AMGE.AMMI: Sum Across Environments of GEI Modelled by AMMI

Description Usage Arguments Details Value References See Also Examples

View source: R/AMGE.AMMI.R

Description

AMGE.AMMI computes the Sum Across Environments of Genotype-Environment Interaction (GEI) Modelled by AMMI (AMGE) (Sneller et al., 1997) considering all significant interaction principal components (IPCs) in the AMMI model. Using AMGE, the Simultaneous Selection Index for Yield and Stability (SSI) is also calculated according to the argument ssi.method.

Usage

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AMGE.AMMI(model, n, alpha = 0.05, ssi.method = c("farshadfar", "rao"), a = 1)

Arguments

model

The AMMI model (An object of class AMMI generated by AMMI).

n

The number of principal components to be considered for computation. The default value is the number of significant IPCs.

alpha

Type I error probability (Significance level) to be considered to identify the number of significant IPCs.

ssi.method

The method for the computation of simultaneous selection index. Either "farshadfar" or "rao" (See SSI).

a

The ratio of the weights given to the stability components for computation of SSI when method = "rao" (See SSI).

Details

The Sum Across Environments of GEI Modelled by AMMI (AMGE) is computed as follows:

AMGE = Ej=1N'n=1 λnγinδjn

Where, N' is the number of significant IPCs (number of IPC that were retained in the AMMI model via F tests); λn is the singular value for nth IPC and correspondingly λ2n is its eigen value; γin is the eigenvector value for ith genotype; and δjn is the eigenvector value for the jth environment.

Value

A data frame with the following columns:

AMGE

The AMGE values.

SSI

The computed values of simultaneous selection index for yield and stability.

rAMGE

The ranks of AMGE values.

rY

The ranks of the mean yield of genotypes.

means

The mean yield of the genotypes.

The names of the genotypes are indicated as the row names of the data frame.

References

\insertRef

sneller_repeatability_1997ammistability

See Also

AMMI, SSI

Examples

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library(agricolae)
data(plrv)

# AMMI model
model <- with(plrv, AMMI(Locality, Genotype, Rep, Yield, console = FALSE))

# ANOVA
model$ANOVA

# IPC F test
model$analysis

# Mean yield and IPC scores
model$biplot

# G*E matrix (deviations from mean)
array(model$genXenv, dim(model$genXenv), dimnames(model$genXenv))

# With default n (N') and default ssi.method (farshadfar)
AMGE.AMMI(model)

# With n = 4 and default ssi.method (farshadfar)
AMGE.AMMI(model, n = 4)

# With default n (N') and ssi.method = "rao"
AMGE.AMMI(model, ssi.method = "rao")

# Changing the ratio of weights for Rao's SSI
AMGE.AMMI(model, ssi.method = "rao", a = 0.43)

ajaygpb/AMMIStbp documentation built on Jan. 27, 2020, 8:53 a.m.