R/covariateM.R

In gcostaneto/envirotype: GIS platforms to support envirorytping in breeding programs

#' Preparing reaction norm models

#' build Jarquin et al (2014) covariate matrix (M)
jarquin_RN = function(covariable.id, df, env.id, stage.id=NULL, digits=8){
  
  .DF = melt(df[,c(covariable.id,env.id,stage.id)],
             id.vars = c(e.ids,stage.id),
             variable.name = "covariable")
  
  if(isTRUE(is.null(stage.id))){
    .DF$variable = .DF$covariable
  }else{.DF$variable = paste(.DF$covariable,.DF[,stage.id],sep="-")}
  
  .DF=acast(ddply(.DF,.(env,variable),summarise,y=mean(value)),env~variable,value.var="y")
  
  return(list(x.origin = round(.DF,digits),
              x.scaled = round(scale(.DF, center=T,scale = T),digits)))
}