R/f_val_calc_all_driver.R
In erikerhardt/isogasex: Isotopic gas exchange using TDL and Licor input. Updated version of package tdllicor
#' This function calls all of the \code{f_val_calc.*} files
#'
#' SECTION Licor data assign variables
#'
#' SECTION Concentrations.
#'
#' Calibration tank concentrations
#'
#' Calibration tank gain. \code{\link{f_val_calc_gain}}
#'
#' Calibration tank offset. \code{\link{f_val_calc_offset}}
#'
#' Corrected reference values. \code{\link{f_val_calc_corrected}}
#'
#' Corrected chamber values. \code{\link{f_val_calc_corrected}}
#'
#' Total reference and chamber values. \code{\link{f_val_calc_total_mol_fraction_CO2}}
#'
#' xi. \code{\link{f_val_calc_xi}}
#'
#' SECTION A Photosynthesis
#'
#' A, TDL photosynthesis. \code{\link{f_val_calc_TDL_A_photosynthesis}}
#'
#' 12A, TDL photosynthesis. \code{\link{f_val_calc_TDL_A_photosynthesis}}
#'
#' 13A, TDL photosynthesis. \code{\link{f_val_calc_TDL_A_photosynthesis}}
#'
#' Total A LI6400 Photo LI6400 header, these values listed because I will likely use them in a plot
#'
#' Delta from ratios in and out?, (Re/Ro)-1, is this really the same? \code{\link{f_val_calc_Delta_from_ratios_in_out}}
#'
#' D from A ratio, (Ro/(13A/12A))-1, should be the same as Dobs above. \code{\link{f_val_calc_Delta_from_A_ratio}}
#'
#' Select TDL or Licor based on switch
#'
#' SECTION Delta
#'
#' delta reference and chamber values. \code{\link{f_val_calc_delta_proportion}}
#'
#' delta diff
#'
#' Delta discrim
#'
#' Dobs observed discrimination. \code{\link{f_val_calc_Delta_obs}}
#'
#' Dobs per mil 1000*Dobs. \code{\link{f_val_calc_Delta_obs_permil}}
#'
#' delta13C Assimilated, isotopic composition of assimilated sugars. \code{\link{f_val_calc_delta_13C_Assim}}
#'
#' p (Co - Ce) / Co. \code{\link{f_val_calc_p}}
#'
#' delta13C Respired, isotopic composition of respired CO2. \code{\link{f_val_calc_delta_13C_Resp}}
#'
#' SECTION g conductance
#'
#' gbw BLcond boundary layer conductance for water, Blcond is LI 6400 header
#'
#' gbc BLcond/1.37 boundary layer conductance for CO2
#'
#' gsw cond stomatal conductance for water, cond is LI6400 header
#'
#' gsc gsw/1.6 stomatal conductance for CO2
#'
#' gtc, total (stomatal and boundary layer) conductance for CO2
#'
#' SECTION Cx and px (concentrations and pressures)
#'
#' Ca = Co, ppm CO2 concentration above the leaf = concentration leaving the leaf chamber = ambient CO2 concentration
#'
#' Cs, ppm CO2 concentration at the leaf surface, cs calculated from eq 40 Ball 1987 Ch 20 Stomatal Function, eds Zeiger, Farquhar, Cowan. \code{\link{f_val_calc_Cs}}
#'
#' pa, partial pressure of CO2 above the leaf, Press is the atmospheric pressure value from the LI6400. \code{\link{f_val_calc_pp}}
#'
#' ps, partial pressure of CO2 at the leaf surface, Press is the atmospheric pressure value from the LI6400. \code{\link{f_val_calc_pp}}
#' NB: same formula as pa, but using Cs instead of Co
#'
#' Ci, ppm CO2 concentration in the sub-stomatal cavities, ci calculated from eq 35 Ball 1987 Ch 20 Stomatal Function, eds Zeiger, Farquhar, Cowan. \code{\link{f_val_calc_Cs}}
#' NB: same formula as Cs, but using gtc instead of gbc
#'
#' pi, partial pressure of CO2 in the substomatal cavities, Press is the atmospheric pressure value from the LI6400. \code{\link{f_val_calc_pp}}
#' NB: same formula as pa, but using Ci instead of Co
#'
#' pi/pa total pi/pa or total Ci/Ca ratio of substomatal CO2 partial pressure to CO2 partial pressure above leaf = Ci/Ca ratio of mol fractions
#'
#' SECTION Delta_i predictions
#'
#' Delta_i simple for gm, predicted discrimination including boundary layer effects but not decarboxylation effects. \code{\link{f_val_calc_Delta_i_simple_for_gm}}
#'
#' Delta_i simple for modeling a + (b-a) pi/pa predicted discrimination including boundary layer effects but using b adjustments to approximate effects of gm and decarboxylations. \code{\link{f_val_calc_Delta_i_simple_for_modeling}}
#'
#' Delta_i complex for gm CHECK DERIVATION predicted discrimination including boundary layer effects AND decarboxylation effects. \code{\link{f_val_calc_Delta_i_complex_for_gm}}
#'
#' Delta_i simple for gm-Dobs (Di simple for gm)-(Dobs per mil)
#'
#' Delta_i complex for gm-Dobs (Di complex for gm)-(Dobs per mil)
#'
#' SECTION gm mesophyll conductance
#'
#' gm point simple, internal leaf (mesophyll) conductance calculated for every D value ignoring decarboxylation effects. \code{\link{f_val_calc_gm_point_simple}}
#'
#' gm point complex, internal leaf (mesophyll) conductance calculated for every D value estimating decarboxylation effects. \code{\link{f_val_calc_gm_point_complex}}
#'
#' select one of the calculated gm values to use
#'
#' SECTION pc
#'
#' pc using gm, total partial pressure of CO2 at the site of carboxylation, Press is the atmospheric pressure value from the LI6400. \code{\link{f_val_calc_pc_using_gm}}
#'
#' pc using simple D for gm, includes boundary layer. \code{\link{f_val_calc_pc_using_simple_Delta_for_gm}}
#'
#' pc using simple D for modeling. \code{\link{f_val_calc_pc_using_simple_Delta_for_modeling}}
#'
#' pc using complex D, no decarboxylation [ab(pa-ps)+a(ps-pi)+pi(bs+al)-Dpa]/(bs+al-b) is this different from two up? They give different values but both may not be derived properly. \code{\link{f_val_calc_pc_using_complex_Delta_no_decarboxylation}}
#'
#' pc using complex D, full model [ab(pa-ps)+a(ps-pi)+pi(bs+al)-(eRd/k+fG*)-Dpa]/(bs+al-b) includes boundary layer and decarboxylation effects. \code{\link{f_val_calc_pc_using_complex_Delta_full_model}}
#'
#' select one of the calculated pc values to use
#'
#' Cc (pc*10^6)/(Press*1000) ppm CO2 concentration at the site of carboxylation, generally meaning inside the chloroplast and ignoring PEPC in cytosol. \code{\link{f_val_calc_pp}}
#' NB: same formula as pa, but using pc instead of Co
#'
#' @param val_TDL xxxPARAMxxx
#' @param val_Licor xxxPARAMxxx
#' @param val_const xxxPARAMxxx
#' @param sw xxxPARAMxxx
#'
#' @return val_temp xxxRETURNxxx
#'
f_val_calc_all_driver <-
function# This function calls all the \code{f_val_calc.*} files
(val_TDL
###
, val_Licor
###
, val_const
###
, sw
###
)
{
# DEBUG DEBUG DEBUG DEBUG DEBUG
# val_TDL <- val$sum$TDL;
# val_Licor <- val$sum$Licor;
# val_const <- val$const;
#
# val_TDL <- val$obs$TDL;
# val_Licor <- val$obs$Licor;
# val_const <- val$const;
# DEBUG DEBUG DEBUG DEBUG DEBUG
val_temp <- list(); # hold current set of calculated values below
#-------------------
##details<<
## SECTION Licor data assign_variables
# LICOR DATA SECTION (moved from bottom to top 9/5/2012, so Licor_flow_uin can replace flow_adjusted)
# VPD VpdL LI6400 header, these values listed because I will likely use them in a plot
val_temp$VPD <- val_Licor$VPD;
# Transpiration Trmmol LI6400 header, these values listed because I will likely use them in a plot
val_temp$E_transpiration <- val_Licor$E;
# Leaf Temp Tleaf LI6400 header, these values listed because I will likely use them in a plot
val_temp$leaf_temp <- val_Licor$temp_leaf;
# Air Temp ? Tair LI6400 header, these values listed because I will likely use them in a plot
val_temp$air_temp <- val_Licor$temp_air;
# Light in PARi LI6400 header, these values listed because I will likely use them in a plot
val_temp$light_in <- val_Licor$par_int;
# Light out PARo LI6400 header, these values listed because I will likely use them in a plot
val_temp$light_out <- val_Licor$par_ext;
# 7/21/2012 added Licor var to save
val_temp$Licor_flow_uin <- val_Licor$uin ;
val_temp$Licor_H2OR_xin <- val_Licor$xin ;
val_temp$Licor_La <- val_Licor$La ;
val_temp$Licor_Atm_press <- val_Licor$Atm_press ;
val_temp$Licor_gsc <- val_Licor$gsc ;
val_temp$Licor_Ci <- val_Licor$Ci ;
val_temp$Licor_StmRat <- val_Licor$StmRat ;
val_temp$Licor_gbw <- val_Licor$gbw ;
val_temp$Licor_temp_block <- val_Licor$temp_block ;
val_temp$Licor_Ce <- val_Licor$Ce ;
val_temp$Licor_Co <- val_Licor$Co ;
val_temp$Licor_xout <- val_Licor$xout ;
val_temp$Licor_rh_ref <- val_Licor$rh_ref ;
val_temp$Licor_rh_sam <- val_Licor$rh_sam ;
val_temp$Licor_CsMch <- val_Licor$CsMch ;
val_temp$Licor_HsMch <- val_Licor$HsMch ;
val_temp$Licor_StableF <- val_Licor$StableF ;
val_temp$Licor_Status <- val_Licor$Status ;
