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Various EDA topics Q2

*Unverified author*
R Software Module: rwasp_hierarchicalclustering.wasp (opens new window with default values)
Title produced by software: Hierarchical Clustering
Date of computation: Sun, 09 Nov 2008 09:10:03 -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/09/t1226247056opsdqs1ixgbbgsb.htm/, Retrieved Sun, 09 Nov 2008 16:10:56 +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/09/t1226247056opsdqs1ixgbbgsb.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:
Van Dooren Leen
 
Dataseries X:
» Textbox « » Textfile « » CSV «
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'Sir Ronald Aylmer Fisher' @ 193.190.124.24


Summary of Dendrogram
LabelHeight
11.41421356237310
21.41421356237310
31.41421356237310
41.73205080756888
52.23606797749979
62.44948974278318
72.44948974278318
82.44948974278318
92.82842712474619
103.65602689891371
113.74165738677394
123.74165738677394
133.74165738677394
143.74165738677394
153.74165738677394
164.12310562561766
174.24264068711928
184.58257569495584
194.89897948556636
205.09901951359278
215.09901951359278
225.53125745811468
235.74456264653803
246.48074069840786
256.96564801457551
267.34846922834953
278.20407816807507
288.48528137423857
299.00353107304067
309.47161567483146
3110.0035541233253
3210.0436084811547
3310.7009376651595
3410.7238052947636
3510.9198183276202
3611.352162112529
3711.3578166916005
3811.7688290727508
3911.9339157331054
4012.2642459334231
4112.3828431695042
4213.2567139436797
4313.5432442106297
4414.0367549301043
4514.7017043493017
4616.6511101865354
4719.1887274389745
4821.5136604490006
4924.4873530190255
5025.3853212333016
5126.5044481470131
5228.2189872358057
5336.5424602768386
5437.2045360954518
5539.0686494559738
5639.5824941977336
5740.7455027169033
5841.9742545325414
5948.030064668399
6070.4703066696427
6174.7229657882031
6287.5786186610769
63133.288365382396
64137.743542236795
65144.620610233962
66217.481031826518
67386.419423258650
68717.95618427546
691667.04090043997
 
Charts produced by software:
http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Nov/09/t1226247056opsdqs1ixgbbgsb/1960j1226246998.png (open in new window)
http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Nov/09/t1226247056opsdqs1ixgbbgsb/1960j1226246998.ps (open in new window)


http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Nov/09/t1226247056opsdqs1ixgbbgsb/21s351226246998.png (open in new window)
http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Nov/09/t1226247056opsdqs1ixgbbgsb/21s351226246998.ps (open in new window)


 
Parameters (Session):
par1 = 50 ; par2 = 50 ; par3 = 0 ; par4 = 0 ; par5 = 0 ; par6 = Y ; par7 = Y ;
 
Parameters (R input):
par1 = ward ; par2 = ALL ; par3 = FALSE ; par4 = FALSE ; par5 = 0 ; par6 = Y ; par7 = Y ;
 
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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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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