PerMANOVA.Simple: PERMANOVA from a matrix of distancies

In PERMANOVA: Multivariate Analysis of Variance Based on Distances and Permutations

Description

This function makes a PERMANOVA from distancies matrix and factor for groups.

Usage

PerMANOVA.Simple(D, grupo, nperm = 999, seed = NULL, C = NULL)

Arguments

D	A matrix containing the distances between individuals.
grupo	A factor containing the groups to compare.
nperm	Number of permutation that want to perform. By default it is 999.
seed	Seed to start permutations. By default it is null.
C	Contrast matrix. By default it is null.

Value

The PERMANOVA.Simple function create a list that return:

call	Function
nperm	Number of permutation.
Inicial	Containing: * TSS -> Total sum of squares. * BSS -> Between groups sum of squares. * WSS -> Within groups sum of squares. * glt -> Total degrees of freedom. * glb -> Between groups degrees of freedom. * glw -> Within groups degrees of freedom. * Fexp -> Experimental F.
Fvals	F values of the permutation.
pval	Estimate p-valor for PERMANOVA.

Author(s)

Laura Vicente-Gonzalez, Jose Luis Vicente-Villardon

References

Anderson, M. J. (2001). A new method for non-parametric multivariate analysis of variance. Austral ecology, 26(1):32–46.

Anderson, M. J. (2005). Permanova: a fortran computer program for permutational multivariate analysis of variance. Department of Statistics, University of Auckland, New Zealand, 24.

Examples

data(wine)
X = wine[,4:21]
Dist = DistContinuous (X)
PerMANOVA.Simple(Dist$D, wine$Group)
  

PERMANOVA documentation built on Sept. 6, 2021, 5:07 p.m.