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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, 13 Nov 2008 11:40:30 -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/t12266025318ion8p87dn5pxhr.htm/, Retrieved Thu, 13 Nov 2008 18:55:31 +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/t12266025318ion8p87dn5pxhr.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 «
493 116 377 481 111 370 462 104 358 457 100 357 442 93 349 439 91 348 488 119 369 521 139 381 501 134 368 485 124 361 464 113 351 460 109 351 467 109 358 460 106 354 448 101 347 443 98 345 436 93 343 431 91 340 484 122 362 510 139 370 513 140 373 503 132 371 471 117 354 471 114 357 476 113 363 475 110 364 470 107 363 461 103 358 455 98 357 456 98 357 517 137 380 525 148 378 523 147 376 519 139 380 509 130 379 512 128 384 519 127 392 517 123 394 510 118 392 509 114 396 501 108 392 507 111 396 569 151 419 580 159 421 578 158 420 565 148 418 547 138 410 555 137 418 562 136 426 561 133 428 555 126 430 544 120 424 537 114 423 543 116 427 594 153 441 611 162 449 613 161 452 611 149 462 594 139 455 595 135 461 591 130 461 589 127 463 584 122 462 573 117 456
 
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'Herman Ole Andreas Wold' @ 193.190.124.10:1001


Summary of Dendrogram
LabelHeight
11
21.41421356237310
32.23606797749979
42.44948974278318
52.44948974278318
63
73.04299673483065
83.3166247903554
93.60555127546399
103.74165738677394
113.74165738677394
123.74165738677394
134.12310562561766
144.12310562561766
154.19531255396809
164.24264068711928
174.24264068711928
184.35889894354067
194.89897948556636
205.09901951359278
215.09901951359278
226.16441400296898
236.16441400296898
246.16441400296898
256.16441400296898
267.28010988928052
278.09190611531691
288.36274151723244
299.47161567483146
309.89949493661167
3110.4783014776451
3210.5046359118436
3311.3578166916005
3413.0250284704506
3513.6055900115565
3614.3180005190900
3714.4328855830626
3815.1172612831014
3919.6176303718507
4021.0466606673232
4121.5079755769913
4222.1209977377159
4322.2118952886881
4422.3529657729801
4522.9261441364216
4623.4596208943976
4726.5044481470131
4827.0038179354249
4929.4437468163541
5029.9705444142465
5131.2023589484089
5246.6502786886399
5352.3844044297933
5457.9344083137191
5561.8961167183344
56114.544243689187
57115.612153596980
58124.720675213633
59127.255064005911
60238.692627276993
61354.178143335913
62820.802661979632
632273.2871274683
 
Charts produced by software:
http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Nov/13/t12266025318ion8p87dn5pxhr/14mcp1226601624.png (open in new window)
http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Nov/13/t12266025318ion8p87dn5pxhr/14mcp1226601624.ps (open in new window)


http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Nov/13/t12266025318ion8p87dn5pxhr/24eki1226601624.png (open in new window)
http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Nov/13/t12266025318ion8p87dn5pxhr/24eki1226601624.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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