PSR-class: Class '"PSR"'

In PVR: Phylogenetic Eigenvectors Regression and Phylogentic Signal-Representation Curve

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"): ...

Author(s)

Santos, T; Diniz-Filho, J.A.F.; Rangel, T.F.; Bini, L.M.

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

showClass("PSR")

Example output

Loading required package: ape
Loading required package: splancs
Loading required package: sp

Spatial Point Pattern Analysis Code in S-Plus
 
 Version 2 - Spatial and Space-Time analysis


Attaching package: 'splancs'

The following object is masked from 'package:ape':

    zoom

PVR 0.2.1 loaded

Class "PSR" [package "PVR"]

Slots:
                                                               
Name:             PSRarea                PSR Expect.area.values
Class:         data.frame         data.frame               list
                                                               
Name:             nullPSR        BrownianPSR              Eigen
Class:             matrix             matrix               list
                                                               
Name:             phyDist              phylo          Selection
Class:             matrix              phylo               list
                                            
Name:                 PVR            VarPart
Class:               list               list

Extends: "PVR"

PVR documentation built on May 2, 2019, 3:23 a.m.