MASI.AMMI: Modified AMMI Stability Index

In ajaygpb/AMMIStbp: Additive Main Effects and Multiplicative Interaction Model Stability Parameters

Modified AMMI Stability Index

Description

MASI.AMMI computes the Modified AMMI Stability Index (MASI) \insertCiteajay_modified_2018ammistability from a modified formula of AMMI Stability Index (ASI) \insertCitejambhulkar_ammi_2014,jambhulkar_genotype_2015,jambhulkar_stability_2017ammistability. Unlike ASI, MASI calculates stability value considering all significant interaction principal components (IPCs) in the AMMI model. Using MASI, the Simultaneous Selection Index for Yield and Stability (SSI) is also calculated according to the argument ssi.method. \loadmathjax

Usage

MASI.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 Modified AMMI Stability Index (\mjseqnMASI) \insertCiteajay_modified_2018ammistability is computed as follows:

\mjsdeqn

MASI = \sqrt \sum_n=1^N' PC_n^2 \times \theta_n^2

Where, \mjseqnPC_n are the scores of \mjseqnnth IPC; and \mjseqn\theta_n is the percentage sum of squares explained by the \mjseqnnth principal component interaction effect.

Value

A data frame with the following columns:

MASI	The MASI values.
SSI	The computed values of simultaneous selection index for yield and stability.
rMASI	The ranks of MASI 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

\insertAllCited

See Also

AMMI, ASI.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)
MASI.AMMI(model)

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

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

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

# ASI.AMMI same as MASI.AMMI with n = 2

a <- ASI.AMMI(model)
b <- MASI.AMMI(model, n = 2)

identical(a$ASI, b$MASI)

ajaygpb/AMMIStbp documentation built on Aug. 21, 2023, 7:59 p.m.