Description Usage Arguments Details Value References See Also Examples

View source: R/ammistability.R

`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.

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
)
``` |

`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 |

`AMGE` |
If |

`ASI` |
If |

`ASV` |
If |

`ASTAB` |
If |

`AVAMGE` |
If |

`DA` |
If |

`DZ` |
If |

`EV` |
If |

`FA` |
If |

`MASI` |
If |

`MASV` |
If |

`SIPC` |
If |

`ZA` |
If |

`force.grouping` |
If |

`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 |

`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 |

`text.size` |
Size of text annotations plotted in the slopegraphs. Must be numeric. |

`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

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. |

zobel_stress_1994ammistability

\insertRefannicchiarico_joint_1997ammistability

\insertRefpurchase_parametric_1997ammistability

\insertRefsneller_repeatability_1997ammistability

\insertRefzhang_analysis_1998ammistability

\insertRefpurchase_use_1999ammistability

\insertRefpurchase_genotype_2000ammistability

\insertRefraju_study_2002ammistability

\insertRefrao_use_2005ammistability

\insertRefzali_evaluation_2012ammistability

\insertRefjambhulkar_ammi_2014ammistability

\insertRefjambhulkar_genotype_2015ammistability

\insertRefjambhulkar_stability_2017ammistability

\insertRefjambhulkar_stability_2017ammistability

\insertRefajay_modified_2018ammistability

\insertRefajay2019ammistabilityammistability

`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)
``` |

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