EV.AMMI {ammistability}R Documentation

Averages of the Squared Eigenvector Values

Description

EV.AMMI computes the Sums of the Averages of the Squared Eigenvector Values (EV) (Zobel 1994) considering all significant interaction principal components (IPCs) in the AMMI model. Using EV, the Simultaneous Selection Index for Yield and Stability (SSI) is also calculated according to the argument ssi.method.

Usage

EV.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 Averages of the Squared Eigenvector Values (\(EV\)) (Zobel 1994) is computed as follows:

\[EV = \sum_{n=1}^{N'}\frac{\gamma_{in}^2}{N'}\]

Where, \(N'\) is the number of significant IPCs (number of IPC that were retained in the AMMI model via F tests); and \(\gamma_{in}\) is the eigenvector value for \(i\)th genotype.

Value

A data frame with the following columns:

EV

The EV values.

SSI

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

rEV

The ranks of EV 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

Zobel RW (1994). “Stress resistance and root systems.” In Proceedings of the Workshop on Adaptation of Plants to Soil Stress. 1-4 August, 1993. INTSORMIL Publication 94-2, 80–99. Institute of Agriculture and Natural Resources, University of Nebraska-Lincoln.

See Also

AMMI, SSI

Examples

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)
EV.AMMI(model)

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

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

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


[Package ammistability version 0.1.2 Index]