# typically not used
# ,"VpdA"
# ,"Ci_Ca"
# ,"pi"
# ,"uc_20_mV"
# ,"uc_21_mV"
# ,"U_S"
# ,"Trans"
# ,"CndCO2"
# ,"Ref_mV"
# ,"xTemp1"
# ,"xTemp2"
#-------------------
##details<<
## SECTION Concentrations.
# also include interp concentration values "0.1-16" "2012-07-10"
##details<<
## Calibration tank concentrations
val_temp$tank_hi_12 <- val_TDL$interp_tank_hi_12 ;
val_temp$tank_hi_13 <- val_TDL$interp_tank_hi_13 ;
val_temp$tank_low_12 <- val_TDL$interp_tank_low_12;
val_temp$tank_low_13 <- val_TDL$interp_tank_low_13;
##details<<
## Calibration tank gain. \code{\link{f_val_calc_gain}}
temp_gain <-
f_val_calc_gain( val_const$true_value_hi_12C, val_const$true_value_hi_13C, val_const$true_value_lo_12C, val_const$true_value_lo_13C
,val_TDL$interp_tank_hi_12, val_TDL$interp_tank_hi_13, val_TDL$interp_tank_low_12, val_TDL$interp_tank_low_13);
val_temp$gain_12C <- temp_gain$gain_12C;
val_temp$gain_13C <- temp_gain$gain_13C;
##details<<
## Calibration tank offset. \code{\link{f_val_calc_offset}}
temp_offset <-
f_val_calc_offset( val_const$true_value_hi_12C, val_const$true_value_hi_13C
,val_temp$gain_12C, val_temp$gain_13C
,val_TDL$interp_tank_hi_12, val_TDL$interp_tank_hi_13);
val_temp$offset_12C <- temp_offset$offset_12C;
val_temp$offset_13C <- temp_offset$offset_13C;
# # Plot active gains, offsets, and corrected magnitudes
# p_o <- paste("Plot active gains, offsets, and corrected magnitudes\n"); wWw <- write_progress(p_o, time_start);
#plot_gain_offset(val_temp$gain_12C, val_temp$gain_13C, val_temp$offset_12C, val_temp$offset_13C, val_TDL$time, plot_format_list);
##details<<
## Corrected reference values. \code{\link{f_val_calc_corrected}}
# 12Ce 12C Site 1 reference Ce is the ppm CO2 concentration entering the leaf chamber, equivalent terms: reference, Site 1, CO2R
# 13Ce 13C Site 1 reference
temp_corrected <-
f_val_calc_corrected(val_TDL$interp_reference_12, val_TDL$interp_reference_13
,val_temp$gain_12C, val_temp$gain_13C
,val_temp$offset_12C, val_temp$offset_13C)
val_temp$reference_12Ce <- temp_corrected$corrected_12C;
val_temp$reference_13Ce <- temp_corrected$corrected_13C;
##details<<
## Corrected chamber values. \code{\link{f_val_calc_corrected}}
# 12Co 12C Site 21 chamber Co is the outgoing ppm CO2 concentration from the leaf chamber: sample, Site 21, CO2S, Ca, also air above the leaf
# 13Co 13C Site 21 chamber
temp_corrected <-
f_val_calc_corrected(val_TDL$chamber_12, val_TDL$chamber_13
,val_temp$gain_12C, val_temp$gain_13C
,val_temp$offset_12C, val_temp$offset_13C)
val_temp$chamber_12Co <- temp_corrected$corrected_12C;
val_temp$chamber_13Co <- temp_corrected$corrected_13C;
##details<<
## Total reference and chamber values. \code{\link{f_val_calc_total_mol_fraction_CO2}}
# Total Ce Total Site 1
# Total Co Total Site 21
val_temp$reference_TotalCe <-
f_val_calc_total_mol_fraction_CO2(val_temp$reference_12Ce, val_temp$reference_13Ce, val_const$fo_13C);
val_temp$chamber_TotalCo <-
f_val_calc_total_mol_fraction_CO2(val_temp$chamber_12Co, val_temp$chamber_13Co, val_const$fo_13C);
# Ce-Co Total Site 1 - Total Site 21 I like having this as an output for diagnostics
val_temp$chamber_reference_Total_diff_CeCo <- val_temp$reference_TotalCe - val_temp$chamber_TotalCo;
val_temp$chamber_reference_12_diff_CeCo <- val_temp$reference_12Ce - val_temp$chamber_12Co;
val_temp$chamber_reference_13_diff_CeCo <- val_temp$reference_13Ce - val_temp$chamber_13Co;
##details<<
## xi. \code{\link{f_val_calc_xi}}
# xi Ce/(Ce-Co) I like having this as an output for diagnostics
val_temp$xi <-
f_val_calc_xi(val_temp$reference_TotalCe, val_temp$chamber_TotalCo)
# # Plot corrected 12CO2 and 13CO2, total, and difference for reference and sample
# p_o <- paste("Plot corrected 12CO2 and 13CO2, total, and difference for reference and sample\n"); wWw <- write_progress(p_o, time_start);
#plot_corrected_total_diff_xi( val_temp$reference_12Ce, val_temp$reference_13Ce
# ,val_temp$chamber_12Co, val_temp$chamber_13Co
# ,val_temp$reference_TotalCe, val_temp$chamber_TotalCo
# ,val_temp$chamber_reference_Total_diff_CeCo, val_temp$xi, val_TDL$time, plot_format_list);
#-------------------
##details<<
## SECTION A Photosynthesis
# # Deprecated (0.1-20, 9/5/2012) ##
# Adjusted flow, LI6400 flow includes water in the entering air but the TDL removes this water before measuring and this effectively reduces the flow (use H2OR to correct it)
#val_temp$flow_adjusted <- # 9/5/2012
# f_val_calc_flow_adjusted(val_Licor$uin, val_Licor$xin); # 9/5/2012
##details<<
## A, TDL photosynthesis. \code{\link{f_val_calc_TDL_A_photosynthesis}}
val_temp$TDL_A_photosynthesis <-
#f_val_calc_TDL_A_photosynthesis( val_temp$flow_adjusted, val_temp$reference_TotalCe # 9/5/2012
f_val_calc_TDL_A_photosynthesis( val_temp$Licor_flow_uin, val_temp$reference_TotalCe # 9/5/2012
,val_temp$chamber_TotalCo, val_Licor$La);
##details<<
## 12A, TDL photosynthesis. \code{\link{f_val_calc_TDL_A_photosynthesis}}
val_temp$TDL_12A_photosynthesis <-
#f_val_calc_TDL_A_photosynthesis( val_temp$flow_adjusted, val_temp$reference_12Ce # 9/5/2012
f_val_calc_TDL_A_photosynthesis( val_temp$Licor_flow_uin, val_temp$reference_12Ce # 9/5/2012
,val_temp$chamber_12Co, val_Licor$La);
##details<<
## 13A, TDL photosynthesis. \code{\link{f_val_calc_TDL_A_photosynthesis}}
val_temp$TDL_13A_photosynthesis <-
#f_val_calc_TDL_A_photosynthesis( val_temp$flow_adjusted, val_temp$reference_13Ce # 9/5/2012
f_val_calc_TDL_A_photosynthesis( val_temp$Licor_flow_uin, val_temp$reference_13Ce # 9/5/2012
,val_temp$chamber_13Co, val_Licor$La);
##details<<
## Total A LI6400 Photo LI6400 header, these values listed because I will likely use them in a plot
val_temp$Licor_A_photosynthesis <- val_Licor$A;
##details<<
## Delta from ratios in and out?, (Re/Ro)-1, is this really the same? \code{\link{f_val_calc_Delta_from_ratios_in_out}}
val_temp$Delta_from_ratios_in_out <-
f_val_calc_Delta_from_ratios_in_out( val_temp$reference_12Ce, val_temp$reference_13Ce
,val_temp$chamber_12Co, val_temp$chamber_13Co)
##details<<
## D from A ratio, (Ro/(13A/12A))-1, should be the same as Dobs above. \code{\link{f_val_calc_Delta_from_A_ratio}}
val_temp$Delta_from_A_ratio <-
f_val_calc_Delta_from_A_ratio( val_temp$chamber_12Co, val_temp$chamber_13Co
,val_temp$TDL_12A_photosynthesis, val_temp$TDL_13A_photosynthesis)
##details<<
## Select TDL or Licor based on switch
# switch added for A_photosynthesis 9/5/2012
if (sw$Licor_or_TDL_A_photosynthesis == 0) { # Licor
# use Licor
val_temp$selected_A_photosynthesis <- val_temp$Licor_A_photosynthesis;
val_temp$selected_12A_photosynthesis <- rep(NA, length(val_temp$TDL_12A_photosynthesis));
val_temp$selected_13A_photosynthesis <- rep(NA, length(val_temp$TDL_13A_photosynthesis));
#val_temp$TDL_A_photosynthesis <- rep(NA, length(val_temp$TDL_A_photosynthesis ));
#val_temp$TDL_12A_photosynthesis <- rep(NA, length(val_temp$TDL_12A_photosynthesis));
#val_temp$TDL_13A_photosynthesis <- rep(NA, length(val_temp$TDL_13A_photosynthesis));
}
if (sw$Licor_or_TDL_A_photosynthesis == 1) { # TDL
# use TDL
val_temp$selected_A_photosynthesis <- val_temp$TDL_A_photosynthesis ;
val_temp$selected_12A_photosynthesis <- val_temp$TDL_12A_photosynthesis;
val_temp$selected_13A_photosynthesis <- val_temp$TDL_13A_photosynthesis;
#val_temp$Licor_A_photosynthesis <- rep(NA, length(val_temp$Licor_A_photosynthesis));
}
# # Plot A photosynthesis
# p_o <- paste("Plot A photosynthesis\n"); wWw <- write_progress(p_o, time_start);
#plot_A_photosynthesis( val_temp$TDL_A_photosynthesis, val_temp$TDL_12A_photosynthesis, val_temp$TDL_13A_photosynthesis
# ,val_temp$Licor_A_photosynthesis, val_temp$Delta_from_ratios_in_out, val_temp$Delta_from_A_ratio
# ,val_TDL$time, plot_format_list)
#
# # Plot Licor Temp Light values
# p_o <- paste("Plot Licor Temp Light values\n"); wWw <- write_progress(p_o, time_start);
#plot_Licor_temp_light(val_temp$VPD, val_temp$E_transpiration, val_temp$leaf_temp, val_temp$air_temp
# ,val_temp$light_in, val_temp$light_out, val_temp$flow_adjusted
# ,val_TDL$time, plot_format_list)
#-------------------
##details<<
## SECTION Delta
##details<<
## delta reference and chamber values. \code{\link{f_val_calc_delta_proportion}}
# de d13C Site 1
val_temp$reference_delta_e <-
f_val_calc_delta_proportion(val_temp$reference_12Ce, val_temp$reference_13Ce, val_const$Rstd_13C);
# do d13C Site 21
val_temp$chamber_delta_o <-
f_val_calc_delta_proportion(val_temp$chamber_12Co, val_temp$chamber_13Co, val_const$Rstd_13C);
##details<<
## delta diff
# do-de d Site 21 - d Site 1 I like having this as an output for diagnostics
val_temp$chamber_reference_delta_diff_CoCe <- val_temp$chamber_delta_o - val_temp$reference_delta_e;
##details<<
## Delta discrim
##details<<
## Dobs observed discrimination. \code{\link{f_val_calc_Delta_obs}}
val_temp$Delta_obs <-
f_val_calc_Delta_obs(val_temp$reference_delta_e, val_temp$chamber_delta_o, val_temp$xi)
##details<<
## Dobs per mil 1000*Dobs. \code{\link{f_val_calc_Delta_obs_permil}}
val_temp$Delta_obs_permil <-
f_val_calc_Delta_obs_permil(val_temp$reference_delta_e, val_temp$chamber_delta_o, val_temp$xi)
##details<<
## delta13C Assimilated, isotopic composition of assimilated sugars. \code{\link{f_val_calc_delta_13C_Assim}}
val_temp$delta_13C_Assim <-
f_val_calc_delta_13C_Assim(val_temp$chamber_delta_o, val_temp$Delta_obs)
##details<<
## p (Co - Ce) / Co. \code{\link{f_val_calc_p}}
val_temp$p <-
f_val_calc_p(val_temp$reference_TotalCe, val_temp$chamber_TotalCo)
##details<<
## delta13C Respired, isotopic composition of respired CO2. \code{\link{f_val_calc_delta_13C_Resp}}
val_temp$delta_13C_Resp <-
f_val_calc_delta_13C_Resp(val_temp$reference_delta_e, val_temp$chamber_delta_o, val_temp$p)
