ammiBayes.sm.plot: Plot Method for Bayesian Stability Mahalanobis Distance...

In ammiBayes: Bayesian Ammi Model for Continuous Data with or without Additive and Dominance Effect

Plot Method for Bayesian Stability Mahalanobis Distance (SM_i)

Description

Plot the SM_i Stability Index and Genotype Posterior Mean for the SM_i

Usage

ammiBayes.sm.plot(x, xlab = "Genotype Posterior Mean",
                               ylab = "Bayesian Stability Index (SM_i)",
                               line.col = "darkblue", main = NULL, text.col = "red",
                               pch = 16, cex = 1.5, lwd = 1.5, lty = 2,
                               ylimits = 0.1, grid.col = "gray50"
                              )

Arguments

x	An object of class ammiBayes.sm.
xlab	Character string for the X-axis label. Default is "Genotype Posterior Mean".
ylab	Character string for the Y-axis label. Default is "Bayesian Stability Index (SM_i)".
line.col	Color for the points and error bars. Default is "darkblue".
main	Character string or expression for the plot title. Default is NULL.
text.col	Color for the genotype text labels. Default is "red".
pch	Plotting character symbol. Default is 16
cex	Font size for genotype labels. Default is 1.5
lwd	Numeric value for the thickness of the HPD error bars. Default is 1.5.
lty	Integer or character for the reference grid lines (quadrants). Default is 2 (dashed).
ylimits	Numeric adjustment padding for the Y-axis limits. Default is 0.1.
grid.col	Color for the reference quadrant lines. Default is "gray50".

Author(s)

Luciano A. Oliveira
Carlos P. Silva
Cristian T. E. Mendes
Alessandra Q. Silva
Joel J. Nuvunga
Larissa C. V. Boas
Julio S. S. Bueno-Filho
Diogenes F. Filho
Fabio M. Correa

Examples

library(ammiBayes)
data(ammiData)

Env  <- factor(ammiData$amb)
Rep <- factor(ammiData$rep)
Gen  <- factor(ammiData$gen)
Y  <- ammiData$prod

model <- ammiBayes(Y=Y, Gen=Gen, Env=Env, Rep=Rep, iter=10, 
									 burn=1, jump=2, chains=2)

out <- sm.index(model)


ammiBayes.sm.plot(out)

ammiBayes documentation built on Aug. 24, 2026, 5:14 p.m.