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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: Wed, 12 Nov 2008 11:58:10 -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/12/t122651661441zvhk2re3jjm2x.htm/, Retrieved Wed, 12 Nov 2008 19:03:37 +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/12/t122651661441zvhk2re3jjm2x.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:
hierarchical
 
Dataseries X:
» Textbox « » Textfile « » CSV «
62.2 43.5 200.7 88.5 37.7 146.5 93.3 36.8 143.6 89.2 24.4 141.5 101.3 31.3 137.5 97 43.9 138.7 102.2 53.6 135.5 100.3 48.9 136.4 78.2 30.9 112.1 105.9 31.8 109 119.9 41.3 123.8 108 43.7 151.2 77 54.1 139.2 93.1 47.8 115.7 109.5 36.7 147.6 100.4 30.8 126.1 99 31.9 122.8 113.9 61.7 137.3 102.1 73 142 101.6 64.7 137.4 84 24.2 89.4 110.7 33.9 108 111.6 32.4 117.7 110.7 63.2 127.3 73.1 71.8 121 87.5 60.4 104.1 109.6 48 119.5 99.3 44.5 116.7 92.1 44.9 96.1 109.3 70.9 125 94.5 72.7 118.8 91.4 59.5 114.9 82.9 35.9 79.3 103.3 40 90.5 96 43.6 87.8 104.8 57.2 109.4 65.8 75.8 88.9 78.7 57.7 97.4 100.3 47.7 112 85 42.3 86.8 94.5 43 82.9 97.9 68 105.2 91.9 70.6 89.1 87.2 54.2 85.5 84.4 38.6 87.1 99.2 40.3 85.2 105.4 49.2 88.2 110.9 68.5 104 69.8 75.9 96.4 86.8 63.2 82.3 106.7 49.8 114.1 88.8 37 88.9 96.9 48.8 93.6 108.1 74.9 101.8 93.7 75.3 96.6 94.8 66.9 93.7 79.8 44.1 68.4 95.6 39.8 68.7 107.9 56.6 81.2 104.9 77.1 85.1 61.9 78.5 75.4 85.7 70.6 71.6 92.4 54.2 83 86.4 47.2 72.3 99.3 55.1 90.2 95.5 74.5 89 97 88 84.9 102.1 80.8 90.9 77.8 54.4 46.6 105.5 55.2 55.4 113.2 73.8 88.7 108.8 85.3 76 66.9 98.7 76.9 89.3 86.1 72.1 93.6 62.5 90 92 58.6 92.3 99.5 67 78 98.6 88.4 93.9 94.6 96.5 84.5 96.7 87.1 80.4 75.3 61.2 60.5 102.5 62.5 75.3 115.1 85.2 91.5 104.7 101.7 105.2 71.4 113.7 92.7
 
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'Gwilym Jenkins' @ 72.249.127.135


Summary of Dendrogram
LabelHeight
13.74966665185053
23.76031913539263
34.59891291502677
44.80208288141718
55.1487862647424
65.15945733580576
75.3084837759948
85.33385414123783
95.67978872846517
105.72632889513846
115.76974869470067
125.77321400954443
136.04483250388297
146.38827050147378
156.65806144472115
166.67083203206317
177.32393336944023
187.42765104188398
198.01311425102625
208.15720540381325
218.20228987643107
228.22834381117324
238.26922003577121
248.50058821494136
258.71894489029493
269.48602495241368
279.50263121456367
2810.2029644138025
2910.9242212456256
3011.3399800956223
3111.3850779531806
3211.5323656253959
3311.7385307321470
3411.8915936694793
3512.2912119092932
3612.444955970077
3713.4866600757934
3813.8811042129643
3914.1088624630053
4014.4920667953194
4115.0410359466301
4215.6748205731358
4315.9204271299485
4416.3908218441782
4517.8266993247784
4618.5741683916382
4718.7680628117252
4818.9832594757116
4919.5452875756097
5020.2885410306815
5120.6052819647626
5220.8636046741688
5321.3449239510999
5423.6397113048711
5523.9900922615064
5625.6854044157377
5727.0159606945415
5831.0573737150870
5931.7750944194458
6031.8555300413931
6132.0179864797182
6233.1860959278244
6333.6504516095465
6433.946598447509
6536.3055062500737
6637.2580674919272
6741.9563652262156
6842.3787672712521
6943.4183873064041
7043.7968622407546
7146.7511332021842
7249.2947627942733
7353.3274303249379
7457.3164566420601
7568.9222504554683
7684.905491216104
77112.476001114202
78124.894875240283
79143.902023138068
80161.794252558235
81175.511990556912
82202.793574212824
83361.942616892302
84922.954746322548
 
Charts produced by software:
http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Nov/12/t122651661441zvhk2re3jjm2x/1pd8g1226516288.png (open in new window)
http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Nov/12/t122651661441zvhk2re3jjm2x/1pd8g1226516288.ps (open in new window)


http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Nov/12/t122651661441zvhk2re3jjm2x/282fr1226516288.png (open in new window)
http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Nov/12/t122651661441zvhk2re3jjm2x/282fr1226516288.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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