GGEModel: Produces genotype plus genotype-by-environment model from a...

In stats4sd/GGEBiplots: GGE Biplots with 'ggplot2'

Produces genotype plus genotype-by-environment model from a 2-way table of means

Description

Calculates the GGE model where presented with a two way table of means with genotypes in rows, where genotype names are set as row names, and environments in columns, where environment names are set as column names. This function serves as a command line interface to the internal code contained within the archived package 'GGEBiplotGUI'. For dealing with missing data then a better implementation is available through gge.

Usage

GGEModel(Data, centering = "tester", scaling = "none", SVP = "column")

Arguments

Data	a data frame or matrix containing genotype by environment means with the genotypes in rows and the environments in columns. row names and column names should be set to indicate the genotype names and environment names.
centering	centering method. Either "tester" for tester centered (G+GE), "global" for global centered (E+G+GE), "double" for double centred (GE) or "none" for no centering. Models produced without centering cannot be used in the GGEPlot function.
scaling	scaling method. Either "sd" for standard deviation or "none" for no scaling.
SVP	method for singular value partitioning. Either "row","column","dual" or "symmetrical".

Value

A list of class GGEModel containing:

coordgenotype	plotting coordinates for genotypes from all components
coordenviroment	plotting coordinates for environments from all components
eigenvalues	vector of eigenvalues from each component
vartotal	overall variance
varexpl	percentage of variance explained by each component
labelgen	genotype names
labelenv	environment names
axes	axis labels
Data	scaled and centered input data
centering	name of centering method
scaling	name of scaling method
SVP	name of SVP method

References

Yan W, Kang M (2003). GGE Biplot Analysis: A Graphical Tool for Breeders, Geneticists, and Agronomists. CRC Press.

Yan W, Kang M (2002). Singular-Value Partitioning in Biplot Analysis of Multienvironment Trial Data. Agronomy Journal, 94, 990-996. http://dx.doi.org/10.2134/agronj2002.0990

Examples

data(Ontario)
GGE1<-GGEModel(Ontario)
GGEPlot(GGE1)

stats4sd/GGEBiplots documentation built on March 18, 2023, 7:54 p.m.