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various EDA Q2 Yannick van schil

*Unverified author*

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 10:01:47 -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/t12265957525atmpa7p4zy0e8k.htm/, Retrieved Thu, 13 Nov 2008 17:02:35 +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/t12265957525atmpa7p4zy0e8k.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 «

110.40 109.20 99.90 72.50 96.40 88.60 99.80 59.40 101.90 94.30 99.80 85.70 106.20 98.30 100.30 88.20 81.00 86.40 99.90 62.80 94.70 80.60 99.90 87.00 101.00 104.10 100.00 79.20 109.40 108.20 100.10 112.00 102.30 93.40 100.10 79.20 90.70 71.90 100.20 132.10 96.20 94.10 100.30 40.10 96.10 94.90 100.60 69.00 106.00 96.40 100.00 59.40 103.10 91.10 100.10 73.80 102.00 84.40 100.20 57.40 104.70 86.40 100.00 81.10 86.00 88.00 100.10 46.60 92.10 75.10 100.10 41.40 106.90 109.70 100.10 71.20 112.60 103.00 100.50 67.90 101.70 82.10 100.50 72.00 92.00 68.00 100.50 145.50 97.40 96.40 96.30 39.70 97.00 94.30 96.30 51.90 105.40 90.00 96.80 73.70 102.70 88.00 96.80 70.90 98.10 76.10 96.90 60.80 104.50 82.50 96.80 61.00 87.40 81.40 96.80 54.50 89.90 66.50 96.80 39.10 109.80 97.20 96.80 66.60 111.70 94.10 97.00 58.50 98.60 80.70 97.00 59.80 96.90 70.50 97.00 80.90 95.10 87.80 96.80 37.30 97.00 89.50 96.90 44.60 112.70 99.60 97.20 48.70 102.90 84.20 97.30 54.00 97.40 75.10 97.30 49.50 111.40 92.00 97.20 61.60 87.40 80.80 97.30 35.00 96.80 73.10 97.30 35.70 114.10 99.80 97.30 51.30 110.30 90.00 97.30 49.00 103.90 83.10 97.30 41.50 101.60 72.40 97.30 72.50 94.60 78.80 98.10 42.10 95.90 87.30 96.80 44.10 104.70 91.00 96.80 45.10 102.80 80.10 96.80 50.30 98.10 73.60 96.80 40.90 113.90 86.40 96.80 47.20 80.90 74.50 96.80 36.90 95.70 71.20 96.80 40.90 113.20 92.40 96.80 38.30 105.90 81.50 96.80 46.30 108.80 85.30 96.80 28.40 102.30 69.90 96.80 78.40 99.00 84.20 96.90 36.80 100.70 90.70 97.10 50.70 115.50 100.30 97.10 42.80 135 125 149 170 170 158 133 114 140 145 150 178 163 172 178 199 199 184 162 146 166 171 180 193 181 183 218 230 242 209 191 172 194 196 196 236 235 229 243 264 272 237 211 180 201 204 188 235 227 234 264 302 293 259 229 203 229 242 233 267 269 270 315 364 347 312 274 237 278 284 277 317 313 318 374 413 405 355 306 271 306 315 301 356 348 355 422 465 467 404 347 305 336 340 318 362 348 363 435 491 505 404 359 310 337 360 342 406 396 420 472 548 559 463 407 362 405 417 391 419 461 472 535 622 606 508 461 390 432

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	2 seconds
R Server	'George Udny Yule' @ 72.249.76.132