# # Plot delta, Delta, and p
# p_o <- paste("Plot delta, Delta, and p\n"); wWw <- write_progress(p_o, time_start);
#plot_delta_Delta_p( val_temp$reference_delta_e, val_temp$chamber_delta_o, val_temp$chamber_reference_delta_diff_CoCe
# ,val_temp$Delta_obs, val_temp$p, val_temp$delta_13C_Assim, val_temp$delta_13C_Resp
# , val_TDL$time, plot_format_list)
#-------------------
##details<<
## SECTION g conductance
# 9/6/2012 moved above Cs when fixed it's calculation
##details<<
## gbw BLcond boundary layer conductance for water, Blcond is LI 6400 header
val_temp$chamber_Totalgbw <- val_Licor$gbw;
##details<<
## gbc BLcond/1.37 boundary layer conductance for CO2
val_temp$chamber_Totalgbc <- val_Licor$gbw / val_const$gbc_1.37;
val_temp$chamber_12gbc <- val_temp$chamber_Totalgbc;
val_temp$chamber_13gbc <- val_temp$chamber_Totalgbc / (1 + (val_const$a_b / 1000));
##details<<
## gsw cond stomatal conductance for water, cond is LI6400 header
val_temp$chamber_Totalgsw <- val_Licor$gsc;
##details<<
## gsc gsw/1.6 stomatal conductance for CO2
val_temp$chamber_Totalgsc <- val_temp$chamber_Totalgsw / val_const$gsc_1.6;
val_temp$chamber_12gsc <- val_temp$chamber_Totalgsc;
val_temp$chamber_13gsc <- val_temp$chamber_Totalgsc / (1 + (val_const$a_b / 1000));
##details<<
## gtc, total (stomatal and boundary layer) conductance for CO2
val_temp$chamber_Totalgtc <- f_val_calc_gtc( val_temp$chamber_Totalgbc, val_temp$chamber_Totalgsc);
val_temp$chamber_12gtc <- val_temp$chamber_Totalgtc;
val_temp$chamber_13gtc <- f_val_calc_gtc( val_temp$chamber_13gbc, val_temp$chamber_13gsc);
# # Plot gbc, gsc, gtc: boundary layer, stomatal, and total conductance for CO2
# p_o <- paste("Plot gbc, gsc, gtc: boundary layer, stomatal, and total conductance for CO2\n"); wWw <- write_progress(p_o, time_start);
#plot_gbc_gsc_gtc(val_temp$chamber_Totalgbc, val_temp$chamber_13gbc
# ,val_temp$chamber_Totalgsc, val_temp$chamber_13gsc
# ,val_temp$chamber_Totalgtc, val_temp$chamber_13gtc
# ,val_TDL$time, plot_format_list)
#-------------------
##details<<
## SECTION Cx and px (concentrations and pressures)
##details<<
## Ca = Co, ppm CO2 concentration above the leaf = concentration leaving the leaf chamber = ambient CO2 concentration
val_temp$chamber_TotalCa <- val_temp$chamber_TotalCo;
val_temp$chamber_12Ca <- val_temp$chamber_12Co ;
val_temp$chamber_13Ca <- val_temp$chamber_13Co ;
##details<<
## Cs, ppm CO2 concentration at the leaf surface, cs calculated from eq 40 Ball 1987 Ch 20 Stomatal Function, eds Zeiger, Farquhar, Cowan. \code{\link{f_val_calc_Cs}}
#val_temp$chamber_TotalCs <- f_val_calc_Cs(val_Licor$gbw, val_Licor$E, val_temp$chamber_TotalCo, val_temp$TDL_A_photosynthesis);
#val_temp$chamber_12Cs <- f_val_calc_Cs(val_Licor$gbw, val_Licor$E, val_temp$chamber_12Co , val_temp$TDL_A_photosynthesis);
#val_temp$chamber_13Cs <- f_val_calc_Cs(val_Licor$gbw, val_Licor$E, val_temp$chamber_13Co , val_temp$TDL_A_photosynthesis);
# 7/28/2012 Using A from Licor until test effect of using A from TDL
# switch added for A_photosynthesis 9/5/2012
# fixed calculation of Cs, was using val_Licor$gbc before I changed name to gbw 9/6/2012
val_temp$chamber_TotalCs <- f_val_calc_Cs(val_temp$chamber_Totalgbc, val_Licor$E, val_temp$chamber_TotalCo, val_temp$selected_A_photosynthesis);
val_temp$chamber_12Cs <- f_val_calc_Cs(val_temp$chamber_12gbc , val_Licor$E, val_temp$chamber_12Co , val_temp$selected_12A_photosynthesis);
val_temp$chamber_13Cs <- f_val_calc_Cs(val_temp$chamber_13gbc , val_Licor$E, val_temp$chamber_13Co , val_temp$selected_13A_photosynthesis);
# # Plot Ca Cs, CO2 concentrations above the leaf and at the leaf surface
# p_o <- paste("Plot Ca Cs, CO2 concentrations above the leaf and at the leaf surface\n"); wWw <- write_progress(p_o, time_start);
#plot_Ca_Cs(val_temp$chamber_TotalCa, val_temp$chamber_12Ca, val_temp$chamber_13Ca
# ,val_temp$chamber_TotalCs, val_temp$chamber_12Cs, val_temp$chamber_13Cs
# ,val_TDL$time, plot_format_list)
##details<<
## pa, partial pressure of CO2 above the leaf, Press is the atmospheric pressure value from the LI6400. \code{\link{f_val_calc_pp}}
val_temp$chamber_Totalpa <- f_val_calc_pp(val_temp$chamber_TotalCo, val_Licor$Atm_press);
val_temp$chamber_12pa <- f_val_calc_pp(val_temp$chamber_12Co , val_Licor$Atm_press);
val_temp$chamber_13pa <- f_val_calc_pp(val_temp$chamber_13Co , val_Licor$Atm_press);
##details<<
## ps, partial pressure of CO2 at the leaf surface, Press is the atmospheric pressure value from the LI6400. \code{\link{f_val_calc_pp}}
## NB: same formula as pa, but using Cs instead of Co
val_temp$chamber_Totalps <- f_val_calc_pp(val_temp$chamber_TotalCs, val_Licor$Atm_press);
val_temp$chamber_12ps <- f_val_calc_pp(val_temp$chamber_12Cs , val_Licor$Atm_press);
val_temp$chamber_13ps <- f_val_calc_pp(val_temp$chamber_13Cs , val_Licor$Atm_press);
# # Plot Pa Ps, partial pressure of CO2 above the leaf and at the leaf surface
# p_o <- paste("Plot Pa Ps, partial pressure of CO2 above the leaf and at the leaf surface\n"); wWw <- write_progress(p_o, time_start);
#plot_pa_ps(val_temp$chamber_Totalpa, val_temp$chamber_12pa, val_temp$chamber_13pa
# ,val_temp$chamber_Totalps, val_temp$chamber_12ps, val_temp$chamber_13ps
# ,val_TDL$time, plot_format_list)
##details<<
## Ci, ppm CO2 concentration in the sub-stomatal cavities, ci calculated from eq 35 Ball 1987 Ch 20 Stomatal Function, eds Zeiger, Farquhar, Cowan. \code{\link{f_val_calc_Cs}}
## NB: same formula as Cs, but using gtc instead of gbc
#val_temp$chamber_TotalCi <- f_val_calc_Cs(val_temp$chamber_Totalgtc, val_Licor$E, val_temp$chamber_TotalCo, val_temp$TDL_A_photosynthesis);
#val_temp$chamber_12Ci <- f_val_calc_Cs(val_temp$chamber_12gtc, val_Licor$E, val_temp$chamber_12Co , val_temp$TDL_A_photosynthesis);
#val_temp$chamber_13Ci <- f_val_calc_Cs(val_temp$chamber_13gtc, val_Licor$E, val_temp$chamber_13Co , val_temp$TDL_A_photosynthesis);
# 7/28/2012 Using A from Licor until test effect of using A from TDL
# switch added for A_photosynthesis 9/5/2012
val_temp$chamber_TotalCi <- f_val_calc_Cs(val_temp$chamber_Totalgtc, val_Licor$E, val_temp$chamber_TotalCo, val_temp$selected_A_photosynthesis);
val_temp$chamber_12Ci <- f_val_calc_Cs(val_temp$chamber_12gtc, val_Licor$E, val_temp$chamber_12Co , val_temp$selected_12A_photosynthesis);
val_temp$chamber_13Ci <- f_val_calc_Cs(val_temp$chamber_13gtc, val_Licor$E, val_temp$chamber_13Co , val_temp$selected_13A_photosynthesis);
##details<<
## pi, partial pressure of CO2 in the substomatal cavities, Press is the atmospheric pressure value from the LI6400. \code{\link{f_val_calc_pp}}
## NB: same formula as pa, but using Ci instead of Co
val_temp$chamber_Totalpi <- f_val_calc_pp(val_temp$chamber_TotalCi, val_Licor$Atm_press);
val_temp$chamber_12pi <- f_val_calc_pp(val_temp$chamber_12Ci , val_Licor$Atm_press);
val_temp$chamber_13pi <- f_val_calc_pp(val_temp$chamber_13Ci , val_Licor$Atm_press);
# # Plot Ci, Pi, CO2 concentration and partial pressure of CO2 in the substomatal cavities
# p_o <- paste("Plot Ci, pi, CO2 concentration and partial pressure of CO2 in the substomatal cavities\n"); wWw <- write_progress(p_o, time_start);
#plot_Ci_pi(val_temp$chamber_TotalCi, val_temp$chamber_12Ci, val_temp$chamber_13Ci
# ,val_temp$chamber_Totalpi, val_temp$chamber_12pi, val_temp$chamber_13pi
# ,val_TDL$time, plot_format_list)
#-------------------
##details<<
## pi/pa total pi/pa or total Ci/Ca ratio of substomatal CO2 partial pressure to CO2 partial pressure above leaf = Ci/Ca ratio of mol fractions
val_temp$chamber_Totalpi_pa <- val_temp$chamber_Totalpi / val_temp$chamber_Totalpa;
# # Plot Totalpi_pa, ratio of substomatal CO2 partial pressure to CO2 partial pressure above leaf = Ci/Ca ratio of mol fractions
# p_o <- paste("Plot Totalpi_pa, ratio of substomatal CO2 partial pressure to CO2 partial pressure above leaf\n"); wWw <- write_progress(p_o, time_start);
#plot_pi_pa(val_temp$chamber_Totalpi, val_temp$chamber_Totalpa, val_temp$chamber_Totalpi_pa
# ,val_TDL$time, plot_format_list)
#-------------------
##details<<
## SECTION Delta_i predictions
##details<<
## Delta_i simple for gm, predicted discrimination including boundary layer effects but not decarboxylation effects. \code{\link{f_val_calc_Delta_i_simple_for_gm}}
val_temp$chamber_Delta_i_simple_for_gm <-
f_val_calc_Delta_i_simple_for_gm( val_const$a, val_const$b_gm, val_const$a_b
,val_temp$chamber_Totalpa, val_temp$chamber_Totalps, val_temp$chamber_Totalpi)
##details<<
## Delta_i simple for modeling a + (b-a) pi/pa predicted discrimination including boundary layer effects but using b adjustments to approximate effects of gm and decarboxylations. \code{\link{f_val_calc_Delta_i_simple_for_modeling}}
val_temp$chamber_Delta_i_simple_for_modeling <-
f_val_calc_Delta_i_simple_for_modeling( val_const$a, val_const$b_modeling
,val_temp$chamber_Totalpa, val_temp$chamber_Totalpi)
##details<<
## Delta_i complex for gm CHECK DERIVATION predicted discrimination including boundary layer effects AND decarboxylation effects. \code{\link{f_val_calc_Delta_i_complex_for_gm}}
val_temp$chamber_Delta_i_complex_for_gm <-
f_val_calc_Delta_i_complex_for_gm( val_const$a, val_const$b_gm, val_const$a_b
,val_temp$chamber_Totalpa, val_temp$chamber_Totalps, val_temp$chamber_Totalpi
,val_const$b_gm
,val_const$f_photo_respiration, val_const$Gamma_star
,val_const$e, val_const$Rd, val_const$k);
# CAN PROBABLY REMOVE THIS COMMENTED CODE TO SELECT DELTA_i
# # select one of the calculated Delta_i values to use
#val_temp$chamber_Delta_i_to_use <- NULL; # as default
#switch(sw$calc_Delta_i_to_use
# # 1 = Delta_i_simple_for_gm
# , val_temp$chamber_Delta_i_to_use <- val_temp$chamber_Delta_i_simple_for_gm
# # 2 = Delta_i_simple_for_modeling
# , val_temp$chamber_Delta_i_to_use <- val_temp$chamber_Delta_i_simple_for_modeling
# # 3 = Delta_i_complex_for_gm
# , val_temp$chamber_Delta_i_to_use <- val_temp$chamber_Delta_i_complex_for_gm
# );
#-------------------
