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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 10:54:36 -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/t1226598964ur2lnnapc1mwwws.htm/, Retrieved Thu, 13 Nov 2008 17:56:04 +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/t1226598964ur2lnnapc1mwwws.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 «
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 98 357 517 137 380 525 148 378 523 147 376 519 139 380 509 130 379 512 128 384 519 127 392 517 123 394 510 118 392 509 114 396 501 108 392 507 111 396 569 151 419 580 159 421 578 158 420 565 148 418 547 138 410 555 137 418 562 136 426 561 133 428 555 126 430 544 120 424 537 114 423 543 116 427 594 153 441 611 162 449 613 161 452 611 149 462 594 139 455 595 135 461 591 130 461 589 127 463 584 122 462 573 117 456 567 112 455 569 113 456 621 149 472 629 157 472 628 157 471 612 147 465 595 137 459 597 132 465 593 125 468 590 123 467 580 117 463 574 114 460 573 111 462 573 112 461 620 144 476 626 150 476 620 149 471 588 134 453 566 123 443 557 116 442 561 117 444 549 111 438 532 105 427 526 102 424 511 95 416 499 93 406 555 124 431 565 130 434 542 124 418 527 115 412 510 106 404 514 105 409 517 105 412 508 101 406 493 95 398 490 93 397 469 84 385 478 87 390 528 116 413 534 120 413 518 117 401 506 109 397
 
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
31.41421356237310
41.41421356237310
51.41421356237310
61.73205080756888
72.23606797749979
82.23606797749979
92.44948974278318
102.44948974278318
112.44948974278318
122.44948974278318
132.82842712474619
143
153.04299673483065
163.3166247903554
173.65602689891371
183.74165738677394
193.74165738677394
203.74165738677394
213.74165738677394
223.74165738677394
233.74165738677394
244.12310562561766
254.12310562561766
264.19531255396809
274.24264068711928
284.24264068711928
294.24264068711928
304.35889894354067
314.58257569495584
324.89897948556636
335.09901951359278
345.09901951359278
355.53125745811468
365.74456264653803
376.16441400296898
386.16441400296898
396.16441400296898
406.16441400296898
416.48074069840786
426.96564801457551
437.34846922834953
448.09190611531691
458.20407816807507
468.48528137423857
479.00353107304067
489.47161567483146
499.89949493661167
5010.0035541233253
5110.0436084811547
5210.4783014776451
5310.7009376651595
5410.7238052947636
5510.9198183276202
5611.352162112529
5711.3578166916005
5811.7688290727508
5911.9339157331054
6012.2642459334231
6112.3828431695042
6213.2567139436797
6313.5432442106297
6414.0367549301043
6514.3180005190900
6614.4328855830626
6714.7017043493017
6815.1172612831014
6916.6511101865354
7019.1887274389745
7119.6176303718507
7221.0466606673232
7321.5136604490006
7422.1209977377159
7522.3529657729801
7622.9261441364216
7724.4873530190255
7825.3853212333016
7926.5044481470131
8026.6336278201362
8127.0038179354249
8228.2189872358057
8336.5424602768386
8437.2045360954518
8539.0686494559738
8639.5824941977336
8740.7455027169033
8841.9742545325414
8948.030064668399
9053.5915919270773
9157.9344083137191
9270.4703066696427
9374.7229657882031
9487.5786186610769
95114.544243689187
96133.288365382396
97137.743542236795
98144.620610233962
99217.481031826518
100238.692627276993
101349.535292878498
102386.419423258650
103858.378118614952
1041734.59640264382
1053010.53634079378
 
Charts produced by software:
http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Nov/13/t1226598964ur2lnnapc1mwwws/1z1cy1226598870.png (open in new window)
http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Nov/13/t1226598964ur2lnnapc1mwwws/1z1cy1226598870.ps (open in new window)


http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Nov/13/t1226598964ur2lnnapc1mwwws/2gwnj1226598870.png (open in new window)
http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Nov/13/t1226598964ur2lnnapc1mwwws/2gwnj1226598870.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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