ammistability (version 0.1.2)

ammistability: 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.

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.

Details

ammistability computes the following stability parameters from an AMMI model.

Sum Across Environments of GEI Modelled by AMMI (AMGE)

sneller_repeatability_1997;textualammistability

AMMI Stability Index (ASI)

jambhulkar_ammi_2014,jambhulkar_genotype_2015,jambhulkar_stability_2017;textualammistability

AMMI Stability Value (ASV)

purchase_parametric_1997,purchase_use_1999,purchase_genotype_2000;textualammistability

AMMI Based Stability Parameter (ASTAB)

rao_use_2005;textualammistability

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

zali_evaluation_2012;textualammistability

Annicchiarico's D Parameter (DA)

annicchiarico_joint_1997;textualammistability

Zhang's D Parameter (DZ)

zhang_analysis_1998;textualammistability

Averages of the Squared Eigenvector Values (EV)

zobel_stress_1994;textualammistability

Stability Measure Based on Fitted AMMI Model (FA)

raju_study_2002;textualammistability

Modified AMMI Stability Index (MASI)

ajay_modified_2018;textualammistability

Modified AMMI Stability Value (MASV)

zali_evaluation_2012,ajay2019ammistability;textualammistability

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

sneller_repeatability_1997;textualammistability

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

zali_evaluation_2012;textualammistability

References

See Also

AMMI, AMGE.AMMI, ASI.AMMI, ASTAB.AMMI, AMGE.AMMI, DA.AMMI, DZ.AMMI, EV.AMMI, FA.AMMI, MASV.AMMI, SIPC.AMMI, ZA.AMMI, SSI

Examples

# NOT RUN {
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)
# }