##details<<
## Delta_i simple for gm-Dobs (Di simple for gm)-(Dobs per mil)
val_temp$chamber_Delta_i_simple_for_gm_Delta_obs <-
val_temp$chamber_Delta_i_simple_for_gm - val_temp$Delta_obs_permil; # val_temp$Delta_obs_permil; # 8/19/2011
##details<<
## Delta_i complex for gm-Dobs (Di complex for gm)-(Dobs per mil)
val_temp$chamber_Delta_i_complex_for_gm_Delta_obs <-
val_temp$chamber_Delta_i_complex_for_gm - val_temp$Delta_obs_permil; # val_temp$Delta_obs_permil; # 8/19/2011
# # Plot Delta_i, predicted discrimination
# p_o <- paste("Plot Delta_i, predicted discrimination\n"); wWw <- write_progress(p_o, time_start);
#plot_Delta_i(val_temp$chamber_Delta_i_simple_for_gm, val_temp$chamber_Delta_i_simple_for_modeling, val_temp$chamber_Delta_i_complex_for_gm
# ,val_temp$chamber_Delta_i_simple_for_gm_Delta_obs, val_temp$chamber_Delta_i_complex_for_gm_Delta_obs
# ,val_TDL$time, plot_format_list)
#-------------------
##details<<
## SECTION gm mesophyll conductance
##details<<
## gm point simple, internal leaf (mesophyll) conductance calculated for every D value ignoring decarboxylation effects. \code{\link{f_val_calc_gm_point_simple}}
val_temp$chamber_Totalgm_point_simple <-
# switch added for A_photosynthesis 9/5/2012
#f_val_calc_gm_point_simple( val_const$b_gm, val_const$b_s, val_const$a_l, val_Licor$A
f_val_calc_gm_point_simple( val_const$b_gm, val_const$b_s, val_const$a_l, val_temp$selected_A_photosynthesis
,val_temp$chamber_Totalpa, val_temp$chamber_Delta_i_simple_for_gm, val_temp$Delta_obs_permil); # 8/19/2011 use permil
# switch added for A_photosynthesis 9/5/2012
#val_temp$chamber_12gm_point_simple <- val_temp$chamber_Totalgm_point_simple;
val_temp$chamber_12gm_point_simple <-
f_val_calc_gm_point_simple( val_const$b_gm, val_const$b_s, val_const$a_l, val_temp$selected_12A_photosynthesis
,val_temp$chamber_12pa, val_temp$chamber_Delta_i_simple_for_gm, val_temp$Delta_obs_permil);
val_temp$chamber_13gm_point_simple <-
# switch added for A_photosynthesis 9/5/2012
#f_val_calc_gm_point_simple( val_const$b_gm, val_const$b_s, val_const$a_l, val_temp$TDL_13A_photosynthesis
f_val_calc_gm_point_simple( val_const$b_gm, val_const$b_s, val_const$a_l, val_temp$selected_13A_photosynthesis
,val_temp$chamber_13pa, val_temp$chamber_Delta_i_simple_for_gm, val_temp$Delta_obs_permil);
##details<<
## gm point complex, internal leaf (mesophyll) conductance calculated for every D value estimating decarboxylation effects. \code{\link{f_val_calc_gm_point_complex}}
val_temp$chamber_Totalgm_point_complex <-
# switch added for A_photosynthesis 9/5/2012
#f_val_calc_gm_point_complex( val_const$b_gm, val_const$b_s, val_const$a_l, val_Licor$A
f_val_calc_gm_point_complex( val_const$b_gm, val_const$b_s, val_const$a_l, val_temp$selected_A_photosynthesis
,val_temp$chamber_Totalpa, val_temp$chamber_Delta_i_complex_for_gm, val_temp$Delta_obs_permil # 8/19/2011 use permil
,val_const$f_photo_respiration, val_const$Gamma_star
,val_const$e, val_const$Rd, val_const$k);
##details<<
## select one of the calculated gm values to use
val_temp$chamber_Totalgm_to_use <- NULL; # as default
switch(sw$calc_gm_to_use
# 1 = gm_point_simple
, val_temp$chamber_Totalgm_to_use <- val_temp$chamber_Totalgm_point_simple
# 2 = gm_point_complex
, val_temp$chamber_Totalgm_to_use <- val_temp$chamber_Totalgm_point_complex
);
# # Plot gm point simple and complex, internal leaf (mesophyll) conductance calculated for every D value ignoring and estimating decarboxylation effects
# p_o <- paste("Plot gm point simple and complex, internal leaf (mesophyll) conductance calculated for every D value ignoring and estimating decarboxylation effects\n"); wWw <- write_progress(p_o, time_start);
#plot_gm(val_temp$chamber_Totalgm_point_simple, val_temp$chamber_12gm_point_simple, val_temp$chamber_13gm_point_simple
# ,val_temp$chamber_Totalgm_point_complex
# ,val_TDL$time, plot_format_list)
#-------------------
##details<<
## SECTION pc
##details<<
## pc using gm, total partial pressure of CO2 at the site of carboxylation, Press is the atmospheric pressure value from the LI6400. \code{\link{f_val_calc_pc_using_gm}}
# switch added for A_photosynthesis 9/5/2012
#val_temp$chamber_Totalpc_using_gm <- f_val_calc_pc_using_gm(val_temp$chamber_Totalpi, val_Licor$A, val_temp$chamber_Totalgm_to_use);
#val_temp$chamber_12pc_using_gm <- f_val_calc_pc_using_gm(val_temp$chamber_12pi , val_Licor$A, val_temp$chamber_Totalgm_to_use);
#val_temp$chamber_13pc_using_gm <- f_val_calc_pc_using_gm(val_temp$chamber_13pi , val_Licor$A, val_temp$chamber_Totalgm_to_use);
val_temp$chamber_Totalpc_using_gm <- f_val_calc_pc_using_gm(val_temp$chamber_Totalpi, val_temp$selected_A_photosynthesis, val_temp$chamber_Totalgm_to_use);
val_temp$chamber_12pc_using_gm <- f_val_calc_pc_using_gm(val_temp$chamber_12pi , val_temp$selected_12A_photosynthesis, val_temp$chamber_Totalgm_to_use);
val_temp$chamber_13pc_using_gm <- f_val_calc_pc_using_gm(val_temp$chamber_13pi , val_temp$selected_13A_photosynthesis, val_temp$chamber_Totalgm_to_use);
##details<<
## pc using simple D for gm, includes boundary layer. \code{\link{f_val_calc_pc_using_simple_Delta_for_gm}}
val_temp$chamber_Totalpc_using_simple_Delta_for_gm <-
f_val_calc_pc_using_simple_Delta_for_gm( val_temp$chamber_Delta_i_simple_for_gm, val_temp$chamber_Totalpa
,val_temp$chamber_Totalps, val_const$a, val_const$b_gm, val_const$a_b);
##details<<
## pc using simple D for modeling. \code{\link{f_val_calc_pc_using_simple_Delta_for_modeling}}
val_temp$chamber_Totalpc_using_simple_Delta_for_modeling <-
f_val_calc_pc_using_simple_Delta_for_modeling( val_temp$chamber_Delta_i_simple_for_modeling, val_temp$chamber_Totalpa
,val_const$a, val_const$b_modeling);
# # # What value of b to use here?
##details<<
## pc using complex D, no decarboxylation [ab(pa-ps)+a(ps-pi)+pi(bs+al)-Dpa]/(bs+al-b) is this different from two up? They give different values but both may not be derived properly. \code{\link{f_val_calc_pc_using_complex_Delta_no_decarboxylation}}
val_temp$chamber_Totalpc_using_complex_Delta_no_decarboxylation <-
f_val_calc_pc_using_complex_Delta_no_decarboxylation( val_temp$chamber_Delta_i_complex_for_gm, val_temp$chamber_Totalpa
,val_temp$chamber_Totalps, val_temp$chamber_Totalpi
,val_const$a, val_const$a_b, val_const$a_l, val_const$b_modeling, val_const$b_s)
# # # What value of b to use here?
##details<<
## pc using complex D, full model [ab(pa-ps)+a(ps-pi)+pi(bs+al)-(eRd/k+fG*)-Dpa]/(bs+al-b) includes boundary layer and decarboxylation effects. \code{\link{f_val_calc_pc_using_complex_Delta_full_model}}
val_temp$chamber_Totalpc_using_complex_Delta_full_model <-
f_val_calc_pc_using_complex_Delta_full_model( val_temp$chamber_Delta_i_complex_for_gm, val_temp$chamber_Totalpa
,val_temp$chamber_Totalps, val_temp$chamber_Totalpi
,val_const$a, val_const$a_b, val_const$a_l, val_const$b_modeling, val_const$b_s
,val_const$e, val_const$Rd, val_const$k, val_const$Gamma_star, val_const$f_photo_respiration)
# # Plot pc, total partial pressure of CO2 at the site of carboxylation
# p_o <- paste("Plot pc, total partial pressure of CO2 at the site of carboxylation\n"); wWw <- write_progress(p_o, time_start);
#plot_pc_total( val_temp$chamber_Totalpc_using_gm, val_temp$chamber_12pc_using_gm, val_temp$chamber_13pc_using_gm
# ,val_TDL$time, plot_format_list)
#
# # Plot pc, simple and complex
# p_o <- paste("Plot pc, simple and complex\n"); wWw <- write_progress(p_o, time_start);
#plot_pc_simple_complex(val_temp$chamber_Totalpc_using_simple_Delta_for_gm, val_temp$chamber_Totalpc_using_simple_Delta_for_modeling
# ,val_temp$chamber_Totalpc_using_complex_Delta_no_decarboxylation, val_temp$chamber_Totalpc_using_complex_Delta_full_model
# ,val_TDL$time, plot_format_list)
##details<<
## select one of the calculated pc values to use
val_temp$chamber_Totalpc_to_use <- NULL; # as default
switch(sw$calc_pc_to_use
# 1 = pc_using_gm
, val_temp$chamber_Totalpc_to_use <- val_temp$chamber_Totalpc_using_gm
# 2 = pc_using_simple_Delta_for_gm
, val_temp$chamber_Totalpc_to_use <- val_temp$chamber_Totalpc_using_simple_Delta_for_gm
# 3 = pc_using_simple_Delta_for_modeling
, val_temp$chamber_Totalpc_to_use <- val_temp$chamber_Totalpc_using_simple_Delta_for_modeling
# 4 = pc_using_complex_Delta_no_decarboxylation
, val_temp$chamber_Totalpc_to_use <- val_temp$chamber_Totalpc_using_complex_Delta_no_decarboxylation
# 5 = pc_using_complex_Delta_full_model
, val_temp$chamber_Totalpc_to_use <- val_temp$chamber_Totalpc_using_complex_Delta_full_model
);
# (after pc -- one of the several pc's)
##details<<
## Cc (pc*10^6)/(Press*1000) ppm CO2 concentration at the site of carboxylation, generally meaning inside the chloroplast and ignoring PEPC in cytosol. \code{\link{f_val_calc_pp}}
## NB: same formula as pa, but using pc instead of Co
val_temp$chamber_TotalCc <- f_val_calc_pp(val_temp$chamber_Totalpc_using_gm, val_Licor$Atm_press);
val_temp$chamber_12Cc <- f_val_calc_pp(val_temp$chamber_12pc_using_gm , val_Licor$Atm_press);
val_temp$chamber_13Cc <- f_val_calc_pp(val_temp$chamber_13pc_using_gm , val_Licor$Atm_press);
# # Plot Cc, ppm CO2 concentration at the site of carboxylation, generally meaning inside the chloroplast and ignoring PEPC in cytosol
# p_o <- paste("Plot Cc, ppm CO2 concentration at the site of carboxylation\n"); wWw <- write_progress(p_o, time_start);
#plot_Cc_total(val_temp$chamber_TotalCc, val_temp$chamber_12Cc, val_temp$chamber_13Cc
# ,val_TDL$time, plot_format_list)
return( val_temp );
### val_temp
}
erikerhardt/isogasex documentation built on July 16, 2019, 5:25 a.m.
