ammiBayes.conf.plot {ammiBayes}

Plot ammiBayes object with confidence region

Description

Plot the confidence regions for genotype and environment effects

Usage

ammiBayes.conf.plot(model, conf=0.95, pars.gen=NULL, pars.env=NULL,
              gen.labels=NULL, env.labels=NULL,
              col.env="red", col.gen="green", 
              alpha.env=80, alpha.gen=80, 
              col.text.env="black", col.text.gen="black",
              border.gen="transparent", border.env="transparent", 
              cex.env=1, cex.gen=1, lty.gen=1, lty.env=1, 
              lwd.gen=1, lwd.env=1, xlab, ylab, col.grid="grey", 
              lty.grid=2, lwd.grid=1, change.signal=FALSE, 
              plot.gen=TRUE, plot.env=TRUE)

Arguments

model

An object of the ammiBayes class

conf

Significant level for the confidence region. By default is 0.95.

pars.gen

An optional character vector of genotype names. If pars is omitted all genotypes are included.

pars.env

An optional character vector of environment names. If pars is omitted all environments are included.

gen.labels

Optional vector for the name of the genotypes.

env.labels

Optional vector for the name of the environments.

col.env

Color for the confidence region of the environment. Default is "red".

col.gen

Color for the confidence region of the genotype. Default is "green".

alpha.env

Specifies the opacity of the confidence region for the environment. Default is 80.

alpha.gen

Specifies the opacity of the confidence region for the genotype. Default is 80.

col.text.env

Define the color of environment names.

col.text.gen

Define the color of genotype names.

border.gen

Define the color for the border of the confidence region of genotype. Default is "transparent".

border.env

Define the color for the border of the confidence region of environment. Default is "transparent".

cex.env

Scale for the font size of the environment names. Default is 1

cex.gen

Scale for the font size of the genotype names. Default is 1

lty.gen

Line type for the border of confidence region of genotype. Default is 1

lty.env

Line type for the border of confidence region of environment. Default is 1

lwd.gen

Line width for the border of confidence region of genotype. Default is 1

lwd.env

Line width for the border of confidence region of environment. Default is 1

xlab

Label for the x-axis

ylab

Label for the y-axis

col.grid

Define the color for the grid. Default is "grey"

lty.grid

Line type of grid. Default is 2

lwd.grid

Line width of grid. Default is 1

change.signal

Changes the signal of the chain for better visualization of the sample. By default is FALSE

plot.gen

Plot effects of genotypes. By default is TRUE

plot.env

PLot effects of environment. By default is TRUE

Details

The confidence regions are defined using the package distfree.cr.

Author(s)

Luciano A. Oliveira
Carlos P. Silva
Cristian T. E. Mendes
Alessandra Q. Silva
Joel J. Nuvunga
Marcio Balestre
Julio S. S. Bueno-Filho
Fabio M. Correa

References

OLIVEIRA,L.A.; SILVA, C. P.; NUVUNGA, J. J.; SILVA, A. Q.; BALESTRE, M. Credible Intervals for Scores in the AMMI with Random Effects for Genotype. Crop Science, v. 55, p. 465-476, 2015. doi: https://doi.org/10.2135/cropsci2014.05.0369

SILVA, C. P.; OLIVEIRA, L. A.; NUVUNGA, J. J.; PAMPLONA, A. K. A.; BALESTRE, M. A Bayesian Shrinkage Approach for AMMI Models. Plos One, v. 10, p. e0131414, 2015. doi: https://doi.org/10.1371/journal.pone.0131414.

See Also

lattice

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)

ammiBayes.conf.plot(model)