PVR-package: Computes *P*hylogenetic eigen*V*ectors *R*egression and...

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

Description

Computes PVR and PSR curve along with some plot utilitties.

Details

Package:	PVR
Type:	Package
Version:	1.0
Date:	2018-05-29
License:	GPL >= 2

Author(s)

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

Maintainer: Thiago Santos <[e-mail]>

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.

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

Examples

library(splancs)
#Creating a 10 tips ultrametric random phylogeny
library(ape)
tree <- rcoal(10)
#Decomposing phylogenetic distance matrix derived from tree into a set of orthogonal vectors
x <- PVRdecomp(tree)
trait <- runif(10)
y <- PSR(x, trait)
y

Example output

PVR 0.3 loaded

Loading required package: sp

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


Attaching package: 'ape'

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

    zoom


Phylogenetic Signal Representation (PSR) curve
	PSR area: -0.2215594
	Probability of PSR area been equal to the null (random) expectancy: NA
	Probability of PSR area been equal to the Brownian expectancy**: NA
	Iterations: 1
	Trait type: continuous

	**: If trait is binary than the null expectancy is equal to the Brownian expectancy

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