PVR (version 0.3)

PVR-class: Class "PVR"

Description

A S4 class that contains eigenvalues and eigenvectors from decomposition of a phylogenetic distance matrix and PVR r squared and residuals.

Objects from the Class

Objects can be created by calls of the form new("PVR", ...).

Slots

Eigen:

Object of class "list" that contains the eigenvalues and eigenvectors generated by phylogenetic distance matrix eigendecomposition.

phyDist:

Object of class "matrix" that contains a phylogenetic distance matrix.

phylo:

Object of class "phylo" that contains a phylogeny.

Selection:

Object of class "list" that contains the selection method (along with its statistics) used to select the vectors, the selected vectors IDs and a matrix that contains the selected vectors.

PVR:

Object of class "list" that contains the Philogenetic EigenVectors Regression r squared and residuals.

VarPart:

Object of class "list" that contains the variation partition components.

Methods

show

signature(object = "PVR"): Always print the Eigen slot.

References

Diniz-Filho, J.A.F., Sant'Ana, C.E.R. and Bini, L.M. (1998). An eigenvector method for estimating phylogenetic inertia. Evolution 52:1247-1262.

Legendre, P. and Legendre, L. (1998). Numerical ecology, 2nd Englished. Elsevier.

Diniz-filho, J.A.F., Rangel, T.F., Santos, T. and Bini, L.M. (2012). Exploring patterns of interespecific variation in quantitative traits using sequential phylogenetic eigenvector regressions. Evolution, 66(4):1079-1090.

Diniz-filho, J.A.F., Bini, L.M., Rangel, T.F., Morales-Castilla, I., Olalla-Tarraga, M.A., Rodriguez, M.A. and Hawkins, B.A. (2012). On the selection of phylogenetic eigenvectors for ecological analyses. Ecography, 35:239-249.

See Also

PSR-class, PVR, PSR, PVRdecomp, PSRplot, VarPartplot

Examples

# NOT RUN {
showClass("PVR")
# }