PVR (version 0.3)

PSR-class: Class "PSR"

Description

A S4 class that extends S4 PVR class in order to accommodate PSR analysis results.

Objects from the Class

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

Slots

PSRarea:

Object of class "data.frame" that contains PSR curve area.

PSR:

Object of class "data.frame" that contais accumulated r squared and eigenvalues.

Expect.area.values:

Object of class "list" that contains the expected null and neutral area values.

nullPSR:

Object of class "matrix" nested in the Expect.area.values slot that contains the expected null area values.

BrownianPSR:

Object of class "matrix" nested in the Expect.area.values slot that contains the expected Brownian (neutral) area values.

Eigen:

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

phyDist:

Object of class "matrix" that contains a phylogenetic distance matrix. Inherited from PVR class.

phylo:

Object of class "phylo" that contains a phylogeny. Inherited from PVR class.

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. Inherited from PVR class.

PVR:

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

VarPart:

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

Extends

Class "'>PVR", directly.

Methods

plot

signature(x = "PSR"): ...

show

signature(object = "PSR"): ...

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

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

Examples

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