FA.AMMI {ammistability} | R Documentation |
Stability Measure Based on Fitted AMMI Model
Description
FA.AMMI
computes the Stability Measure Based on Fitted AMMI Model (FA)
(Raju 2002) considering all significant
interaction principal components (IPCs) in the AMMI model. Using FA, the
Simultaneous Selection Index for Yield and Stability (SSI) is also calculated
according to the argument ssi.method
.
Usage
FA.AMMI(model, n, alpha = 0.05, ssi.method = c("farshadfar", "rao"), a = 1)
Arguments
model |
The AMMI model (An object of class |
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 |
a |
The ratio of the weights given to the stability components for
computation of SSI when |
Details
The Stability Measure Based on Fitted AMMI Model (\(FA\)) (Raju 2002) is computed as follows:
\[FA = \sum_{n=1}^{N'}\lambda_{n}^{2}\gamma_{in}^{2}\]Where, \(N'\) is the number of significant IPCs (number of IPC that were retained in the AMMI model via F tests); \(\lambda_{n}\) is the singular value for \(n\)th IPC and correspondingly \(\lambda_{n}^{2}\) is its eigen value; and \(\gamma_{in}\) is the eigenvector value for \(i\)th genotype.
When \(N'\) is replaced by 1 (only first IPC axis is considered for computation), then the parameter \(FP\) can be estimated (Zali et al. 2012).
\[FP = \lambda_{1}^{2}\gamma_{i1}^{2}\]When \(N'\) is replaced by 2 (only first two IPC axes are considered for computation), then the parameter \(B\) can be estimated (Zali et al. 2012).
\[B = \sum_{n=1}^{2}\lambda_{n}^{2}\gamma_{in}^{2}\]When \(N'\) is replaced by \(N\) (All the IPC axes are considered for computation), then the parameter estimated is equivalent to Wricke's ecovalence (\(W_{(AMMI)}\)) (Wricke 1962; Zali et al. 2012).
\[W_{(AMMI)} = \sum_{n=1}^{N}\lambda_{n}^{2}\gamma_{in}^{2}\]Value
A data frame with the following columns:
FA |
The FA values. |
SSI |
The computed values of simultaneous selection index for yield and stability. |
rFA |
The ranks of FA 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
Raju BMK (2002).
“A study on AMMI model and its biplots.”
Journal of the Indian Society of Agricultural Statistics, 55(3), 297–322.
Wricke G (1962).
“On a method of understanding the biological diversity in field research.”
Zeitschrift fur Pflanzenzuchtung, 47, 92–146.
Zali H, Farshadfar E, Sabaghpour SH, Karimizadeh R (2012).
“Evaluation of genotype × environment interaction in chickpea using measures of stability from AMMI model.”
Annals of Biological Research, 3(7), 3126–3136.
See Also
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)
FA.AMMI(model)
# With n = 4 and default ssi.method (farshadfar)
FA.AMMI(model, n = 4)
# With default n (N') and ssi.method = "rao"
FA.AMMI(model, ssi.method = "rao")
# Changing the ratio of weights for Rao's SSI
FA.AMMI(model, ssi.method = "rao", a = 0.43)