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

ammistability

R Documentation

Estimate multiple AMMI 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

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): \insertCite
sneller_repeatability_1997;textualammistability
AMMI Stability Index (ASI): \insertCite
jambhulkar_ammi_2014,jambhulkar_genotype_2015,jambhulkar_stability_2017;textualammistability
AMMI Stability Value (ASV): \insertCite
purchase_parametric_1997,purchase_use_1999,purchase_genotype_2000;textualammistability
AMMI Based Stability Parameter (ASTAB): \insertCite
rao_use_2005;textualammistability
Sum Across Environments of Absolute Value of GEI Modelled by AMMI (AVAMGE): \insertCite
zali_evaluation_2012;textualammistability
Annicchiarico's D Parameter (DA): \insertCite
annicchiarico_joint_1997;textualammistability
Zhang's D Parameter (DZ): \insertCite
zhang_analysis_1998;textualammistability
Averages of the Squared Eigenvector Values (EV): \insertCite
zobel_stress_1994;textualammistability
Stability Measure Based on Fitted AMMI Model (FA): \insertCite
raju_study_2002;textualammistability
Modified AMMI Stability Index (MASI): \insertCite
ajay_modified_2018;textualammistability
Modified AMMI Stability Value (MASV): \insertCite
zali_evaluation_2012,ajay2019ammistability;textualammistability
Sums of the Absolute Value of the IPC Scores (SIPC): \insertCite
sneller_repeatability_1997;textualammistability
Absolute Value of the Relative Contribution of IPCs to the Interaction (Za): \insertCite
zali_evaluation_2012;textualammistability

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

\insertAllCited

Examples

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)

ajaygpb/ammistability documentation built on Aug. 24, 2023, 8:09 a.m.