R/recalculate.R

In cdmuir/bayCi: Bayesian Photosynthetic Response Curves Using Stan

#' Recalculate LI-6800 values
#' 
#' @param .x A \code{data.frame} containing output from the LI-6800.
#' 
#' @examples 
#' 
#' library(bayCi)
#' 
#' @name recalculate
#' @export
#' 
recalc_licor68 <- function(.x) {
  
  message("Constant values printed in the header of the licor output file are ignored in this recalculation.\nThis means that the values for deltaTw (0), fT1 (1), fT2 (0) or fTeb (0) are set as denoted in brackets.")
  
  .x %>%
    dplyr::select(-(.data$A:.data$EBSum)) %>%
    dplyr::mutate(
      E = .data$Flow * .data$CorrFact * (.data$H2O_s - .data$H2O_r) / 
        (100 * .data$S * (1000 - .data$CorrFact * .data$H2O_s)),
      A = .data$Flow * .data$CorrFact * 
        (.data$CO2_r - .data$CO2_s * (1000 - .data$CorrFact * .data$H2O_r) / 
           (1000 - .data$CorrFact * .data$H2O_s)) / (100 * .data$S),
      Ca = .data$CO2_s - 
        ifelse(.data$CorrFact > 1, .data$A * .data$S * 100 / 
                 (.data$Fan * .data$Fan_speed), 0),
      gbw = .data$blfa_3 + .data$blfa_2 * .data$S + .data$blfa_1 * .data$S * .data$S,
      Rabs = (.data$Qabs * .data$convert),
      TleafEB = (.data$Tair + 
                   (.data$Rabs + 2 * 0.95 * 0.0000000567 * 
                      (((.data$Tair + 0) + 273) ^ 4 - (.data$Tair + 273) ^ 4) -
                      44100 * .data$E) / 
                   (1.84 * 29.3 * .data$gbw + 8 * 0.95 * 0.0000000567 * 
                      (.data$Tair + 273) ^ 3)),
      ## n.b. deltaTw set at 0
      TleafCnd = (1 * .data$Tleaf + 0 * .data$Tleaf2 + 0 * .data$TleafEB),
      ## n.b. fT1, fT2 and fTeb set at 1, 0, 0
      gtw = .data$E * 
        (1000 - (1000 * 0.61365 * exp(17.502 * .data$TleafCnd / 
                                        (240.97 + .data$TleafCnd)) / 
                   (.data$Pa + .data$ΔPcham) + .data$H2O_s) / 2) / 
        (1000 * 0.61365 * exp(17.502 * .data$TleafCnd / 
                                (240.97 + .data$TleafCnd)) / 
           (.data$Pa + .data$ΔPcham) - .data$H2O_s),
      gsw = 2 / 
        ((1 / .data$gtw - 1 / .data$gbw) + sign(.data$gtw) * 
           sqrt((1 / .data$gtw - 1 / .data$gbw) * 
                  (1 / .data$gtw - 1 / .data$gbw) + 
                  4 * .data$K / ((.data$K + 1) * (.data$K + 1)) * 
                  (2 * 1 / .data$gtw * 1 / .data$gbw - 
                     1 / .data$gbw * 1 / .data$gbw))),
      gtc = 1 / ((.data$K + 1) / (.data$gsw / 1.6) + 1 / (.data$gbw / 1.37)) + 
        .data$K /((.data$K + 1) / (.data$gsw / 1.6) + 
                    .data$K / (.data$gbw / 1.37)),
      Ci = ((.data$gtc - .data$E / 2) * .data$Ca - .data$A) /
        (.data$gtc + .data$E / 2),
      Pci = .data$Ci * (.data$Pa + .data$ΔPcham) / 1000,
      Pca = (.data$CO2_s - 
               ifelse(.data$CorrFact > 1, .data$A * .data$S * 100 /
                        (.data$Fan * .data$Fan_speed), 0)) * 
        (.data$Pa + .data$ΔPcham) / 1000,
      SVPleaf = 0.61365 * 
        exp(17.502 * .data$TleafCnd / (240.97 + .data$TleafCnd)),
      VPcham = .data$H2O_s * (.data$Pa + .data$ΔPcham) / 1000,
      SVPcham = 0.61365 * exp(17.502 * .data$Tair / (240.97 + .data$Tair)),
      RHcham = (.data$VPcham / .data$SVPcham * 100),
      VPDleaf = (.data$SVPleaf - .data$H2O_s * (.data$Pa + .data$ΔPcham) / 1000),
      LatHFlux = (-.data$E * 44100),
      SenHFlux = 2 * 29.3 * .data$gbw * 0.92 * (.data$Tair - .data$TleafCnd),
      NetTherm = 2 * 0.95 * 0.0000000567 * (((.data$Tair + 0) + 273) ^ 4 - 
                                              (.data$TleafCnd + 273) ^ 4),
      ## n.b. deltaTw set at 0
      EBSum = .data$Rabs + .data$NetTherm + .data$LatHFlux + .data$SenHFlux
    )
  
}