PERMANOVA from a matrix of distancies
This function makes a PERMANOVA from distancies matrix and factor for groups.
PerMANOVA.Simple(D, grupo, nperm = 999, seed = NULL, C = NULL)
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. |
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. |
Laura Vicente-Gonzalez, Jose Luis Vicente-Villardon
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.
## Not run: data(wine) X = wine[,4:21] Dist = DistContinuous (X) PerMANOVA.Simple(Dist$D, wine$Group) ## End(Not run)
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