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#' This function calls all of the \code{f_val_calc.*} files
#'
#' SECTION Licor data assign variables
#'
#' SECTION Concentrations.
#'
#' Calibration tank concentrations
#'
#' Calibration tank gain. \code{\link{f_val_calc_gain}}
#'
#' Calibration tank offset. \code{\link{f_val_calc_offset}}
#'
#' Corrected reference values. \code{\link{f_val_calc_corrected}}
#'
#' Corrected chamber values. \code{\link{f_val_calc_corrected}}
#'
#' Total reference and chamber values. \code{\link{f_val_calc_total_mol_fraction_CO2}}
#'
#' xi. \code{\link{f_val_calc_xi}}
#'
#' SECTION A Photosynthesis
#'
#' A, TDL photosynthesis. \code{\link{f_val_calc_TDL_A_photosynthesis}}
#'
#' 12A, TDL photosynthesis. \code{\link{f_val_calc_TDL_A_photosynthesis}}
#'
#' 13A, TDL photosynthesis. \code{\link{f_val_calc_TDL_A_photosynthesis}}
#'
#' Total A LI6400 Photo LI6400 header, these values listed because I will likely use them in a plot
#'
#' Delta from ratios in and out?, (Re/Ro)-1, is this really the same? \code{\link{f_val_calc_Delta_from_ratios_in_out}}
#'
#' D from A ratio, (Ro/(13A/12A))-1, should be the same as Dobs above. \code{\link{f_val_calc_Delta_from_A_ratio}}
#'
#' Select TDL or Licor based on switch
#'
#' SECTION Delta
#'
#' delta reference and chamber values. \code{\link{f_val_calc_delta_proportion}}
#'
#' delta diff
#'
#' Delta discrim
#'
#' Dobs observed discrimination. \code{\link{f_val_calc_Delta_obs}}
#'
#' Dobs per mil 1000*Dobs. \code{\link{f_val_calc_Delta_obs_permil}}
#'
#' delta13C Assimilated, isotopic composition of assimilated sugars. \code{\link{f_val_calc_delta_13C_Assim}}
#'
#' p (Co - Ce) / Co. \code{\link{f_val_calc_p}}
#'
#' delta13C Respired, isotopic composition of respired CO2. \code{\link{f_val_calc_delta_13C_Resp}}
#'
#' SECTION g conductance
#'
#' gbw BLcond boundary layer conductance for water, Blcond is LI 6400 header
#'
#' gbc BLcond/1.37 boundary layer conductance for CO2
#'
#' gsw cond stomatal conductance for water, cond is LI6400 header
#'
#' gsc gsw/1.6 stomatal conductance for CO2
#'
#' gtc, total (stomatal and boundary layer) conductance for CO2
#'
#' SECTION Cx and px (concentrations and pressures)
#'
#' Ca = Co, ppm CO2 concentration above the leaf = concentration leaving the leaf chamber = ambient CO2 concentration
#'
#' Cs, ppm CO2 concentration at the leaf surface, cs calculated from eq 40 Ball 1987 Ch 20 Stomatal Function, eds Zeiger, Farquhar, Cowan. \code{\link{f_val_calc_Cs}}
#'
#' pa, partial pressure of CO2 above the leaf, Press is the atmospheric pressure value from the LI6400. \code{\link{f_val_calc_pp}}
#'
#' ps, partial pressure of CO2 at the leaf surface, Press is the atmospheric pressure value from the LI6400. \code{\link{f_val_calc_pp}}
#' NB: same formula as pa, but using Cs instead of Co
#'
#' Ci, ppm CO2 concentration in the sub-stomatal cavities, ci calculated from eq 35 Ball 1987 Ch 20 Stomatal Function, eds Zeiger, Farquhar, Cowan. \code{\link{f_val_calc_Cs}}
#' NB: same formula as Cs, but using gtc instead of gbc
#'
#' pi, partial pressure of CO2 in the substomatal cavities, Press is the atmospheric pressure value from the LI6400. \code{\link{f_val_calc_pp}}
#' NB: same formula as pa, but using Ci instead of Co
#'
#' pi/pa total pi/pa or total Ci/Ca ratio of substomatal CO2 partial pressure to CO2 partial pressure above leaf = Ci/Ca ratio of mol fractions
#'
#' SECTION Delta_i predictions
#'
#' Delta_i simple for gm, predicted discrimination including boundary layer effects but not decarboxylation effects. \code{\link{f_val_calc_Delta_i_simple_for_gm}}
#'
#' Delta_i simple for modeling a + (b-a) pi/pa predicted discrimination including boundary layer effects but using b adjustments to approximate effects of gm and decarboxylations. \code{\link{f_val_calc_Delta_i_simple_for_modeling}}
#'
#' Delta_i complex for gm CHECK DERIVATION predicted discrimination including boundary layer effects AND decarboxylation effects. \code{\link{f_val_calc_Delta_i_complex_for_gm}}
#'
#' Delta_i simple for gm-Dobs (Di simple for gm)-(Dobs per mil)
#'
#' Delta_i complex for gm-Dobs (Di complex for gm)-(Dobs per mil)
#'
#' SECTION gm mesophyll conductance
#'
#' gm point simple, internal leaf (mesophyll) conductance calculated for every D value ignoring decarboxylation effects. \code{\link{f_val_calc_gm_point_simple}}
#'
#' gm point complex, internal leaf (mesophyll) conductance calculated for every D value estimating decarboxylation effects. \code{\link{f_val_calc_gm_point_complex}}
#'
#' select one of the calculated gm values to use
#'
#' SECTION pc
#'
#' pc using gm, total partial pressure of CO2 at the site of carboxylation, Press is the atmospheric pressure value from the LI6400. \code{\link{f_val_calc_pc_using_gm}}
#'
#' pc using simple D for gm, includes boundary layer. \code{\link{f_val_calc_pc_using_simple_Delta_for_gm}}
#'
#' pc using simple D for modeling. \code{\link{f_val_calc_pc_using_simple_Delta_for_modeling}}
#'
#' pc using complex D, no decarboxylation [ab(pa-ps)+a(ps-pi)+pi(bs+al)-Dpa]/(bs+al-b) is this different from two up? They give different values but both may not be derived properly. \code{\link{f_val_calc_pc_using_complex_Delta_no_decarboxylation}}
#'
#' pc using complex D, full model [ab(pa-ps)+a(ps-pi)+pi(bs+al)-(eRd/k+fG*)-Dpa]/(bs+al-b) includes boundary layer and decarboxylation effects. \code{\link{f_val_calc_pc_using_complex_Delta_full_model}}
#'
#' select one of the calculated pc values to use
#'
#' Cc (pc*10^6)/(Press*1000) ppm CO2 concentration at the site of carboxylation, generally meaning inside the chloroplast and ignoring PEPC in cytosol. \code{\link{f_val_calc_pp}}
#' NB: same formula as pa, but using pc instead of Co
#'
#' @param val_TDL xxxPARAMxxx
#' @param val_Licor xxxPARAMxxx
#' @param val_const xxxPARAMxxx
#' @param sw xxxPARAMxxx
#'
#' @return val_temp xxxRETURNxxx
#'
f_val_calc_all_driver <-
function# This function calls all the \code{f_val_calc.*} files
(val_TDL
###
, val_Licor
###
, val_const
###
, sw
###
)
{
# DEBUG DEBUG DEBUG DEBUG DEBUG
# val_TDL <- val$sum$TDL;
# val_Licor <- val$sum$Licor;
# val_const <- val$const;
#
# val_TDL <- val$obs$TDL;
# val_Licor <- val$obs$Licor;
# val_const <- val$const;
# DEBUG DEBUG DEBUG DEBUG DEBUG
val_temp <- list(); # hold current set of calculated values below
#-------------------
##details<<
## SECTION Licor data assign_variables
# LICOR DATA SECTION (moved from bottom to top 9/5/2012, so Licor_flow_uin can replace flow_adjusted)
# VPD VpdL LI6400 header, these values listed because I will likely use them in a plot
val_temp$VPD <- val_Licor$VPD;
# Transpiration Trmmol LI6400 header, these values listed because I will likely use them in a plot
val_temp$E_transpiration <- val_Licor$E;
# Leaf Temp Tleaf LI6400 header, these values listed because I will likely use them in a plot
val_temp$leaf_temp <- val_Licor$temp_leaf;
# Air Temp ? Tair LI6400 header, these values listed because I will likely use them in a plot
val_temp$air_temp <- val_Licor$temp_air;
# Light in PARi LI6400 header, these values listed because I will likely use them in a plot
val_temp$light_in <- val_Licor$par_int;
# Light out PARo LI6400 header, these values listed because I will likely use them in a plot
val_temp$light_out <- val_Licor$par_ext;
# 7/21/2012 added Licor var to save
val_temp$Licor_flow_uin <- val_Licor$uin ;
val_temp$Licor_H2OR_xin <- val_Licor$xin ;
val_temp$Licor_La <- val_Licor$La ;
val_temp$Licor_Atm_press <- val_Licor$Atm_press ;
val_temp$Licor_gsc <- val_Licor$gsc ;
val_temp$Licor_Ci <- val_Licor$Ci ;
val_temp$Licor_StmRat <- val_Licor$StmRat ;
val_temp$Licor_gbw <- val_Licor$gbw ;
val_temp$Licor_temp_block <- val_Licor$temp_block ;
val_temp$Licor_Ce <- val_Licor$Ce ;
val_temp$Licor_Co <- val_Licor$Co ;
val_temp$Licor_xout <- val_Licor$xout ;
val_temp$Licor_rh_ref <- val_Licor$rh_ref ;
val_temp$Licor_rh_sam <- val_Licor$rh_sam ;
val_temp$Licor_CsMch <- val_Licor$CsMch ;
val_temp$Licor_HsMch <- val_Licor$HsMch ;
val_temp$Licor_StableF <- val_Licor$StableF ;
val_temp$Licor_Status <- val_Licor$Status ;
