Principal coordinates Analysis for a matrix of proximities obtained from binary, categorical, continuous or mixed data
PrincipalCoordinates(Proximities, w = NULL, dimension = 2,
method = "eigen", tolerance = 1e-04, Bootstrap = FALSE,
BootstrapType = c("Distances", "Products"), nB = 200,
ProcrustesRot = TRUE, BootstrapMethod = c("Sampling", "Permutation"))An object of class Principal.Coordinates. The function adds the information of the Principal Coordinates to the object of class proximities. Together with the information about the proximities the object has:
The type of analysis performed, "Principal Coordinates" in this case
The eigenvalues of the PCoA
The Inertia of the PCoA
Coordinates for the objects in the PCoA
Qualities of representation for the objects in the PCoA
Raw Stress values
stress formula 1
stress formula 2
sstress formula 1
sstress formula 2
Squared correlation between disparities and distances
Spearman correlation between disparities and distances
Kendall correlation between disparities and distances
The result of the bootstrap calculations
An object of class proximities.
An set of weights.
Dimension of the solution
Method to calculate the eigenvalues and eigenvectors. The default is the usual eigen function although the Power Method to calculate only tre first eigenvectors can be used.
Tolerance for the eigenvalues
Should Bootstrap be calculated?
Bootstrap on the residuals of the "distance" or "scalar products" matrix.
Number of Bootstrap replications
Should each replication be rotated to match the initial solution?
The replications are obtained "Sampling" or "Permutating" the residuals.
Jose Luis Vicente-Villardon
Principal Coordinates Analysis for a proximity matrix previously calculated from a matrix of raw data or directly obsrved proximities.
Gower, J. C. (2006) Similarity dissimilarity and Distance, measures of. Encyclopedia of Statistical Sciences. 2nd. ed. Volume 12. Wiley
Gower, J.C. (1966). Some distance properties of latent root and vector methods used in multivariate analysis. Biometrika 53: 325-338.
J.R. Demey, J.L. Vicente-Villardon, M.P. Galindo, A.Y. Zambrano, Identifying molecular markers associated with classifications of genotypes by external logistic biplot, Bioinformatics 24 (2008) 2832.
BinaryProximities, BootstrapDistance, BootstrapDistance, BinaryProximities
data(spiders)
Dis=BinaryProximities(spiders)
pco=PrincipalCoordinates(Dis)
Dis=BinaryProximities(spiders)
pco=PrincipalCoordinates(Dis, Bootstrap=TRUE)
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