# ammistability: Estimate multiple AMMI model Stability Parameters In ajaygpb/AMMIStbp: Additive Main Effects and Multiplicative Interaction Model Stability Parameters

## Description

`ammistability` computes multiple stability parameters from an AMMI model. Further, the corresponding Simultaneous Selection Indices for Yield and Stability (SSI) are also calculated according to the argument `ssi.method`. From the results, correlation between the computed indices will also be computed. The resulting correlation matrices will be plotted as correlograms. For visual comparisons of ranks of genotypes for different indices, slopegraphs and heatmaps will also be generated by this function.

## Usage

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28``` ```ammistability( model, n, alpha = 0.05, ssi.method = c("farshadfar", "rao"), a = 1, AMGE = TRUE, ASI = TRUE, ASV = TRUE, ASTAB = TRUE, AVAMGE = TRUE, DA = TRUE, DZ = TRUE, EV = TRUE, FA = TRUE, MASI = TRUE, MASV = TRUE, SIPC = TRUE, ZA = TRUE, force.grouping = TRUE, line.size = 1, line.alpha = 0.5, line.col = NULL, point.size = 1, point.alpha = 0.5, point.col = NULL, text.size = 2 ) ```

## 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`). `AMGE` If `TRUE`, computes AMGE (see Details). Default is `TRUE`. `ASI` If `TRUE`, computes ASI (see Details). `n = 2` will be used in this case. Default is `TRUE`. `ASV` If `TRUE`, computes ASV (see Details). `n = 2` will be used in this case. Default is `TRUE`. `ASTAB` If `TRUE`, computes ASTAB (see Details). Default is `TRUE`. `AVAMGE` If `TRUE`, computes AVAMGE (see Details). Default is `TRUE`. `DA` If `TRUE`, computes DA (see Details). Default is `TRUE`. `DZ` If `TRUE`, computes DZ (see Details). Default is `TRUE`. `EV` If `TRUE`, computes EV (see Details). Default is `TRUE`. `FA` If `TRUE`, computes FA (see Details). Default is `TRUE`. `MASI` If `TRUE`, computes MASI (see Details). Default is `TRUE`. `MASV` If `TRUE`, computes MASV (see Details). Default is `TRUE`. `SIPC` If `TRUE`, computes SIPC (see Details). Default is `TRUE`. `ZA` If `TRUE`, computes ZA (see Details). Default is `TRUE`. `force.grouping` If `TRUE`, genotypes will be considered as a grouping variable for plotting the slopegraphs. (Each genotype will be represented by a different colour in the slopegraphs). Default is `TRUE`. `line.size` Size of lines plotted in the slopegraphs. Must be numeric. `line.alpha` Transparency of lines plotted in the slopegraphs. Must be numeric. `line.col` Default is `TRUE`. Overrides colouring by `force.grouping` argument. `point.size` Size of points plotted in the slopegraphs. Must be numeric. `point.alpha` Transparency of points plotted in the slopegraphs. Must be numeric. `point.col` Default is `TRUE`. Overrides colouring by `force.grouping` argument. `text.size` Size of text annotations plotted in the slopegraphs. Must be numeric.

## Details

`ammistability` computes the following stability parameters from an AMMI model.

Sum Across Environments of GEI Modelled by AMMI (AMGE)

Sneller et al., 1997

AMMI Stability Index (ASI)

Jambhulkar et al., 2014; Jambhulkar et al., 2015; Jambhulkar et al., 2017

AMMI Stability Value (ASV)

Purchase 1997; Purchase et al., 1999; Purchase et al., 2000

AMMI Based Stability Parameter (ASTAB)

Rao and Prabhakaran, 2005

Sum Across Environments of Absolute Value of GEI Modelled by AMMI (AVAMGE)

Zali et al., 2012

Annicchiarico's D Parameter (DA)

Annicchiarico, 1997

Zhang's D Parameter (DZ)

Zhang, 1998

Averages of the Squared Eigenvector Values (EV)

Zobel, 1994

Stability Measure Based on Fitted AMMI Model (FA)

Raju, 2002

Modified AMMI Stability Index (MASI)

Ajay et al., 2018

Modified AMMI Stability Value (MASV)

Zali et al., 2012; Ajay et al., 2019

Sums of the Absolute Value of the IPC Scores (SIPC)

Sneller et al., 1997

Absolute Value of the Relative Contribution of IPCs to the Interaction (Za)

Zali et al., 2012

## Value

A list with the following components:

 `Details` A data frame indicating the stability parameters computed and the method used for computing the SSI. `Stability Parameters` A data frame of computed stability parameters. `Simultaneous Selection Indices` A data frame of computed SSIs. `SP Correlation` A data frame of correlation between stability parameters. `SSI Correlation` A data frame of correlation between SSIs. `SP and SSI Correlation` A data frame of correlation between stability parameters and SSIs. ```SP Correlogram``` Correlogram of stability parameters. ```SSI Correlogram``` Correlogram of SSIs. ```SP and SSI Correlogram``` Correlogram of stability parameters and SSIs. ```SP Slopegraph``` Slopegraph of stability parameter ranks. ```SSI Slopegraph``` Slopegraph of SSI ranks. ```SP Heatmap``` Heatmap of stability parameter ranks. ```SSI Heatmap``` Heatmap of SSI ranks.

## References

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zobel_stress_1994ammistability

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annicchiarico_joint_1997ammistability

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purchase_parametric_1997ammistability

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sneller_repeatability_1997ammistability

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zhang_analysis_1998ammistability

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purchase_use_1999ammistability

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purchase_genotype_2000ammistability

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raju_study_2002ammistability

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rao_use_2005ammistability

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zali_evaluation_2012ammistability

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jambhulkar_ammi_2014ammistability

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jambhulkar_genotype_2015ammistability

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jambhulkar_stability_2017ammistability

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jambhulkar_stability_2017ammistability

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ajay_modified_2018ammistability

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ajay2019ammistabilityammistability

`AMMI`, `AMGE.AMMI`, `ASI.AMMI`, `ASTAB.AMMI`, `AMGE.AMMI`, `DA.AMMI`, `DZ.AMMI`, `EV.AMMI`, `FA.AMMI`, `MASV.AMMI`, `SIPC.AMMI`, `ZA.AMMI`, `SSI`
 ``` 1 2 3 4 5 6 7 8 9 10``` ```library(agricolae) data(plrv) # AMMI model model <- with(plrv, AMMI(Locality, Genotype, Rep, Yield, console = FALSE)) ammistability(model, AMGE = TRUE, ASI = FALSE, ASV = TRUE, ASTAB = FALSE, AVAMGE = FALSE, DA = FALSE, DZ = FALSE, EV = TRUE, FA = FALSE, MASI = FALSE, MASV = TRUE, SIPC = TRUE, ZA = FALSE) ```