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Various EDA Topics Q1 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 07:05:20 -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/t1226412519wvgbi7kyymdeksi.htm/, Retrieved Tue, 11 Nov 2008 14:08:42 +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/t1226412519wvgbi7kyymdeksi.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 «
1045,9 1593 0,8721 4,5 1401,9 1477,9 0,8552 4,7 1027,6 1733,7 0,8564 4,75 1703,8 1569,7 0,8973 4,75 1481,3 1843,7 0,9383 4,75 1422,7 1950,3 0,9217 4,75 1304,7 1657,5 0,9095 4,75 1246,1 1772,1 0,892 4,75 1417,8 1568,3 0,8742 4,58 1459,1 1809,8 0,8532 4,5 1156,4 1646,7 0,8607 4,5 1304,5 1808,5 0,9005 4,49 1336,9 1763,9 0,9111 4,03 1372,3 1625,5 0,9059 3,75 975,5 1538,8 0,8883 3,39 1180,8 1342,4 0,8924 3,25 1361,3 1645,1 0,8833 3,25 1428,1 1619,9 0,87 3,25 1355,9 1338,1 0,8758 3,25 1781,2 1505,5 0,8858 3,25 1697 1529,1 0,917 3,25 1852 1511,9 0,9554 3,25 1844,1 1656,7 0,9922 3,25 1967,2 1694,4 0,9778 3,25 1747,1 1662,3 0,9808 3,25 1863,9 1588,7 0,9811 3,25 1559,3 1483,3 1,0014 3,25 1675 1585,6 1,0183 2,85 2237,5 1658,9 1,0622 2,75 1965,2 1584,4 1,0773 2,75 1871,5 1470,6 1,0807 2,55 1752,2 1618,7 1,0848 2,5 1360,7 1407,6 1,1582 2,5 1444,3 1473,9 1,1663 2,1 1621,6 1515,3 1,1372 2 1368 1485,4 1,1139 2 1553,9 1496,1 1,1222 2 1695,3 1493,5 1,1692 2 1397,1 1298,4 1,1702 2 1848,4 1375,3 1,2286 2 1809,2 1507,9 1,2613 2 1551,1 1455,3 1,2646 2 1546,6 1363,3 1,2262 2 1467,9 1392,8 1,1985 2 1662,4 1348,8 1,2007 2 1972,3 1880,3 1,2138 2 1673,5 1669,2 1,2266 2 1762 1543,6 1,2176 2 2019,8 1701,2 1,2218 2 1754,3 1516,5 1,249 2 1400,4 1466,8 1,2991 2 1453,6 1484,1 1,3408 2 1740,9 1577,2 1,3119 2 1694,6 1684,5 1,3014 2 1541,2 1414,7 1,3201 2 1482,3 1674,5 1,2938 2 1632,1 1598,7 1,2694 2 1837,3 1739,1 1,2165 2 1797 1674,6 1,2037 2 2066,2 1671,8 1,2292 2 1983,8 1802 1,2256 2 1601,7 1526,8 1,2015 2 1660,3 1580,9 1,1786 2 1954 1634,8 1,1856 2,21 1991,9 1610,3 1,2103 2,25 1881,4 1712 1,1938 2,25 2345,5 1678,8 1,202 2,45 1773,1 1708,1 1,2271 2,5 1719,2 1680,6 1,277 2,5 2240,9 2056 1,265 2,64 1816,4 1624 1,2684 2,75 2171,3 2021,4 1,2811 2,93 1823,3 1861,1 1,2727 3 2022,5 1750,8 1,2611 3,17 1991 1767,5 1,2881 3,25 1920 1710,3 1,3213 3,39 2168,4 2151,5 1,2999 3,5 2013,5 2047,9 1,3074 3,5 1790,8 1915,4 1,3242 3,65 1855,7 1984,7 1,3516 3,75 2074 1896,5 1,3511 3,75 2535,8 2170,8 1,3419 3,9 1837,2 2139,9 1,3716 4 1805,1 2330,5 1,3622 4 1785,7 2121,8 1,3896 4 2250 2226,8 1,4227 4 1959,7 1857,9 1,4684 4 1890,8 2155,9 1,457 4 2405,7 2341,7 1,4718 4 2090,3 2290,2 1,4748 4 1666,5 2006,5 1,5527 4 1803,5 2111,9 1,575 4 1793,8 1731,3 1,5557 4 1488,8 1762,2 1,5553 4 1545 1863,2 1,577 4,18 1369,9 1943,5 1,4975 4,25 1451,6 1975,2 1,4369 4,25
 
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 time2 seconds
R Server'Gwilym Jenkins' @ 72.249.127.135


Summary of Dendrogram
LabelHeight
111.5302665715066
213.8047256492114
313.9490893122095
415.4573023548742
520.3687106405879
622.4813369433403
722.9839973566391
824.9122579337965
925.7795426871772
1028.1329610999269
1128.1726993019838
1231.1301779301051
1335.2655129871947
1435.6633720340631
1537.2017162104115
1637.9525281524171
1738.1541011038132
1838.6544416108937
1940.4736453767965
2040.5230766602193
2141.7896288599216
2242.8591447236175
2343.9037961456637
2444.2801220798038
2545.6776280041993
2646.9890916410238
2749.6872261702139
2852.1072816064509
2952.6347690945825
3054.9441003025444
3155.1283204202704
3255.937172731199
3357.2291811173283
3463.2863741436498
3565.1098233079864
3671.4650695334922
3772.3852109029949
3874.2762056862895
3977.7264714187514
4078.4672749382898
4181.0128424126517
4281.1992427051352
4381.9320977684893
4488.2825357086792
4588.8539946341188
4693.0987947436962
47101.374086111812
48101.516424424151
49102.374874530380
50109.818575587375
51110.527109081135
52111.035647788627
53111.929881576374
54113.676925133847
55115.17598346574
56116.605127210698
57127.386579903197
58133.368265814836
59140.499674937595
60141.250623625962
61151.984219489065
62155.430056676597
63158.567731298477
64183.656323558882
65194.423737141212
66195.64116579808
67198.229555432800
68214.78558348737
69216.422451432605
70219.872691930392
71224.984066614386
72231.533848275424
73234.834897626026
74244.847878445762
75288.098965940868
76311.344465810703
77315.582044341469
78348.600651502825
79389.174582784162
80403.83039589531
81454.295850036313
82507.332521393584
83560.698062638709
84614.207481351393
85755.120420562977
86806.897565964837
87938.311506821412
88977.52853169423
891011.51704364708
901046.74537339903
911618.62939014278
922296.92442092311
932593.30099827492
943564.94550253035
957035.60095892096
9612535.9084782997
 
Charts produced by software:
http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Nov/11/t1226412519wvgbi7kyymdeksi/1me481226412318.png (open in new window)
http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Nov/11/t1226412519wvgbi7kyymdeksi/1me481226412318.ps (open in new window)


http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Nov/11/t1226412519wvgbi7kyymdeksi/2m8kg1226412318.png (open in new window)
http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Nov/11/t1226412519wvgbi7kyymdeksi/2m8kg1226412318.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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