# typically not used
# ,"VpdA"
# ,"Ci_Ca"
# ,"pi"
# ,"uc_20_mV"
# ,"uc_21_mV"
# ,"U_S"
# ,"Trans"
# ,"CndCO2"
# ,"Ref_mV"
# ,"xTemp1"
# ,"xTemp2"
#-------------------
##details<<
## SECTION Concentrations.
# also include interp concentration values "0.1-16" "2012-07-10"
##details<<
## Calibration tank concentrations
val_temp$tank_hi_12 <- val_TDL$interp_tank_hi_12 ;
val_temp$tank_hi_13 <- val_TDL$interp_tank_hi_13 ;
val_temp$tank_low_12 <- val_TDL$interp_tank_low_12;
val_temp$tank_low_13 <- val_TDL$interp_tank_low_13;
##details<<
## Calibration tank gain. \code{\link{f_val_calc_gain}}
temp_gain <-
f_val_calc_gain( val_const$true_value_hi_12C, val_const$true_value_hi_13C, val_const$true_value_lo_12C, val_const$true_value_lo_13C
,val_TDL$interp_tank_hi_12, val_TDL$interp_tank_hi_13, val_TDL$interp_tank_low_12, val_TDL$interp_tank_low_13);
val_temp$gain_12C <- temp_gain$gain_12C;
val_temp$gain_13C <- temp_gain$gain_13C;
##details<<
## Calibration tank offset. \code{\link{f_val_calc_offset}}
temp_offset <-
f_val_calc_offset( val_const$true_value_hi_12C, val_const$true_value_hi_13C
,val_temp$gain_12C, val_temp$gain_13C
,val_TDL$interp_tank_hi_12, val_TDL$interp_tank_hi_13);
val_temp$offset_12C <- temp_offset$offset_12C;
val_temp$offset_13C <- temp_offset$offset_13C;
# # Plot active gains, offsets, and corrected magnitudes
# p_o <- paste("Plot active gains, offsets, and corrected magnitudes\n"); wWw <- write_progress(p_o, time_start);
#plot_gain_offset(val_temp$gain_12C, val_temp$gain_13C, val_temp$offset_12C, val_temp$offset_13C, val_TDL$time, plot_format_list);
##details<<
## Corrected reference values. \code{\link{f_val_calc_corrected}}
# 12Ce 12C Site 1 reference Ce is the ppm CO2 concentration entering the leaf chamber, equivalent terms: reference, Site 1, CO2R
# 13Ce 13C Site 1 reference
temp_corrected <-
f_val_calc_corrected(val_TDL$interp_reference_12, val_TDL$interp_reference_13
,val_temp$gain_12C, val_temp$gain_13C
,val_temp$offset_12C, val_temp$offset_13C)
val_temp$reference_12Ce <- temp_corrected$corrected_12C;
val_temp$reference_13Ce <- temp_corrected$corrected_13C;
##details<<
## Corrected chamber values. \code{\link{f_val_calc_corrected}}
# 12Co 12C Site 21 chamber Co is the outgoing ppm CO2 concentration from the leaf chamber: sample, Site 21, CO2S, Ca, also air above the leaf
# 13Co 13C Site 21 chamber
temp_corrected <-
f_val_calc_corrected(val_TDL$chamber_12, val_TDL$chamber_13
,val_temp$gain_12C, val_temp$gain_13C
,val_temp$offset_12C, val_temp$offset_13C)
val_temp$chamber_12Co <- temp_corrected$corrected_12C;
val_temp$chamber_13Co <- temp_corrected$corrected_13C;
##details<<
## Total reference and chamber values. \code{\link{f_val_calc_total_mol_fraction_CO2}}
# Total Ce Total Site 1
# Total Co Total Site 21
val_temp$reference_TotalCe <-
f_val_calc_total_mol_fraction_CO2(val_temp$reference_12Ce, val_temp$reference_13Ce, val_const$fo_13C);
val_temp$chamber_TotalCo <-
f_val_calc_total_mol_fraction_CO2(val_temp$chamber_12Co, val_temp$chamber_13Co, val_const$fo_13C);
# Ce-Co Total Site 1 - Total Site 21 I like having this as an output for diagnostics
val_temp$chamber_reference_Total_diff_CeCo <- val_temp$reference_TotalCe - val_temp$chamber_TotalCo;
val_temp$chamber_reference_12_diff_CeCo <- val_temp$reference_12Ce - val_temp$chamber_12Co;
val_temp$chamber_reference_13_diff_CeCo <- val_temp$reference_13Ce - val_temp$chamber_13Co;
##details<<
## xi. \code{\link{f_val_calc_xi}}
# xi Ce/(Ce-Co) I like having this as an output for diagnostics
val_temp$xi <-
f_val_calc_xi(val_temp$reference_TotalCe, val_temp$chamber_TotalCo)
# # Plot corrected 12CO2 and 13CO2, total, and difference for reference and sample
# p_o <- paste("Plot corrected 12CO2 and 13CO2, total, and difference for reference and sample\n"); wWw <- write_progress(p_o, time_start);
#plot_corrected_total_diff_xi( val_temp$reference_12Ce, val_temp$reference_13Ce
# ,val_temp$chamber_12Co, val_temp$chamber_13Co
# ,val_temp$reference_TotalCe, val_temp$chamber_TotalCo
# ,val_temp$chamber_reference_Total_diff_CeCo, val_temp$xi, val_TDL$time, plot_format_list);
#-------------------
##details<<
## SECTION A Photosynthesis
# # Deprecated (0.1-20, 9/5/2012) ##
# Adjusted flow, LI6400 flow includes water in the entering air but the TDL removes this water before measuring and this effectively reduces the flow (use H2OR to correct it)
#val_temp$flow_adjusted <- # 9/5/2012
# f_val_calc_flow_adjusted(val_Licor$uin, val_Licor$xin); # 9/5/2012
##details<<
## A, TDL photosynthesis. \code{\link{f_val_calc_TDL_A_photosynthesis}}
val_temp$TDL_A_photosynthesis <-
#f_val_calc_TDL_A_photosynthesis( val_temp$flow_adjusted, val_temp$reference_TotalCe # 9/5/2012
f_val_calc_TDL_A_photosynthesis( val_temp$Licor_flow_uin, val_temp$reference_TotalCe # 9/5/2012
,val_temp$chamber_TotalCo, val_Licor$La);
##details<<
## 12A, TDL photosynthesis. \code{\link{f_val_calc_TDL_A_photosynthesis}}
val_temp$TDL_12A_photosynthesis <-
#f_val_calc_TDL_A_photosynthesis( val_temp$flow_adjusted, val_temp$reference_12Ce # 9/5/2012
f_val_calc_TDL_A_photosynthesis( val_temp$Licor_flow_uin, val_temp$reference_12Ce # 9/5/2012
,val_temp$chamber_12Co, val_Licor$La);
##details<<
## 13A, TDL photosynthesis. \code{\link{f_val_calc_TDL_A_photosynthesis}}
val_temp$TDL_13A_photosynthesis <-
#f_val_calc_TDL_A_photosynthesis( val_temp$flow_adjusted, val_temp$reference_13Ce # 9/5/2012
f_val_calc_TDL_A_photosynthesis( val_temp$Licor_flow_uin, val_temp$reference_13Ce # 9/5/2012
,val_temp$chamber_13Co, val_Licor$La);
##details<<
## Total A LI6400 Photo LI6400 header, these values listed because I will likely use them in a plot
val_temp$Licor_A_photosynthesis <- val_Licor$A;
##details<<
## Delta from ratios in and out?, (Re/Ro)-1, is this really the same? \code{\link{f_val_calc_Delta_from_ratios_in_out}}
val_temp$Delta_from_ratios_in_out <-
f_val_calc_Delta_from_ratios_in_out( val_temp$reference_12Ce, val_temp$reference_13Ce
,val_temp$chamber_12Co, val_temp$chamber_13Co)
##details<<
## D from A ratio, (Ro/(13A/12A))-1, should be the same as Dobs above. \code{\link{f_val_calc_Delta_from_A_ratio}}
val_temp$Delta_from_A_ratio <-
f_val_calc_Delta_from_A_ratio( val_temp$chamber_12Co, val_temp$chamber_13Co
,val_temp$TDL_12A_photosynthesis, val_temp$TDL_13A_photosynthesis)
##details<<
## Select TDL or Licor based on switch
# switch added for A_photosynthesis 9/5/2012
if (sw$Licor_or_TDL_A_photosynthesis == 0) { # Licor
# use Licor
val_temp$selected_A_photosynthesis <- val_temp$Licor_A_photosynthesis;
val_temp$selected_12A_photosynthesis <- rep(NA, length(val_temp$TDL_12A_photosynthesis));
val_temp$selected_13A_photosynthesis <- rep(NA, length(val_temp$TDL_13A_photosynthesis));
#val_temp$TDL_A_photosynthesis <- rep(NA, length(val_temp$TDL_A_photosynthesis ));
#val_temp$TDL_12A_photosynthesis <- rep(NA, length(val_temp$TDL_12A_photosynthesis));
#val_temp$TDL_13A_photosynthesis <- rep(NA, length(val_temp$TDL_13A_photosynthesis));
}
if (sw$Licor_or_TDL_A_photosynthesis == 1) { # TDL
# use TDL
val_temp$selected_A_photosynthesis <- val_temp$TDL_A_photosynthesis ;
val_temp$selected_12A_photosynthesis <- val_temp$TDL_12A_photosynthesis;
val_temp$selected_13A_photosynthesis <- val_temp$TDL_13A_photosynthesis;
#val_temp$Licor_A_photosynthesis <- rep(NA, length(val_temp$Licor_A_photosynthesis));
}
# # Plot A photosynthesis
# p_o <- paste("Plot A photosynthesis\n"); wWw <- write_progress(p_o, time_start);
#plot_A_photosynthesis( val_temp$TDL_A_photosynthesis, val_temp$TDL_12A_photosynthesis, val_temp$TDL_13A_photosynthesis
# ,val_temp$Licor_A_photosynthesis, val_temp$Delta_from_ratios_in_out, val_temp$Delta_from_A_ratio
# ,val_TDL$time, plot_format_list)
#
# # Plot Licor Temp Light values
# p_o <- paste("Plot Licor Temp Light values\n"); wWw <- write_progress(p_o, time_start);
#plot_Licor_temp_light(val_temp$VPD, val_temp$E_transpiration, val_temp$leaf_temp, val_temp$air_temp
# ,val_temp$light_in, val_temp$light_out, val_temp$flow_adjusted
# ,val_TDL$time, plot_format_list)
#-------------------
##details<<
## SECTION Delta
##details<<
## delta reference and chamber values. \code{\link{f_val_calc_delta_proportion}}
# de d13C Site 1
val_temp$reference_delta_e <-
f_val_calc_delta_proportion(val_temp$reference_12Ce, val_temp$reference_13Ce, val_const$Rstd_13C);
# do d13C Site 21
val_temp$chamber_delta_o <-
f_val_calc_delta_proportion(val_temp$chamber_12Co, val_temp$chamber_13Co, val_const$Rstd_13C);
##details<<
## delta diff
# do-de d Site 21 - d Site 1 I like having this as an output for diagnostics
val_temp$chamber_reference_delta_diff_CoCe <- val_temp$chamber_delta_o - val_temp$reference_delta_e;
##details<<
## Delta discrim
##details<<
## Dobs observed discrimination. \code{\link{f_val_calc_Delta_obs}}
val_temp$Delta_obs <-
f_val_calc_Delta_obs(val_temp$reference_delta_e, val_temp$chamber_delta_o, val_temp$xi)
##details<<
## Dobs per mil 1000*Dobs. \code{\link{f_val_calc_Delta_obs_permil}}
val_temp$Delta_obs_permil <-
f_val_calc_Delta_obs_permil(val_temp$reference_delta_e, val_temp$chamber_delta_o, val_temp$xi)
##details<<
## delta13C Assimilated, isotopic composition of assimilated sugars. \code{\link{f_val_calc_delta_13C_Assim}}
val_temp$delta_13C_Assim <-
f_val_calc_delta_13C_Assim(val_temp$chamber_delta_o, val_temp$Delta_obs)
##details<<
## p (Co - Ce) / Co. \code{\link{f_val_calc_p}}
val_temp$p <-
f_val_calc_p(val_temp$reference_TotalCe, val_temp$chamber_TotalCo)
##details<<
## delta13C Respired, isotopic composition of respired CO2. \code{\link{f_val_calc_delta_13C_Resp}}
val_temp$delta_13C_Resp <-
f_val_calc_delta_13C_Resp(val_temp$reference_delta_e, val_temp$chamber_delta_o, val_temp$p)
