BootDisMANOVA: Multivariate Analysis of Variance based on Distances and...

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

Description

Multivariate Analysis of variance based on distances and Bootstrap.

Usage

BootDisMANOVA(Distance, groups, C = NULL, Effects = NULL, nB = 1000, seed = NULL,
CoordPrinc = FALSE, dimens = 2, PCoA = "Standard", ProjectInd = TRUE, tol = 1e-04,
DatosIni = TRUE)

Arguments

Distance	A matrix of distances.
groups	A factor containing the groups to compare.
C	A matrix of contrasts (if null the identity is used).
Effects	A vector of effects.
nB	Number of Bootstrap replicates.
seed	Seed for the random numbers.
CoordPrinc	Should Principal Coordinates be calculated.
dimens	Dimension of the solution.
PCoA	Type of Principal Coordinates to calulate.
ProjectInd	Should the individuals be projected onto the graph.
tol	Tolerance for convergence of the algorithms.
DatosIni	Should the initial data be included in the results.

Details

Multivariate Analysis of Variance based on distances and Bootstrap.

Value

call	Function
Title	Title of the study
Type	BootMANOVA
Distances	A matrix containing the distances between individuals.
C	Contrasts Matrix.
Initial	Containing two matrices: * Global -> Global contrast. * Contrastes ->Contrasts for groups.
DistMuestral	Sample distribution of F-exp from permutations.
pvalue	Estimate p-valor for PERMANOVA.
ExplainedVariance	Explained variance by Principal Coordinates selected.
Inertias	Eigenvalue, Explained variance, Cumulative explained variance.
MeanCoordinates	Mean Coordinates by groups for the dimensions obtained in the Principal Coordinates Analysis.
Qualities	Qualities representation by groups for the dimensions of PCoA.
CummulativeQualities	Cummulative qualities representation.
ClusterType	Cluster type selected.
Clusters	Clusters created.
ClusterNames	Names of clusters
ClusterColors	Colors of clusters, color name and HTML code.

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]
D = DistContinuous (X)
bootwine=BootDisMANOVA(D, wine$Group)
bootwine

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