R/DSI.mean.R

In omarbenites/sbformula: Formulas for crop breeding and standart evaluation trial

#'Function to calculate the Drought Suceptibility Index (DSI) using mean yield values
#'
#'@param ylmeans A data frame with yield means. Included genotypes and Factor.
#'@param clabel The label of water control factor. Example: "irrigation","normal irrigation"
#'@param slabel The label of water stress factor. Example: "stress", "inttermitent 
#'@return The drought suceptible index using means
#'@author Omar Benites
#'@details This function returns the drought suceptible index (DSI) using means.
#'@references Comparison of yield based drought tolerance indices in improved varieties, genetic stocks and landraces
#'of potato (Solanum tuberosum L.)
#'@keywords index, drought
#'@family index
#'@export

#DSI <- function(dfmeans,clabel=NA, slabel=NA)
DSI.means<- function(ylmeans,clabel=NA, slabel=NA)
{
  if(missing(ylmeans)){
    stop("Please enter data frame of yield means") 
  }
  
  if(missing(clabel)){
    stop("Please enter the control condition")
  }
  
  if(missing(slabel)){
    stop("Please enter the stress condition")
  }
  
#   mysubset <- function(df, ...) {
#     ssubset <- deparse(substitute(...))
#     subset(df, eval(parse(text = ssubset)))
#   }
  mysubset <- function(df, ssubset) {
    subset(df, eval(parse(text=ssubset)))
  }

  yield.mean<- function(yf){ 
    ym <- mean(yf[,3],na.rm = TRUE) 
    ym
  }
  
  if(!is.na(clabel)){
    #wc <- subset(ylmeans,FACTOR==clabel) #control
    wc <- mysubset(ylmeans,paste("FACTOR","==",paste("'",clabel,"'",sep = ""),sep = ""))
    names(wc) <- c("INSTN", "FACTOR_C", "TTWP_Mean_C")
  }
  if(!is.na(slabel)){
    #ws <- subset(ylmeans,FACTOR==slabel) #stress
    #ws <- mysubset(ylmeans,FACTOR==slabel)
    ws <- mysubset(ylmeans,paste("FACTOR","==",paste("'",slabel,"'",sep = ""),sep = ""))
    names(ws) <- c("INSTN", "FACTOR_S", "TTWP_Mean_S")
  }
  
  #yfactor: yield mean by factor
  
#   indextable$DTI <- NA
#   indextable$TOL <- NA
#   indextable$MP <- NA
#   indextable$GM <- NA
#   indextable$TDWS <- NA
    
  Mc <- yield.mean(wc) #control
  Ms <- yield.mean(ws) #stress

  indextable<- merge(wc,ws,by = "INSTN") #merge the two tables by INSTN
  indextable$DSI <- NA

  if(length(indextable$TTWP_Mean_S)>0 & length(indextable$TTWP_Mean_C)>0) indextable=within(indextable,{    
    DSI  <- round((1-(indextable$TTWP_Mean_S/indextable$TTWP_Mean_C))/(1-(Ms/Mc)),2)
#     DTI <- round((TTWP_Mean_S*TTWP_Mean_C)/(Mc)^2,2)
#     TOL <- round((TTWP_Mean_C-TTWP_Mean_S),2)
#     MP <- round((TTWP_Mean_C+TTWP_Mean_S)/2,2)
#     GM <-  sqrt(TTWP_Mean_S*TTWP_Mean_C)
#     TDWS <- (TTWP_Mean_S/TTWP_Mean_C)*100
  })

return(indextable)
}