# # Plot delta, Delta, and p
# p_o <- paste("Plot delta, Delta, and p\n"); wWw <- write_progress(p_o, time_start);
#plot_delta_Delta_p( val_temp$reference_delta_e, val_temp$chamber_delta_o, val_temp$chamber_reference_delta_diff_CoCe
# ,val_temp$Delta_obs, val_temp$p, val_temp$delta_13C_Assim, val_temp$delta_13C_Resp
# , val_TDL$time, plot_format_list)
#-------------------
##details<<
## SECTION g conductance
# 9/6/2012 moved above Cs when fixed it's calculation
##details<<
## gbw BLcond boundary layer conductance for water, Blcond is LI 6400 header
val_temp$chamber_Totalgbw <- val_Licor$gbw;
##details<<
## gbc BLcond/1.37 boundary layer conductance for CO2
val_temp$chamber_Totalgbc <- val_Licor$gbw / val_const$gbc_1.37;
val_temp$chamber_12gbc <- val_temp$chamber_Totalgbc;
val_temp$chamber_13gbc <- val_temp$chamber_Totalgbc / (1 + (val_const$a_b / 1000));
##details<<
## gsw cond stomatal conductance for water, cond is LI6400 header
val_temp$chamber_Totalgsw <- val_Licor$gsc;
##details<<
## gsc gsw/1.6 stomatal conductance for CO2
val_temp$chamber_Totalgsc <- val_temp$chamber_Totalgsw / val_const$gsc_1.6;
val_temp$chamber_12gsc <- val_temp$chamber_Totalgsc;
val_temp$chamber_13gsc <- val_temp$chamber_Totalgsc / (1 + (val_const$a_b / 1000));
##details<<
## gtc, total (stomatal and boundary layer) conductance for CO2
val_temp$chamber_Totalgtc <- f_val_calc_gtc( val_temp$chamber_Totalgbc, val_temp$chamber_Totalgsc);
val_temp$chamber_12gtc <- val_temp$chamber_Totalgtc;
val_temp$chamber_13gtc <- f_val_calc_gtc( val_temp$chamber_13gbc, val_temp$chamber_13gsc);
# # Plot gbc, gsc, gtc: boundary layer, stomatal, and total conductance for CO2
# p_o <- paste("Plot gbc, gsc, gtc: boundary layer, stomatal, and total conductance for CO2\n"); wWw <- write_progress(p_o, time_start);
#plot_gbc_gsc_gtc(val_temp$chamber_Totalgbc, val_temp$chamber_13gbc
# ,val_temp$chamber_Totalgsc, val_temp$chamber_13gsc
# ,val_temp$chamber_Totalgtc, val_temp$chamber_13gtc
# ,val_TDL$time, plot_format_list)
#-------------------
##details<<
## SECTION Cx and px (concentrations and pressures)
##details<<
## Ca = Co, ppm CO2 concentration above the leaf = concentration leaving the leaf chamber = ambient CO2 concentration
val_temp$chamber_TotalCa <- val_temp$chamber_TotalCo;
val_temp$chamber_12Ca <- val_temp$chamber_12Co ;
val_temp$chamber_13Ca <- val_temp$chamber_13Co ;
##details<<
## Cs, ppm CO2 concentration at the leaf surface, cs calculated from eq 40 Ball 1987 Ch 20 Stomatal Function, eds Zeiger, Farquhar, Cowan. \code{\link{f_val_calc_Cs}}
#val_temp$chamber_TotalCs <- f_val_calc_Cs(val_Licor$gbw, val_Licor$E, val_temp$chamber_TotalCo, val_temp$TDL_A_photosynthesis);
#val_temp$chamber_12Cs <- f_val_calc_Cs(val_Licor$gbw, val_Licor$E, val_temp$chamber_12Co , val_temp$TDL_A_photosynthesis);
#val_temp$chamber_13Cs <- f_val_calc_Cs(val_Licor$gbw, val_Licor$E, val_temp$chamber_13Co , val_temp$TDL_A_photosynthesis);
# 7/28/2012 Using A from Licor until test effect of using A from TDL
# switch added for A_photosynthesis 9/5/2012
# fixed calculation of Cs, was using val_Licor$gbc before I changed name to gbw 9/6/2012
val_temp$chamber_TotalCs <- f_val_calc_Cs(val_temp$chamber_Totalgbc, val_Licor$E, val_temp$chamber_TotalCo, val_temp$selected_A_photosynthesis);
val_temp$chamber_12Cs <- f_val_calc_Cs(val_temp$chamber_12gbc , val_Licor$E, val_temp$chamber_12Co , val_temp$selected_12A_photosynthesis);
val_temp$chamber_13Cs <- f_val_calc_Cs(val_temp$chamber_13gbc , val_Licor$E, val_temp$chamber_13Co , val_temp$selected_13A_photosynthesis);
# # Plot Ca Cs, CO2 concentrations above the leaf and at the leaf surface
# p_o <- paste("Plot Ca Cs, CO2 concentrations above the leaf and at the leaf surface\n"); wWw <- write_progress(p_o, time_start);
#plot_Ca_Cs(val_temp$chamber_TotalCa, val_temp$chamber_12Ca, val_temp$chamber_13Ca
# ,val_temp$chamber_TotalCs, val_temp$chamber_12Cs, val_temp$chamber_13Cs
# ,val_TDL$time, plot_format_list)
##details<<
## pa, partial pressure of CO2 above the leaf, Press is the atmospheric pressure value from the LI6400. \code{\link{f_val_calc_pp}}
val_temp$chamber_Totalpa <- f_val_calc_pp(val_temp$chamber_TotalCo, val_Licor$Atm_press);
val_temp$chamber_12pa <- f_val_calc_pp(val_temp$chamber_12Co , val_Licor$Atm_press);
val_temp$chamber_13pa <- f_val_calc_pp(val_temp$chamber_13Co , val_Licor$Atm_press);
##details<<
## ps, partial pressure of CO2 at the leaf surface, Press is the atmospheric pressure value from the LI6400. \code{\link{f_val_calc_pp}}
## NB: same formula as pa, but using Cs instead of Co
val_temp$chamber_Totalps <- f_val_calc_pp(val_temp$chamber_TotalCs, val_Licor$Atm_press);
val_temp$chamber_12ps <- f_val_calc_pp(val_temp$chamber_12Cs , val_Licor$Atm_press);
val_temp$chamber_13ps <- f_val_calc_pp(val_temp$chamber_13Cs , val_Licor$Atm_press);
# # Plot Pa Ps, partial pressure of CO2 above the leaf and at the leaf surface
# p_o <- paste("Plot Pa Ps, partial pressure of CO2 above the leaf and at the leaf surface\n"); wWw <- write_progress(p_o, time_start);
#plot_pa_ps(val_temp$chamber_Totalpa, val_temp$chamber_12pa, val_temp$chamber_13pa
# ,val_temp$chamber_Totalps, val_temp$chamber_12ps, val_temp$chamber_13ps
# ,val_TDL$time, plot_format_list)
##details<<
## Ci, ppm CO2 concentration in the sub-stomatal cavities, ci calculated from eq 35 Ball 1987 Ch 20 Stomatal Function, eds Zeiger, Farquhar, Cowan. \code{\link{f_val_calc_Cs}}
## NB: same formula as Cs, but using gtc instead of gbc
#val_temp$chamber_TotalCi <- f_val_calc_Cs(val_temp$chamber_Totalgtc, val_Licor$E, val_temp$chamber_TotalCo, val_temp$TDL_A_photosynthesis);
#val_temp$chamber_12Ci <- f_val_calc_Cs(val_temp$chamber_12gtc, val_Licor$E, val_temp$chamber_12Co , val_temp$TDL_A_photosynthesis);
#val_temp$chamber_13Ci <- f_val_calc_Cs(val_temp$chamber_13gtc, val_Licor$E, val_temp$chamber_13Co , val_temp$TDL_A_photosynthesis);
# 7/28/2012 Using A from Licor until test effect of using A from TDL
# switch added for A_photosynthesis 9/5/2012
val_temp$chamber_TotalCi <- f_val_calc_Cs(val_temp$chamber_Totalgtc, val_Licor$E, val_temp$chamber_TotalCo, val_temp$selected_A_photosynthesis);
val_temp$chamber_12Ci <- f_val_calc_Cs(val_temp$chamber_12gtc, val_Licor$E, val_temp$chamber_12Co , val_temp$selected_12A_photosynthesis);
val_temp$chamber_13Ci <- f_val_calc_Cs(val_temp$chamber_13gtc, val_Licor$E, val_temp$chamber_13Co , val_temp$selected_13A_photosynthesis);
##details<<
## pi, partial pressure of CO2 in the substomatal cavities, Press is the atmospheric pressure value from the LI6400. \code{\link{f_val_calc_pp}}
## NB: same formula as pa, but using Ci instead of Co
val_temp$chamber_Totalpi <- f_val_calc_pp(val_temp$chamber_TotalCi, val_Licor$Atm_press);
val_temp$chamber_12pi <- f_val_calc_pp(val_temp$chamber_12Ci , val_Licor$Atm_press);
val_temp$chamber_13pi <- f_val_calc_pp(val_temp$chamber_13Ci , val_Licor$Atm_press);
# # Plot Ci, Pi, CO2 concentration and partial pressure of CO2 in the substomatal cavities
# p_o <- paste("Plot Ci, pi, CO2 concentration and partial pressure of CO2 in the substomatal cavities\n"); wWw <- write_progress(p_o, time_start);
#plot_Ci_pi(val_temp$chamber_TotalCi, val_temp$chamber_12Ci, val_temp$chamber_13Ci
# ,val_temp$chamber_Totalpi, val_temp$chamber_12pi, val_temp$chamber_13pi
# ,val_TDL$time, plot_format_list)
#-------------------
##details<<
## pi/pa total pi/pa or total Ci/Ca ratio of substomatal CO2 partial pressure to CO2 partial pressure above leaf = Ci/Ca ratio of mol fractions
val_temp$chamber_Totalpi_pa <- val_temp$chamber_Totalpi / val_temp$chamber_Totalpa;
# # Plot Totalpi_pa, ratio of substomatal CO2 partial pressure to CO2 partial pressure above leaf = Ci/Ca ratio of mol fractions
# p_o <- paste("Plot Totalpi_pa, ratio of substomatal CO2 partial pressure to CO2 partial pressure above leaf\n"); wWw <- write_progress(p_o, time_start);
#plot_pi_pa(val_temp$chamber_Totalpi, val_temp$chamber_Totalpa, val_temp$chamber_Totalpi_pa
# ,val_TDL$time, plot_format_list)
#-------------------
##details<<
## SECTION Delta_i predictions
##details<<
## Delta_i simple for gm, predicted discrimination including boundary layer effects but not decarboxylation effects. \code{\link{f_val_calc_Delta_i_simple_for_gm}}
val_temp$chamber_Delta_i_simple_for_gm <-
f_val_calc_Delta_i_simple_for_gm( val_const$a, val_const$b_gm, val_const$a_b
,val_temp$chamber_Totalpa, val_temp$chamber_Totalps, val_temp$chamber_Totalpi)
##details<<
## Delta_i simple for modeling a + (b-a) pi/pa predicted discrimination including boundary layer effects but using b adjustments to approximate effects of gm and decarboxylations. \code{\link{f_val_calc_Delta_i_simple_for_modeling}}
val_temp$chamber_Delta_i_simple_for_modeling <-
f_val_calc_Delta_i_simple_for_modeling( val_const$a, val_const$b_modeling
,val_temp$chamber_Totalpa, val_temp$chamber_Totalpi)
##details<<
## Delta_i complex for gm CHECK DERIVATION predicted discrimination including boundary layer effects AND decarboxylation effects. \code{\link{f_val_calc_Delta_i_complex_for_gm}}
val_temp$chamber_Delta_i_complex_for_gm <-
f_val_calc_Delta_i_complex_for_gm( val_const$a, val_const$b_gm, val_const$a_b
,val_temp$chamber_Totalpa, val_temp$chamber_Totalps, val_temp$chamber_Totalpi
,val_const$b_gm
,val_const$f_photo_respiration, val_const$Gamma_star
,val_const$e, val_const$Rd, val_const$k);
# CAN PROBABLY REMOVE THIS COMMENTED CODE TO SELECT DELTA_i
# # select one of the calculated Delta_i values to use
#val_temp$chamber_Delta_i_to_use <- NULL; # as default
#switch(sw$calc_Delta_i_to_use
# # 1 = Delta_i_simple_for_gm
# , val_temp$chamber_Delta_i_to_use <- val_temp$chamber_Delta_i_simple_for_gm
# # 2 = Delta_i_simple_for_modeling
# , val_temp$chamber_Delta_i_to_use <- val_temp$chamber_Delta_i_simple_for_modeling
# # 3 = Delta_i_complex_for_gm
# , val_temp$chamber_Delta_i_to_use <- val_temp$chamber_Delta_i_complex_for_gm
# );
#-------------------