Summary of Dendrogram
Label	Height
1	0.984885780179617
2	1.51657508881032
3	2.51197133741609
4	2.9086079144498
5	2.94618397253124
6	2.96141857899216
7	3.39411254969542
8	3.43074335968169
9	3.76164857476080
10	3.772267222772
11	3.92683078321437
12	4.08411557133243
13	4.17133072292284
14	4.45196585791041
15	4.56289381861994
16	4.73497624070069
17	4.78434948556228
18	4.85180378828328
19	4.94267134250296
20	5.00199960015992
21	5.11985360729854
22	5.25071423713004
23	5.33197899470731
24	5.36003731330296
25	5.4230987451825
26	5.86770824087224
27	5.98414572015086
28	6.04069532421558
29	6.08687111741328
30	6.08769250208976
31	6.25065996541364
32	6.40234332100365
33	6.48999229583518
34	6.52548865032021
35	6.74907401055878
36	6.85598684882411
37	7.07106781186548
38	7.24844810976806
39	7.31862934082526
40	7.35798885565886
41	7.54055700860354
42	7.56960620527561
43	7.64068059795723
44	7.82370024247937
45	7.9031639233917
46	8.14243881330763
47	8.29638475481942
48	8.56051278084377
49	8.83232698670062
50	8.85934844935958
51	9.14632994752397
52	9.21954445729289
53	9.26282894152753
54	9.32152916309868
55	9.48720883650591
56	9.65038859321219
57	9.7906642531135
58	9.80116422703554
59	10.0717426496113
60	10.2717397717901
61	10.3662915259026
62	10.6977783089397
63	10.9004587059444
64	10.9175633333175
65	10.9475302735850
66	11.1749887841323
67	11.9998557297210
68	12.4550566032831
69	12.7365437294496
70	12.8814001172322
71	13.1753978982080
72	13.3416640641263
73	13.5042881778377
74	13.5843397662809
75	13.7105442514842
76	14.0196290963777
77	14.2228689089086
78	14.4740197839994
79	14.6004513882873
80	14.7528628152703
81	14.7624888662622
82	15.1019866242823
83	15.2801814647016
84	15.3896454665556
85	15.5241746962600
86	15.6637791142937
87	15.7329885315009
88	15.9843268216369
89	16.2638446536299
90	16.4012194668567
91	16.7357873183021
92	17.9057134540054
93	19.1451676950719
94	19.7149003674515
95	19.9749843554382
96	20.6909168174239
97	21.3201783624796
98	22.1359436211787
99	22.6497280015666
100	22.8315762376692
101	23.4330811510197
102	23.9161328160879
103	24.1012522657793
104	25.2909898511548
105	26.6779054441941
106	27.1661554144122
107	27.7542232927572
108	30.1496268633627
109	30.4027879379277
110	31.0644491340181
111	31.1600667086278
112	31.6543835826888
113	32.4786719273815
114	33.0970428319562
115	33.4050629295510
116	33.5065226775146
117	33.6154726279432
118	33.734255586866
119	38.2616088179198
120	40.1621712560464
121	40.4563433677724
122	41.8360593901745
123	42.2863700223221
124	42.3083916026124
125	42.9484552536474
126	42.9997724529726
127	43.0379231790051
128	43.4200153140677
129	43.7492857084547
130	43.9733326835754
131	45.0555060849483
132	45.5112366211433
133	47.5815090134813
134	47.8647852269159
135	48.7749935930288
136	51.6494546509497
137	51.720402163943
138	52.3999530900087
139	55.3263047744922
140	57.1486548087513
141	57.2684936628814
142	58.7622327690158
143	64.4971223320583
144	64.8780776060888
145	69.8280410170927
146	73.3397304190025
147	79.1075217662644
148	79.7084079161374
149	81.1976333884486
150	84.4705196604339
151	84.8357954178091
152	85.1679100131984
153	85.5859536406968
154	96.3661047576742
155	101.044832444436
156	103.678403646185
157	104.840902584218
158	105.315763872571
159	105.434617403245
160	109.623790559329
161	127.098967718465
162	135.744608610011
163	145.12435511728
164	146.287404030175
165	148.416484447378
166	150.575770048106
167	155.008957058639
168	155.041960402745
169	172.263995693086
170	181.541047768840
171	181.626816924787
172	233.033982134435
173	237.599172577599
174	252.043858034607
175	303.899423253562
176	321.434626996701
177	324.466469762285
178	379.332308413272
179	395.181506512553
180	543.444927165786
181	565.373345402758
182	597.650021877275
183	603.453886235506
184	933.150426088258
185	1168.88433589466
186	2241.31063402949
187	2429.60611121347
188	6652.00085273747
189	22918.1768561001

Charts produced by software:

http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Nov/13/t12265957525atmpa7p4zy0e8k/1kkxv1226595704.png (open in new window)

http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Nov/13/t12265957525atmpa7p4zy0e8k/1kkxv1226595704.ps (open in new window)

http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Nov/13/t12265957525atmpa7p4zy0e8k/2v7lz1226595704.png (open in new window)

http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Nov/13/t12265957525atmpa7p4zy0e8k/2v7lz1226595704.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')

}

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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