R/recomp_6400.R

In zhujiedong/readphoto: read LI-6800 and LI-6400 raw data file in batch

#' recompute the raw data in one file measured by LI-6400
#' @description help to read all raw data files with a command.
#'
#' @param file_dir is the file directory only contains all the measured
#' raw data.
#' @param data_start the start of your data(without headline)
#' @param header_line ther start of your data with header.
#' @param S area of the leaf measured
#' @param K stomatal ratio
#' @examples
#' \dontrun{
#' library(readphoto)
#' recomp_6400('./6400')
#' }
#'
#' @export
#' 
#' 
recomp_6400 <- function(file_dir, header_line = 17, data_start = 27, S = 6, K = 0.5){
  
  read_bat_6400 <- match.fun(read_bat_6400) 
  
  df <- read_bat_6400(file_dir, header_line = header_line, data_start = data_start)
  
  # A and E in mmol ---------------------------------------------------------
  
  df$Trmmol =df$Flow *(df$H2OS-df$H2OR)/(1000-df$H2OS)/(100*S)*1000
  
  df$Photo = df$Flow*(df$CO2R-df$CO2S*(1000-df$H2OR)/(1000-df$H2OS))/(100*S)
  
  # gtw ---------------------------------------------------------------------
  
  df$SVTleaf = 0.61365*exp(17.502*df$CTleaf/(240.97+df$CTleaf))
  df$h2o_i = df$SVTleaf*1000/df$Press
  df$CndTotal = df$Trmmol*((1000-(df$h2o_i+df$H2OS)/2))/(df$h2o_i-df$H2OS)/1000
  
  
  
  # gbw single side ---------------------------------------------------------
  df$BLC_1=S*df$BLCslope+df$BLCoffst
  
  
  # gsw ---------------------------------------------------------------------
  df$Kf = (K^2+1)/(K+1)^2
  df$Cond = 1/(1/df$CndTotal-df$Kf/df$BLC_1)
  
  
  # Ci ----------------------------------------------------------------------
  df$gtc = 1/(1.6/df$Cond + 1.378*df$Kf/df$BLC_1)
  df$Ci=((df$gtc-df$Trmmol/2000)*df$CO2S-df$Photo)/(df$gtc+df$Trmmol/2000)
  
  return(df)
}