R/orderPvalue.R

In myaseen208/agricolae: Statistical Procedures for Agricultural Research

#' Grouping the treatments averages in a comparison with a minimum value
#' 
#' When there are treatments and their respective values, these can be compared
#' with a minimal difference of meaning.
#' 
#' 
#' @param treatment treatment
#' @param means means of treatment
#' @param alpha Alpha value, significante value to comparison
#' @param pvalue Matrix of probabilities to comparison
#' @param console logical, print output
#' @return The means and groups for treatments.
#' @note It is considered 81 labels as maximum for the formation of groups,
#' greater number will not have label.
#' @author Felipe de Mendiburu
#' @keywords manip
#' @export
#' @examples
#' 
#' library(agricolae)
#' treatments <- c("A","B","C")
#' means<-c(2,5,3)
#' alpha <- 0.05
#' pvalue<-matrix(1,nrow=3,ncol=3)
#' pvalue[1,2]<-pvalue[2,1]<-0.03
#' pvalue[1,3]<-pvalue[3,1]<-0.10
#' pvalue[2,3]<-pvalue[3,2]<-0.06
#' out<-orderPvalue(treatments,means,alpha,pvalue,console=TRUE)
#' barplot(out[,1],names.arg = row.names(out),col=colors()[84:87])
#' legend("topright",as.character(out$groups),pch=15,col=colors()[84:87],box.col=0)
#' 
orderPvalue <-
function (treatment, means, alpha, pvalue, console) 
{
  n <- length(means)
  z <- data.frame(treatment, means)
  letras<-c(letters[1:26],LETTERS[1:26],1:9,c(".","+","-","*","/","#","$",
"%","&","^","[","]",":","@",";","_","?","!","=","#",rep(" ",2000)))
  w <- z[order(z[, 2], decreasing = TRUE), ]
  M<-rep("",n)
  k<-1
  k1<-0
  j<-1
  i<-1
  cambio<-n
  cambio1<-0
  chequeo=0
  M[1]<-letras[k]
  q <- as.numeric(rownames(w)) #Check
  while(j<n) {
    chequeo<-chequeo+1
    if (chequeo > n) break
    for(i in j:n) {
      s<-pvalue[q[i],q[j]]>alpha
      if(s) {
        if(lastC(M[i]) != letras[k])M[i]<-paste(M[i],letras[k],sep="")
      }
      else {
        k<-k+1
        cambio<-i
        cambio1<-0
        ja<-j
        for(jj in cambio:n) M[jj]<-paste(M[jj],"",sep="") # El espacio
        M[cambio]<-paste(M[cambio],letras[k],sep="")
        for( v in ja:cambio) {
          if(pvalue[q[v],q[cambio]]<=alpha) {j<-j+1
          cambio1<-1
          }
          else break
        }
        break
      }
    }
    if (cambio1 ==0 )j<-j+1
  }
  #-----------
  w<-data.frame(w,stat=M)
  trt <- as.character(w$treatment)
  means <- as.numeric(w$means)
  output <- data.frame(means, groups=M)
  rownames(output)<-trt
  if(k>81) 
    cat("\n",k,"groups are estimated.The number of groups exceeded the maximum of 81 labels. change to group=FALSE.\n")
    invisible(output)
}