PrincipalCoordinates: Principal Coordinates Analysis

In MultBiplotR: Multivariate Analysis Using Biplots in R

Principal Coordinates Analysis

Description

Principal coordinates Analysis for a matrix of proximities obtained from binary, categorical, continuous or mixed data

Usage

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"))

Arguments

Proximities	An object of class proximities.
w	An set of weights.
dimension	Dimension of the solution
method	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	Tolerance for the eigenvalues
Bootstrap	Should Bootstrap be calculated?
BootstrapType	Bootstrap on the residuals of the "distance" or "scalar products" matrix.
nB	Number of Bootstrap replications
ProcrustesRot	Should each replication be rotated to match the initial solution?
BootstrapMethod	The replications are obtained "Sampling" or "Permutating" the residuals.

Details

Principal Coordinates Analysis for a proximity matrix previously calculated from a matrix of raw data or directly obsrved proximities.

Value

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:

Analysis	The type of analysis performed, "Principal Coordinates" in this case
Eigenvalues	The eigenvalues of the PCoA
Inertia	The Inertia of the PCoA
RowCoordinates	Coordinates for the objects in the PCoA
RowQualities	Qualities of representation for the objects in the PCoA
RawStress	Raw Stress values
stress1	stress formula 1
stress2	stress formula 2
sstress1	sstress formula 1
sstress2	sstress formula 2
rsq	Squared correlation between disparities and distances
Spearman	Spearman correlation between disparities and distances
Kendall	Kendall correlation between disparities and distances
BootstrapInfo	The result of the bootstrap calculations

Author(s)

Jose Luis Vicente-Villardon

References

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.

See Also

BinaryProximities, BootstrapDistance, BootstrapDistance, BinaryProximities

Examples

data(spiders)
Dis=BinaryProximities(spiders)
pco=PrincipalCoordinates(Dis)
Dis=BinaryProximities(spiders)
pco=PrincipalCoordinates(Dis, Bootstrap=TRUE)

MultBiplotR documentation built on Nov. 21, 2023, 5:08 p.m.