[R] Help: Mahalanobis distances between 'Species' from iris
Jose Claudio Faria
joseclaudio.faria at terra.com.br
Wed Jul 6 23:28:37 CEST 2005
Dear R list,
I'm trying to calculate Mahalanobis distances for 'Species' of 'iris' data
as obtained below:
Squared Distance to Species From Species:
Setosa Versicolor Virginica
Setosa 0 89.86419 179.38471
Versicolor 89.86419 0 17.20107
Virginica 179.38471 17.20107 0
This distances above were obtained with proc 'CANDISC' of SAS, please,
see Output 21.1.2: Iris Data: Squared Mahalanobis Distances from
http://www.id.unizh.ch/software/unix/statmath/sas/sasdoc/stat/chap21/sect19.htm
From this distance my intention is to make a cluster analysis as below, using
the package 'mclust':
#
# --- Begin R script ---
#
# For units compatibility of 'iris' from R dataset and 'iris' data used in
# the SAS example:
Measures = iris[,1:4]*10
Species = iris[,5]
irisSAS = data.frame(Measures, Species)
n = 3
Mah = c( 0,
89.86419, 0,
179.38471, 17.20107, 0)
# My Question is: how to obtain 'Mah' with R from 'irisSAS' data?
D = matrix(0, n, n)
nam = c('Set', 'Ver', 'Vir')
rownames(D) = nam
colnames(D) = nam
k = 0
for (i in 1:n) {
for (j in 1:i) {
k = k+1
D[i,j] = Mah[k]
D[j,i] = Mah[k]
}
}
D=sqrt(D) #D2 -> D
library(mclust)
dendroS = hclust(as.dist(D), method='single')
dendroC = hclust(as.dist(D), method='complete')
win.graph(w = 3.5, h = 6)
split.screen(c(2, 1))
screen(1)
plot(dendroS, main='Single', sub='', xlab='', ylab='', col='blue')
screen(2)
plot(dendroC, main='Complete', sub='', xlab='', col='red')
#
# --- End R script ---
#
I always need of this type of analysis and I'm not founding how to make it in
the CRAN documentation (Archives, packages: mclust, cluster, fpc and mva).
Regards,
--
Jose Claudio Faria
Brasil/Bahia/UESC/DCET
Estatistica Experimental/Prof. Adjunto
mails:
joseclaudio.faria at terra.com.br
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