275.103616842818
4292.207118325341
5333.971555675031
6363.953293706761
7374.951996927607
8375.11198327966
9415.955526468876
10430.373093954536
11440.228349836764
12442.09501241249
13461.10302536418
14465.153520844928
15468.527480517419
16469.281365494092
17478.608677674509
18492.376888165966
19510.124494608914
20515.583164969532
21534.876621287564
22536.604146836154
23595.763552150006
24608.735701024141
25609.937701736825
26621.549327826321
27636.619980836291
28653.226142370041
29664.990225492074
30689.755814301529
31719.943053303523
32721.979224077812
33727.859505335838
34837.533169370442
35948.969370592874
36964.420920371878
371045.26518327050
381159.29195548825
391243.43787819931
401245.47991090852
411304.25411816487
421356.50041135105
431567.77986203648
441695.14495786733
451707.91564411596
461814.84927877855
471881.52930613628
482002.10119141975
492125.13228697934
502266.77301053279
512572.18680793074
522840.90117897524
533378.03999300915
544393.30109108845
555015.88188543551
565800.74098770837
579006.24792009481
589975.83416938366
5928532.0226658569
 
Charts produced by software:
http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Nov/11/t1226431210e7ujjl2l3gn56ue/12yvo1226431118.png (open in new window)
http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Nov/11/t1226431210e7ujjl2l3gn56ue/12yvo1226431118.ps (open in new window)


http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Nov/11/t1226431210e7ujjl2l3gn56ue/242zg1226431118.png (open in new window)
http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Nov/11/t1226431210e7ujjl2l3gn56ue/242zg1226431118.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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