ZA.AMMI: Absolute Value of the Relative Contribution of IPCs to the...

Description Usage Arguments Details Value References See Also Examples

View source: R/Za.AMMI.R

Description

ZA.AMMI computes the Absolute Value of the Relative Contribution of IPCs to the Interaction (\mjseqn\textrmZ_\textrma) \insertCitezali_evaluation_2012ammistability considering all significant interaction principal components (IPCs) in the AMMI model. Using \mjseqn\textrmZ_\textrma, the Simultaneous Selection Index for Yield and Stability (SSI) is also calculated according to the argument ssi.method. \loadmathjax

Usage

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ZA.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 Absolute Value of the Relative Contribution of IPCs to the Interaction (\mjseqnZa) \insertCitezali_evaluation_2012ammistability is computed as follows:

\mjsdeqn

Za = \sum_i=1^N'\left | \theta_n\gamma_in \right |

Where, \mjseqnN' is the number of significant IPCAs (number of IPC that were retained in the AMMI model via F tests); \mjseqn\gamma_in is the eigenvector value for \mjseqnith genotype; 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:

Za

The Za values.

SSI

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

rZa

The ranks of Za 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, 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)
ZA.AMMI(model)

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

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

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

ajaygpb/AMMIStbp documentation built on March 8, 2021, 4:23 a.m.