PERMANOVA (version 0.2.0)

PerMANOVA.Simple: PERMANOVA from a matrix of distancies

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.

References

Anderson, M. J. (2001). A new method for non-parametric multivariate analysis of variance. Austral ecology, 26(1):32<U+2013>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

# NOT RUN {
data(wine)
X = wine[,4:21]
Dist = DistContinuous (X)
PerMANOVA.Simple(Dist$D, wine$Group)
  
# }