R/chill_days.R

In EduardoFernandezC/dormancyR: Functions to Compute Chill Metrics

#' Chill days (Cesaraccio \emph{et al.}, 2004)
#'
#' This function computes the Chill Days according to the model proposed by Cesaraccio \emph{et al.} (2004) developed
#' for several tree species including pears, kiwifruit and sweet cherries. In this function chill days are
#' computed without the negative (-) transformation made in the original paper.
#'
#' @param ExtrDailyTemp Dataframe containing columns "Tmax" and "Tmin". These values must correspond to daily
#' records
#' 
#' @param summ Boolean parameter indicating whether the computed metric should be provided as cumulative values
#' over the period or as the actual accumulation for each hour
#'
#' @references Cesaraccio C., Spano D., Snyder R. and Duce P. 2004. Chilling and forcing model to predict
#' bud - burst of crop and forest species. Agric. For. Meteorol. 126(1-2): 1-13. \href{https://www.sciencedirect.com/science/article/pii/S0168192304000632}{doi:10.1016/j.agrformet.2004.03.002}
#' 
#' @examples
#' library(chillR)
#' 
#' #Example 1
#' 
#' chill_days(KA_weather, summ = TRUE)
#' 
#' #Example 2
#' 
#' data <- KA_weather
#' data[,"Chill_Days"] <- chill_days(data, summ = FALSE)
#' 
#' #Example 3
#' 
#' tempResponse_daily(KA_weather, Start_JDay = 345, End_JDay = 58,
#'                     models = list(Chill_Days = chill_days))
#'                     
#' @export chill_days

chill_days <- function (ExtrDailyTemp, summ = TRUE){
    
  #Threshold used in the model. Several values were reported in the paper according to the trees for which
  #the model was developed. In this case I used values reported for fruit trees (Kiwi, Sweet Cherry and
  #Pears).
  
    threshold <- mean(c(7.0, 6.8, 6.9, 7.0, 7.9, 7.5, 7.0, 7.0, 7.3, 7.1, 7.1, 7.2))
    
  #Computing Tmean from Tmin and Tmax
    
    if (!("Tmean" %in% names(ExtrDailyTemp))) 
      ExtrDailyTemp[,"Tmean"] <- (ExtrDailyTemp["Tmax"] + ExtrDailyTemp["Tmin"]) / 2
    
  #As for Condition 1 (0 <= Threshold <= Tmin <= Tmax) I set the Chill Days as 0 for the whole record and
  #then the relevant days were changed
    
    ExtrDailyTemp[,"Chill_Days"] <- 0 
    
  #Relevant days which fit the condition 2: 0 <= Tmin <= Threshold < Tmax
    
    rel_days_cond2 <- which(ExtrDailyTemp$Tmin >= 0 &
                            ExtrDailyTemp$Tmin <= threshold &
                            threshold < ExtrDailyTemp$Tmax) 
    
    #Value of Chill Days according to the condition 2
    
      ExtrDailyTemp[rel_days_cond2,"Chill_Days"] <- 
        (ExtrDailyTemp[rel_days_cond2,"Tmean"] - 
           ExtrDailyTemp[rel_days_cond2,"Tmin"]) - 
        ((ExtrDailyTemp[rel_days_cond2,"Tmax"] - threshold)^2) /
        (2 * (ExtrDailyTemp[rel_days_cond2,"Tmax"] -
            ExtrDailyTemp[rel_days_cond2,"Tmin"]))
  
  #Relevant days which fit the condition 3: 0 <= Tmin <= Tmax <= Threshold
    
    rel_days_cond3 <- which(0 <= ExtrDailyTemp$Tmin & 
                              threshold >= ExtrDailyTemp$Tmax) 
    
    #Value of Chill Days according to the condition 3
    
      ExtrDailyTemp[rel_days_cond3,"Chill_Days"] <- ExtrDailyTemp[rel_days_cond3,"Tmean"] - 
        ExtrDailyTemp[rel_days_cond3,"Tmin"]
    
  #Relevant days which fit the condition 4: Tmin <= 0 <= Tmax <= Threshold
    
    rel_days_cond4 <- which(ExtrDailyTemp$Tmin < 0 & ExtrDailyTemp$Tmax >= 0 & 
                              threshold >= ExtrDailyTemp$Tmax) 
    
    #Value of Chill Days according to the condition 4
    
      ExtrDailyTemp[rel_days_cond4,"Chill_Days"] <- (ExtrDailyTemp[rel_days_cond4,"Tmax"]^2) /
        (2 * (ExtrDailyTemp[rel_days_cond4,"Tmax"] - ExtrDailyTemp[rel_days_cond4,"Tmin"]))
    
  #Relevant days which fit the condition 5: Tmin < 0 < Threshold < Tmax
    
    rel_days_cond5 <- which(ExtrDailyTemp$Tmin < 0 & threshold > 0 &
                              threshold < ExtrDailyTemp$Tmax) 
    
    #Value of Chill Days according to the condition 5
    
      ExtrDailyTemp[rel_days_cond5,"Chill_Days"] <- (ExtrDailyTemp[rel_days_cond5,"Tmax"]^2) /
        (2 * (ExtrDailyTemp[rel_days_cond5,"Tmax"] - ExtrDailyTemp[rel_days_cond5,"Tmin"])) -
        (((ExtrDailyTemp[rel_days_cond5,"Tmax"] - threshold)^2) /
           (2 * (ExtrDailyTemp[rel_days_cond5,"Tmax"] -
                   ExtrDailyTemp[rel_days_cond5,"Tmin"])))
  
  #End of the function
    if (summ == TRUE)
      return(cumsum(ExtrDailyTemp$Chill_Days)) else return(ExtrDailyTemp$Chill_Days)
}