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Hierarchical Clustering- Q2

*Unverified author*
R Software Module: rwasp_hierarchicalclustering.wasp (opens new window with default values)
Title produced by software: Hierarchical Clustering
Date of computation: Thu, 13 Nov 2008 14:34:21 -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/13/t1226612147coc9ses9zxg8vl2.htm/, Retrieved Thu, 13 Nov 2008 21:35:47 +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/13/t1226612147coc9ses9zxg8vl2.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)
 
Feedback Forum:

Post a new message
 
Original text written by user:
 
IsPrivate?
No (this computation is public)
 
User-defined keywords:
 
Dataseries X:
» Textbox « » Textfile « » CSV «
8 -7 -6 -10 -13 -17 -24 -11 -44 -19 -9 -36 8 8 4 24 24 29 14 4 8 7 7 3 9 16 8 -26 -30 -49 19 26 32 15 19 25 -1 2 -1 -10 -12 -20 -21 -29 -34 -14 -24 -31 -27 -16 -12 26 25 25 23 22 25 5 -7 7 19 17 13 -19 -29 -40 24 18 32 17 15 14 1 1 -5 -9 6 -14 -16 -21 -42 -21 -23 -24 -14 -15 -11 31 24 20 27 15 7 10 15 12 12 14 4 -23 -25 -37 13 14 19 26 21 16 -1 13 2 4 4 -9 -16 -16 -36 -5 13 -29 9 20 3 23 27 33 9 -8 9 2 13 13 10 12 3 -29 -25 -47 17 20 18 9 22 7 9 16 16 -10 -12 -12 -23 -13 -23 13 7 -18 13 12 11 -9 -8 -4 9 12 17 5 -13 -4 8 12 -1 -18 -25 -41 7 0 26 4 18 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 time2 seconds
R Server'Sir Ronald Aylmer Fisher' @ 193.190.124.24


Summary of Dendrogram
LabelHeight
11.73205080756888
23
33
43.16227766016838
54.12310562561766
64.24264068711928
74.24264068711928
84.24264068711928
94.24264068711928
104.47213595499958
114.58257569495584
124.58257569495584
134.69588736423469
145.09901951359278
155.3851648071345
165.48172765326135
175.76046855827592
186.16441400296898
196.4535599249993
207
217.07106781186548
227.13262084327031
237.34846922834953
247.49081315919221
257.61577310586391
268.78887653890689
279.9498743710662
2810.2312416249102
2910.8468451912246
3011.3083336271833
3111.4017542509914
3211.9112311450360
3312.0830459735946
3412.1367207232760
3513.1038723559249
3613.4498297869780
3713.6651476105399
3813.7194335193147
3915.7578353437117
4016.3170691166258
4117.0293863659264
4217.3389407039620
4321.9234741874105
4422.0141990079642
4522.3966541889198
4623.8278459936162
4726.0093030634111
4828.8107034727402
4930.3119990427042
5032.9367756335492
5138.2704933646133
5241.2117988278412
5356.8306799024852
5457.9446486426321
5569.7680669850267
5677.0245219960672
57166.680399988993
58328.024290680700
59941.16651422093
 
Charts produced by software:
http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Nov/13/t1226612147coc9ses9zxg8vl2/1plyk1226612056.png (open in new window)
http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Nov/13/t1226612147coc9ses9zxg8vl2/1plyk1226612056.ps (open in new window)


http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Nov/13/t1226612147coc9ses9zxg8vl2/2kmlt1226612056.png (open in new window)
http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Nov/13/t1226612147coc9ses9zxg8vl2/2kmlt1226612056.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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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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