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dendrogram

*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: Sun, 21 Dec 2008 07:09:41 -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/Dec/21/t12298703186yahe6lr6tk0vh7.htm/, Retrieved Sun, 21 Dec 2008 15:38:40 +0100

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/Dec/21/t12298703186yahe6lr6tk0vh7.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},
}

Original text written by user:

IsPrivate?

No (this computation is public)

User-defined keywords:

Dataseries X:

» Textbox « » Textfile « » CSV «

524 552 532 511 492 492 493 481 462 457 442 439 488 521 501 485 464 460 467 460 448 443 436 431 484 510 513 503 471 471 476 475 470 461 455 456 517 525 523 519 509 512 519 517 510 509 501 507 569 580 578 565 547 555 562 561 555 544 537 543 594 611 613 611 594 595 591 589 584 573 567 569 621 629 628 612 595 597 593 590 580 574 573 573 620 626 620 588 566 557 561 549 532 526 511 499 555 565 542 527 510 514 517 508 493 490 469 478

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 Input	view raw input (R code)
Raw Output	view raw output of R engine
Computing time	1 seconds
R Server	'Gwilym Jenkins' @ 72.249.127.135

Summary of Dendrogram
Label	Height
1	0
2	0
3	0
4	0
5	0
6	0
7	0
8	0
9	0
10	0
11	0
12	0
13	0
14	0
15	0
16	0
17	0
18	0
19	0
20	0
21	0
22	0
23	0
24	0
25	0
26	1
27	1
28	1
29	1
30	1
31	1
32	1
33	1
34	1
35	1
36	1
37	1
38	1
39	1
40	1
41	1
42	1.33333333333333
43	1.33333333333333
44	1.33333333333333
45	1.5
46	1.66666666666667
47	1.66666666666667
48	1.66666666666667
49	1.66666666666667
50	2
51	2
52	2
53	2.4
54	2.5
55	2.5
56	2.5
57	2.5
58	2.5
59	2.66666666666667
60	2.66666666666667
61	2.66666666666667
62	2.66666666666667
63	3
64	3
65	3
66	3
67	3
68	3
69	3.33333333333333
70	4
71	4.33333333333333
72	4.66666666666667
73	6
74	6.33333333333333
75	6.54444444444445
76	6.66666666666667
77	6.66666666666667
78	7
79	7.33333333333333
80	7.5
81	7.66666666666667
82	9.5
83	10.8888888888889
84	14.3333333333333
85	14.6666666666667
86	17.4444444444444
87	17.6666666666667
88	18.2222222222222
89	18.6
90	19.3333333333333
91	23.75
92	25.3333333333333
93	33.5333333333333
94	33.6333333333333
95	38.2666666666667
96	45.5238095238095
97	46.8333333333333
98	68.4428104575163
99	100.311111111111
100	118.835164835165
101	173.551633986928
102	186.066666666667
103	211.7
104	218.152136752137
105	647.647990543735
106	1009.92604735883
107	3187.55929543076

Summary of Cut Dendrogram
Label	Height
1	5.16666666666663
2	6.66666666666663
3	7.25
4	7.33333333333326
5	9.33333333333331
6	9.33333333333337
7	9.58333333333331
8	13.3809523809523
9	14.2166666666667
10	14.3235294117647
11	17.3939393939394
12	17.8040935672514
13	36.5838779956427
14	37.0270175438597
15	45.0399230399231
16	54.6333333333334
17	145.130890464933
18	166.793054037644
19	616.103277719645

Charts produced by software:

http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Dec/21/t12298703186yahe6lr6tk0vh7/1nxin1229868579.png (open in new window)

http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Dec/21/t12298703186yahe6lr6tk0vh7/1nxin1229868579.ps (open in new window)

http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Dec/21/t12298703186yahe6lr6tk0vh7/2fuv21229868579.png (open in new window)

http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Dec/21/t12298703186yahe6lr6tk0vh7/2fuv21229868579.ps (open in new window)

Parameters (Session):

par1 = ward ; par2 = 20 ; par3 = FALSE ; par4 = FALSE ;

Parameters (R input):

par1 = ward ; par2 = 20 ; 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')

}

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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