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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: Tue, 11 Nov 2008 09:12:17 -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/11/t1226420069nj3mn0zrmpcllko.htm/, Retrieved Tue, 11 Nov 2008 16:14:30 +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/11/t1226420069nj3mn0zrmpcllko.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 «
2173 2752 572 582 2363 2373 582 552 2126 1415 574 436 1905 2466 461 602 2121 2318 576 640 1983 2346 460 551 1734 1644 455 421 2074 1421 444 382 2049 1423 488 382 2406 1930 513 427 2558 2694 468 542 2251 4938 488 708 2059 1727 536 465 2397 1899 486 474 1747 1364 460 371 1707 1992 376 463 2319 2051 503 515 1631 2082 369 509 1627 1746 353 380 1791 1271 359 313 2034 1363 400 313 1997 1664 374 359 2169 2179 430 427 2028 2305 433 415 2253 2098 418 402 2218 2231 438 388 1855 1407 389 353 2187 1966 368 464 1852 2293 386 429 1570 2045 261 398 1851 1532 294 291 1954 1333 263 272 1828 1583 293 241 2251 1712 303 288 2277 2641 326 365 2085 2267 314 312 2282 2126 332 325 2266 2231 347 346 1878 1517 290 282 2267 2010 340 362 2069 2628 371 369 1746 2115 340 340 2299 1829 376 308 2360 1636 322 294 2214 1787 364 306 2825 2122 379 328 2355 2620 343 351 2333 2555 358 366 3016 2337 433 350 2155 2524 344 356 2172 1801 357 295 2150 2417 385 359 2533 2389 392 380 2058 2267 308 360 2160 2135 294 336 2259 1760 300 299 2498 1905 302 262 2695 2176 400 299 2799 2344 392 313 2945 2673 373 357 2930 2766 379 356 2318 2785 303 368 2540 2003 324 284 2570 2588 353 338 2669 2739 392 352 2450 2703 327 342 2842 2464 376 315 3439 1974 329 277 2677 2164 359 317 2979 2385 413 291 2257 2936 338 326 2842 2700 421 353 2546 2855 390 371 2455 2764 370 356 2293 1808 366 274 2379 2588 405 352 2478 2600 418 347 2054 2526 346 345 2272 2259 349 336 2351 1738 326 276 2271 1902 318 312 2542 2137 379 330 2304 2460 336 325 2194 2495 372 328 2722 2525 420 332 2395 2465 425 341 2146 1828 422 316 1894 2273 396 377 2548 2377 457 380 2087 2344 313 373 2063 2071 334 346 2481 1611 384 272 2476 1671 342 283 2212 2256 385 302 2834 1983 435 301 2148 1921 405 303 2598 2027 454 320
 
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
130.3973683071413
232.4191301548947
341.6293165929973
446.1519230368573
549.7292670366254
649.9799959983992
750.6458290484024
855.3985559378582
962.6897120746299
1063.08724118235
1167.7790528113222
1270.4840407468244
1371.8261790714221
1474.2293742395825
1575.184724644052
1676.0986202240225
1781.7924201867141
1886.913750350563
1994.3980932010811
2095.4515583948214
2197.2308587241395
22100.850001501952
23102.674110511567
24104.043260233424
25108.765803449430
26111.067547015319
27113.639781766774
28119.363501590225
29121.095004025765
30122.270192606375
31123.308556069723
32124.968066493446
33126.653069445632
34128.386136323203
35128.487353463288
36128.902948993368
37137.397234324422
38140.301389399715
39144.779142144164
40151.429851746609
41152.535241829552
42160.886901063743
43163.405753937546
44170.146995271736
45171.787659626645
46174.573654396415
47180.599566325888
48184.222691327643
49185.321868328806
50203.161633296266
51209.171689618688
52210.127384181347
53212.222375235778
54212.821521468107
55219.652223727361
56227.187663726935
57235.572929253534
58239.496256243073
59242.469361391211
60251.620091586140
61257.488796002958
62258.362205450719
63263.379953679091
64266.538896689265
65275.527313926972
66328.818726995389
67343.995228451656
68344.214835353125
69390.811205663008
70400.785725534446
71456.004818755424
72460.090701392321
73463.874198909259
74505.222440962843
75539.102939441339
76564.126410825905
77615.769316128549
78627.68445157788
79713.90438738075
80762.221259548995
81789.159816363466
82814.109603036147
83891.596814623578
84901.324329387116
85953.609707005061
861012.12756920841
871049.18845133695
881213.17718744536
892239.5031153197
902574.80538434628
912746.79247330567
924164.06032441671
935218.79829262991
945670.35141122717
958058.11811292189
9616076.4706102691
 
Charts produced by software:
http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Nov/11/t1226420069nj3mn0zrmpcllko/19g4s1226419931.png (open in new window)
http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Nov/11/t1226420069nj3mn0zrmpcllko/19g4s1226419931.ps (open in new window)


http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Nov/11/t1226420069nj3mn0zrmpcllko/2rl9a1226419931.png (open in new window)
http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Nov/11/t1226420069nj3mn0zrmpcllko/2rl9a1226419931.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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