IniTransform: Initial transformation of a data matrix

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

Description

Initial transformation of data before the construction of a biplot (or any other technique).

Usage

IniTransform(X, InitTransform = "None", transform = "Standardize columns")

Arguments

X	Original Raw Data Matrix.
InitTransform	Previous transformation (Logarithm or logit).
transform	Transformation to use. See details.

Details

Possible Transformations are:

1.- "Raw Data": When no transformation is required.

2.- "Subtract the global mean": Eliminate an effect common to all the observations

3.- "Double centering" : Interaction residuals. When all the elements of the table are comparable. Useful for AMMI models.

4.- "Column centering": Remove the column means.

5.- "Standardize columns": Remove the column means and divide by its standard deviation.

6.- "Row centering": Remove the row means.

7.- "Standardize rows": Divide each row by its standard deviation.

8.- "Divide by the column means and center": The resulting dispersion is the coefficient of variation.

9.- "Normalized residuals from independence" for a contingency table.

The transformation can be provided to the function by using the string between the quotes or just the associated number.

The supplementary rows and columns are not used to calculate the parameters (means, standard deviations, etc). Some of the transformations are not compatible with supplementary data.

Value

X	Transformed data matrix.

Author(s)

Jose Luis Vicente-Villardon

References

M. J. Baxter (1995) Standardization and Transformation in Principal Component Analysis, with Applications to Archaeometry. Journal of the Royal Statistical Society. Series C (Applied Statistics). Vol. 44, No. 4 (1995) , pp. 513-527

Kroonenberg, P. M. (1983). Three-mode principal component analysis: Theory and applications (Vol. 2). DSWO press. (Chapter 6)

Examples

data(iris)
x=as.matrix(iris[,1:4])
x=IniTransform(x, transform=4)
x

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