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

Description Usage Arguments Value References Examples

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 GGEBiplot. For dealing with missing data then a better implementation is available through gge.

Usage

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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

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

Example output

Loading required package: rgl
Loading required package: tcltk
Loading required package: tkrplot
Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl_init' failed, running with rgl.useNULL = TRUE 
3: .onUnload failed in unloadNamespace() for 'rgl', details:
  call: fun(...)
  error: object 'rgl_quit' not found 
4: no DISPLAY variable so Tk is not available 
5: loading Rplot failed 

GGEBiplots documentation built on May 2, 2019, 6:03 a.m.