pco | R Documentation |
pco
is a program for Principal Coordinate Analysis.
pco(Dis)
Dis |
A distance or dissimilarity matrix |
The program pco
does a principal coordinates analysis of a
dissimilarity (or distance) matrix (Dij) where the diagonal elements,
Dii, are zero.
Note that when we dispose of a similarity matrix rather that a distance matrix, a transformation is needed before calling coorprincipal. For instance, if Sij is a similarity matrix, Dij might be obtained as Dij = 1 - Sij/diag(Sij)
Goodness of fit calculations need to be revised such as to deal (in different ways) with negative eigenvalues.
PC |
the principal coordinates |
Dl |
all eigenvalues of the solution |
Dk |
the positive eigenvalues of the solution |
B |
double centred matrix for the eigenvalue decomposition |
decom |
the goodness of fit table |
Jan Graffelman (jan.graffelman@upc.edu)
cmdscale
citynames <- c("Aberystwyth","Brighton","Carlisle","Dover","Exeter","Glasgow","Hull", "Inverness","Leeds","London","Newcastle", "Norwich") A <-matrix(c( 0,244,218,284,197,312,215,469,166,212,253,270, 244,0,350,77,167,444,221,583,242,53,325,168, 218,350,0,369,347,94,150,251,116,298,57,284, 284,77,369,0,242,463,236,598,257,72,340,164, 197,167,347,242,0,441,279,598,269,170,359,277, 312,444,94,463,441,0,245,169,210,392,143,378, 215,221,150,236,279,245,0,380,55,168,117,143, 469,583,251,598,598,169,380,0,349,531,264,514, 166,242,116,257,269,210,55,349,0,190,91,173, 212,53,298,72,170,392,168,531,190,0,273,111, 253,325,57,340,359,143,117,264,91,273,0,256, 270,168,284,164,277,378,143,514,173,111,256,0),ncol=12) rownames(A) <- citynames colnames(A) <- citynames out <- pco(A) plot(out$PC[,2],-out$PC[,1],pch=19,asp=1) textxy(out$PC[,2],-out$PC[,1],rownames(A))
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