View source: R/ammistability.R
ammistability | R Documentation |
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.
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.
sneller_repeatability_1997;textualammistability
jambhulkar_ammi_2014,jambhulkar_genotype_2015,jambhulkar_stability_2017;textualammistability
purchase_parametric_1997,purchase_use_1999,purchase_genotype_2000;textualammistability
rao_use_2005;textualammistability
zali_evaluation_2012;textualammistability
annicchiarico_joint_1997;textualammistability
zhang_analysis_1998;textualammistability
zobel_stress_1994;textualammistability
raju_study_2002;textualammistability
ajay_modified_2018;textualammistability
zali_evaluation_2012,ajay2019ammistability;textualammistability
sneller_repeatability_1997;textualammistability
zali_evaluation_2012;textualammistability
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. |
AMMI
,
AMGE.AMMI
,
ASI.AMMI
,
ASTAB.AMMI
,
AMGE.AMMI
,
DA.AMMI
, DZ.AMMI
,
EV.AMMI
, FA.AMMI
,
MASV.AMMI
,
SIPC.AMMI
,
ZA.AMMI
, SSI
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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