R/AMMI.contour.R

In myaseen208/agricolae: Statistical Procedures for Agricultural Research

#' @name    AMMI.contour
#' @aliases AMMI.contour
#' @title AMMI contour
#' @description
#' Draws a polygon or a circumference around the center of the Biplot with a
#' proportional radio at the longest distance of the genotype.
#' 
#' First, it is necessary to execute the AMMI function. It is only valid for
#' the BIPLOT function but not for the TRIPLOT one.
#' 
#' @param model Object
#' @param distance Circumference radius >0 and <=1
#' @param shape Numerical, relating to the shape of the polygon outline.
#' @param \dots Parameters corresponding to the R lines function
#' 
#' @return \strong{Genotypes} Genotypes within and outside the area.
#' @return  \strong{distance} Distance from genotype to origin (0,0)
#' 
#' @note Complement graphics AMMI
#' 
#' @author
#' \enumerate{
#'          \item Felipe de Mendiburu (\email{fmendiburu@@lamolina.edu.pe})
#'          \item Muhammad Yaseen (\email{myaseen208@@gmail.com})
#'          }
#' 
#' @seealso
#'  \code{\link{AMMI}}
#' 
#' @keywords aplot
#' 
#' @importFrom graphics lines
#' 
#' @export
#' 
#' @examples
#' 
#' library(agricolae)
#' # see AMMI.
#' data(sinRepAmmi)
#' Environment <- sinRepAmmi$ENV
#' Genotype <- sinRepAmmi$GEN
#' Yield <- sinRepAmmi$YLD
#' REP <- 3
#' MSerror <- 93.24224
#' model<-AMMI(Environment, Genotype, REP, Yield, MSerror)
#' plot(model)
#' AMMI.contour(model,distance=0.7,shape=8,col="red",lwd=2,lty=5)
#' 
#' 
#' 
AMMI.contour <-  
function(model,distance,shape,...)
{
G<- subset(model$biplot,model$biplot$type=="GEN")
x<-G$PC1
y<-G$PC2
d<-sqrt(x^2+y^2)
r <-distance*max(d)
x<-seq(-r,r,length=shape)
A<-cbind(x,y=sqrt(r^2-x^2))
B<-cbind(x,y=-sqrt(r^2-x^2))
lines(A,type="l",...)
lines(B,type="l",...)
Gin <- d<=r
Gout<- d >r
GEN.in<-row.names(G)[Gin]
GEN.out<-row.names(G)[Gout]
cat("\nLimit, radio:",r)
cat("\nGenotype  in:",length(GEN.in))
cat("\nGenotype out:",length(GEN.out),"\n\n")
distance<-data.frame(row.names=row.names(G),distance=d)
return(list("GENOTYPE IN"=GEN.in, "GENOTYPE OUT"=GEN.out,Distance=distance))
}