##details<<
## Delta_i simple for gm-Dobs (Di simple for gm)-(Dobs per mil)
val_temp$chamber_Delta_i_simple_for_gm_Delta_obs <-
val_temp$chamber_Delta_i_simple_for_gm - val_temp$Delta_obs_permil; # val_temp$Delta_obs_permil; # 8/19/2011
##details<<
## Delta_i complex for gm-Dobs (Di complex for gm)-(Dobs per mil)
val_temp$chamber_Delta_i_complex_for_gm_Delta_obs <-
val_temp$chamber_Delta_i_complex_for_gm - val_temp$Delta_obs_permil; # val_temp$Delta_obs_permil; # 8/19/2011
# # Plot Delta_i, predicted discrimination
# p_o <- paste("Plot Delta_i, predicted discrimination\n"); wWw <- write_progress(p_o, time_start);
#plot_Delta_i(val_temp$chamber_Delta_i_simple_for_gm, val_temp$chamber_Delta_i_simple_for_modeling, val_temp$chamber_Delta_i_complex_for_gm
# ,val_temp$chamber_Delta_i_simple_for_gm_Delta_obs, val_temp$chamber_Delta_i_complex_for_gm_Delta_obs
# ,val_TDL$time, plot_format_list)
#-------------------
##details<<
## SECTION gm mesophyll conductance
##details<<
## gm point simple, internal leaf (mesophyll) conductance calculated for every D value ignoring decarboxylation effects. \code{\link{f_val_calc_gm_point_simple}}
val_temp$chamber_Totalgm_point_simple <-
# switch added for A_photosynthesis 9/5/2012
#f_val_calc_gm_point_simple( val_const$b_gm, val_const$b_s, val_const$a_l, val_Licor$A
f_val_calc_gm_point_simple( val_const$b_gm, val_const$b_s, val_const$a_l, val_temp$selected_A_photosynthesis
,val_temp$chamber_Totalpa, val_temp$chamber_Delta_i_simple_for_gm, val_temp$Delta_obs_permil); # 8/19/2011 use permil
# switch added for A_photosynthesis 9/5/2012
#val_temp$chamber_12gm_point_simple <- val_temp$chamber_Totalgm_point_simple;
val_temp$chamber_12gm_point_simple <-
f_val_calc_gm_point_simple( val_const$b_gm, val_const$b_s, val_const$a_l, val_temp$selected_12A_photosynthesis
,val_temp$chamber_12pa, val_temp$chamber_Delta_i_simple_for_gm, val_temp$Delta_obs_permil);
val_temp$chamber_13gm_point_simple <-
# switch added for A_photosynthesis 9/5/2012
#f_val_calc_gm_point_simple( val_const$b_gm, val_const$b_s, val_const$a_l, val_temp$TDL_13A_photosynthesis
f_val_calc_gm_point_simple( val_const$b_gm, val_const$b_s, val_const$a_l, val_temp$selected_13A_photosynthesis
,val_temp$chamber_13pa, val_temp$chamber_Delta_i_simple_for_gm, val_temp$Delta_obs_permil);
##details<<
## gm point complex, internal leaf (mesophyll) conductance calculated for every D value estimating decarboxylation effects. \code{\link{f_val_calc_gm_point_complex}}
val_temp$chamber_Totalgm_point_complex <-
# switch added for A_photosynthesis 9/5/2012
#f_val_calc_gm_point_complex( val_const$b_gm, val_const$b_s, val_const$a_l, val_Licor$A
f_val_calc_gm_point_complex( val_const$b_gm, val_const$b_s, val_const$a_l, val_temp$selected_A_photosynthesis
,val_temp$chamber_Totalpa, val_temp$chamber_Delta_i_complex_for_gm, val_temp$Delta_obs_permil # 8/19/2011 use permil
,val_const$f_photo_respiration, val_const$Gamma_star
,val_const$e, val_const$Rd, val_const$k);
##details<<
## select one of the calculated gm values to use
val_temp$chamber_Totalgm_to_use <- NULL; # as default
switch(sw$calc_gm_to_use
# 1 = gm_point_simple
, val_temp$chamber_Totalgm_to_use <- val_temp$chamber_Totalgm_point_simple
# 2 = gm_point_complex
, val_temp$chamber_Totalgm_to_use <- val_temp$chamber_Totalgm_point_complex
);
# # Plot gm point simple and complex, internal leaf (mesophyll) conductance calculated for every D value ignoring and estimating decarboxylation effects
# p_o <- paste("Plot gm point simple and complex, internal leaf (mesophyll) conductance calculated for every D value ignoring and estimating decarboxylation effects\n"); wWw <- write_progress(p_o, time_start);
#plot_gm(val_temp$chamber_Totalgm_point_simple, val_temp$chamber_12gm_point_simple, val_temp$chamber_13gm_point_simple
# ,val_temp$chamber_Totalgm_point_complex
# ,val_TDL$time, plot_format_list)
#-------------------
##details<<
## SECTION pc
##details<<
## pc using gm, total partial pressure of CO2 at the site of carboxylation, Press is the atmospheric pressure value from the LI6400. \code{\link{f_val_calc_pc_using_gm}}
# switch added for A_photosynthesis 9/5/2012
#val_temp$chamber_Totalpc_using_gm <- f_val_calc_pc_using_gm(val_temp$chamber_Totalpi, val_Licor$A, val_temp$chamber_Totalgm_to_use);
#val_temp$chamber_12pc_using_gm <- f_val_calc_pc_using_gm(val_temp$chamber_12pi , val_Licor$A, val_temp$chamber_Totalgm_to_use);
#val_temp$chamber_13pc_using_gm <- f_val_calc_pc_using_gm(val_temp$chamber_13pi , val_Licor$A, val_temp$chamber_Totalgm_to_use);
val_temp$chamber_Totalpc_using_gm <- f_val_calc_pc_using_gm(val_temp$chamber_Totalpi, val_temp$selected_A_photosynthesis, val_temp$chamber_Totalgm_to_use);
val_temp$chamber_12pc_using_gm <- f_val_calc_pc_using_gm(val_temp$chamber_12pi , val_temp$selected_12A_photosynthesis, val_temp$chamber_Totalgm_to_use);
val_temp$chamber_13pc_using_gm <- f_val_calc_pc_using_gm(val_temp$chamber_13pi , val_temp$selected_13A_photosynthesis, val_temp$chamber_Totalgm_to_use);
##details<<
## pc using simple D for gm, includes boundary layer. \code{\link{f_val_calc_pc_using_simple_Delta_for_gm}}
val_temp$chamber_Totalpc_using_simple_Delta_for_gm <-
f_val_calc_pc_using_simple_Delta_for_gm( val_temp$chamber_Delta_i_simple_for_gm, val_temp$chamber_Totalpa
,val_temp$chamber_Totalps, val_const$a, val_const$b_gm, val_const$a_b);
##details<<
## pc using simple D for modeling. \code{\link{f_val_calc_pc_using_simple_Delta_for_modeling}}
val_temp$chamber_Totalpc_using_simple_Delta_for_modeling <-
f_val_calc_pc_using_simple_Delta_for_modeling( val_temp$chamber_Delta_i_simple_for_modeling, val_temp$chamber_Totalpa
,val_const$a, val_const$b_modeling);
# # # What value of b to use here?
##details<<
## pc using complex D, no decarboxylation [ab(pa-ps)+a(ps-pi)+pi(bs+al)-Dpa]/(bs+al-b) is this different from two up? They give different values but both may not be derived properly. \code{\link{f_val_calc_pc_using_complex_Delta_no_decarboxylation}}
val_temp$chamber_Totalpc_using_complex_Delta_no_decarboxylation <-
f_val_calc_pc_using_complex_Delta_no_decarboxylation( val_temp$chamber_Delta_i_complex_for_gm, val_temp$chamber_Totalpa
,val_temp$chamber_Totalps, val_temp$chamber_Totalpi
,val_const$a, val_const$a_b, val_const$a_l, val_const$b_modeling, val_const$b_s)
# # # What value of b to use here?
##details<<
## pc using complex D, full model [ab(pa-ps)+a(ps-pi)+pi(bs+al)-(eRd/k+fG*)-Dpa]/(bs+al-b) includes boundary layer and decarboxylation effects. \code{\link{f_val_calc_pc_using_complex_Delta_full_model}}
val_temp$chamber_Totalpc_using_complex_Delta_full_model <-
f_val_calc_pc_using_complex_Delta_full_model( val_temp$chamber_Delta_i_complex_for_gm, val_temp$chamber_Totalpa
,val_temp$chamber_Totalps, val_temp$chamber_Totalpi
,val_const$a, val_const$a_b, val_const$a_l, val_const$b_modeling, val_const$b_s
,val_const$e, val_const$Rd, val_const$k, val_const$Gamma_star, val_const$f_photo_respiration)
# # Plot pc, total partial pressure of CO2 at the site of carboxylation
# p_o <- paste("Plot pc, total partial pressure of CO2 at the site of carboxylation\n"); wWw <- write_progress(p_o, time_start);
#plot_pc_total( val_temp$chamber_Totalpc_using_gm, val_temp$chamber_12pc_using_gm, val_temp$chamber_13pc_using_gm
# ,val_TDL$time, plot_format_list)
#
# # Plot pc, simple and complex
# p_o <- paste("Plot pc, simple and complex\n"); wWw <- write_progress(p_o, time_start);
#plot_pc_simple_complex(val_temp$chamber_Totalpc_using_simple_Delta_for_gm, val_temp$chamber_Totalpc_using_simple_Delta_for_modeling
# ,val_temp$chamber_Totalpc_using_complex_Delta_no_decarboxylation, val_temp$chamber_Totalpc_using_complex_Delta_full_model
# ,val_TDL$time, plot_format_list)
##details<<
## select one of the calculated pc values to use
val_temp$chamber_Totalpc_to_use <- NULL; # as default
switch(sw$calc_pc_to_use
# 1 = pc_using_gm
, val_temp$chamber_Totalpc_to_use <- val_temp$chamber_Totalpc_using_gm
# 2 = pc_using_simple_Delta_for_gm
, val_temp$chamber_Totalpc_to_use <- val_temp$chamber_Totalpc_using_simple_Delta_for_gm
# 3 = pc_using_simple_Delta_for_modeling
, val_temp$chamber_Totalpc_to_use <- val_temp$chamber_Totalpc_using_simple_Delta_for_modeling
# 4 = pc_using_complex_Delta_no_decarboxylation
, val_temp$chamber_Totalpc_to_use <- val_temp$chamber_Totalpc_using_complex_Delta_no_decarboxylation
# 5 = pc_using_complex_Delta_full_model
, val_temp$chamber_Totalpc_to_use <- val_temp$chamber_Totalpc_using_complex_Delta_full_model
);
# (after pc -- one of the several pc's)
##details<<
## Cc (pc*10^6)/(Press*1000) ppm CO2 concentration at the site of carboxylation, generally meaning inside the chloroplast and ignoring PEPC in cytosol. \code{\link{f_val_calc_pp}}
## NB: same formula as pa, but using pc instead of Co
val_temp$chamber_TotalCc <- f_val_calc_pp(val_temp$chamber_Totalpc_using_gm, val_Licor$Atm_press);
val_temp$chamber_12Cc <- f_val_calc_pp(val_temp$chamber_12pc_using_gm , val_Licor$Atm_press);
val_temp$chamber_13Cc <- f_val_calc_pp(val_temp$chamber_13pc_using_gm , val_Licor$Atm_press);
# # Plot Cc, ppm CO2 concentration at the site of carboxylation, generally meaning inside the chloroplast and ignoring PEPC in cytosol
# p_o <- paste("Plot Cc, ppm CO2 concentration at the site of carboxylation\n"); wWw <- write_progress(p_o, time_start);
#plot_Cc_total(val_temp$chamber_TotalCc, val_temp$chamber_12Cc, val_temp$chamber_13Cc
# ,val_TDL$time, plot_format_list)
return( val_temp );
### val_temp
}
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