R/assign_param_variables.R
In erikerhardt/isogasex: Isotopic gas exchange using TDL and Licor input. Updated version of package tdllicor
#' Assign PARAM_RAW values from input file to variable names
#'
#' initialize lists to hold all data/output
#'
#' Template version
#'
#' switches to use and filenames for TDL and Licor files
#'
#' Prefix for output filenames
#'
#' TIME WINDOW SECTION
#'
#' OUTPUT SECTION
#'
#' plot formats
#'
#' interpolation: 1 = smooth_spline() like tanks
#' 2 = use last reference mean until next measurement (horizontal interp) - for abrupt ref gas changes
#'
#' Bootstrap
#'
#' TDL sampling information
#'
#' CONSTANTS SECTION
#'
#' True calibration tank values
#'
#' Which values to use
#'
#' constants in formulas not given names
#'
#' Calculation information
#'
#' create a list to all returned parameters
#'
#' @param D xxxPARAMxxx
#' @param path xxxPARAMxxx
#'
#' @return PARAM list of all inputs from Excel template
#'
assign_param_variables <-
function# Assign variables from input file to variable names
###
(D
###
, path
###
)
{
################################################################################
# Assign variables from input file to variable names
# When making changes to the workbook, need to:
# 1. read_template_param.R define sheet names
# 2. assign_param_variables.R define variables
## DEBUG
# D <- DATA
##details<<
## initialize lists to hold all data/output
sw <- list(); # create a list for option switches
# Conventions, ultimately put everything in val
val <- list();
# Constants prefix: val$const$*
val$const <- list();
## Results (output) are in val$calc variables
# Calculated prefix: val$calc$*
val$calc <- list();
val$calc$obs <- list(); # for calculated observed values to use in NP bootstrap
val$calc$all <- list(); # for all calculated values in time window "0.1-16" "2012-07-11"
val$calc$sum <- list(); # for calculated summarized (mean) values to use as estimates
val$write <- list(); # to create tables to write_out to files
##details<<
## Template version
sw$template_version <- as.numeric(D$Template_version); # Version of template must match isogasex
# blank spreadsheet line
# Parameter
##details<<
## switches to use and filenames for TDL and Licor files
# blank spreadsheet line
sw$use_TDL <- as.numeric(D$sw_use_TDL); # 1 = process TDL data, 0 = do not use TDL data
TDL_fn <- paste(path, "/", as.character(D$TDL_fn), sep="");
sw$use_Licor <- as.numeric(D$sw_use_Licor); # 1 = process Licor data, 0 = do not use Licor data
Licor_fn <- paste(path, "/", as.character(D$Licor_fn), sep="");
# blank spreadsheet line
# blank spreadsheet line
##details<<
## Prefix for output filenames
# blank spreadsheet line
output_fn_prefix <- as.character(D$output_fn_prefix); # this prefix will appear on all output files
##details<<
## TIME WINDOW SECTION
# blank spreadsheet line
# two rows at a time
val$timewindow$start_time <- strptime(paste(D$Start_date,D$Start_time), "%m/%d/%y %H:%M:%S");
# row in start_time
val$timewindow$end_time <- strptime(paste(D$End_date,D$End_time), "%m/%d/%y %H:%M:%S");
# row in end_time
##details<<
## OUTPUT SECTION
# blank spreadsheet line
sw$print_TDL_missing <- as.numeric(D$print_TDL_missing); # high tank
sw$print_TDL_cycle_timing <- as.numeric(D$print_TDL_cycle_timing); # low tank
sw$write_all_obs_file <- as.numeric(D$write_all_obs_file); # leaf reference
sw$save_RData <- as.numeric(D$save_RData); # leaf reference
# blank spreadsheet line
# blank spreadsheet line
##details<<
## plot formats
# blank spreadsheet line
plot_format_list <- NULL; # 1=png, 2=eps, 3=pdf, 4=bmp, 5=jpeg, 6=tiff
if ( as.numeric(D$
# plot formats
png) ) { plot_format_list <- c(plot_format_list, 1); }; # png
if ( as.numeric(D$eps) ) { plot_format_list <- c(plot_format_list, 2); }; # eps
if ( as.numeric(D$pdf) ) { plot_format_list <- c(plot_format_list, 3); }; # pdf
if ( as.numeric(D$bmp) ) { plot_format_list <- c(plot_format_list, 4); }; # bmp
if ( as.numeric(D$jpeg) ) { plot_format_list <- c(plot_format_list, 5); }; # jpeg
if ( as.numeric(D$tiff) ) { plot_format_list <- c(plot_format_list, 6); }; # tiff
#if (sw$use_TDL ) { output_summary_TDL_fn <- paste(output_fn_prefix, "_summary_TDL.csv", sep=""); };
#if (sw$use_Licor) { output_summary_Licor_fn <- paste(output_fn_prefix, "_summary_Licor.csv", sep=""); };
output_summary_TDL_fn <- paste(output_fn_prefix, "_summary_TDL.csv", sep="");
output_summary_Licor_fn <- paste(output_fn_prefix, "_summary_Licor.csv", sep="");
output_summary_Calc_fn <- paste(output_fn_prefix, "_summary_Calc.csv", sep="");
output_summary_Calc_last_fn <- paste(output_fn_prefix, "_summary_Calc_last.csv", sep="");
output_all_Calc_fn <- paste(output_fn_prefix, "_all_Calc.csv", sep=""); # "0.1-16" "2012-07-11"
output_CI_TDL_fn <- paste(output_fn_prefix, "_CI_TDL.csv", sep="");
output_CI_Licor_fn <- paste(output_fn_prefix, "_CI_Licor.csv", sep="");
output_CI_Calc_fn <- paste(output_fn_prefix, "_CI_Calc.csv", sep="");
output_CI_Calc_last_fn <- paste(output_fn_prefix, "_CI_Calc_last.csv", sep="");
##details<<
## interpolation: 1 = smooth.spline() like tanks
## 2 = use last reference mean until next measurement (horizontal interp) - for abrupt ref gas changes
# blank spreadsheet line
# blank spreadsheet line
sw$interp_tank_hi <- as.numeric(D$interp_tank_hi); # high tank
sw$interp_tank_low <- as.numeric(D$interp_tank_low); # low tank
sw$interp_reference <- as.numeric(D$interp_reference); # leaf reference
##details<<
## Bootstrap
# blank spreadsheet line
R_bootstrap <- as.numeric(D$R_bootstrap); # Number of bootstrap samples to assess uncertainty of estimates
sig_CI <- as.numeric(D$sig_CI); # Confidence level for central confidence interval
seed <- as.numeric(D$seed); # pseudorandom number seed, 0 is random based on clock, set to integer for results to be repeatable
# blank spreadsheet line
# blank spreadsheet line
##details<<
## TDL sampling information
TDL_cycle <- list(); # create a list to return with data
# number.* is TDL field "PrevSite"
TDL_cycle$number_tank_hi <- as.numeric(D$number_tank_hi); # 9; # high tank
TDL_cycle$number_tank_low <- as.numeric(D$number_tank_low); #10; # low tank
TDL_cycle$number_reference <- as.numeric(D$number_reference); # 1; # leaf reference
TDL_cycle$number_chamber <- as.numeric(D$number_chamber); #21; # leaf chamber
TDL_cycle$name_tank_hi <- as.character(D$name_tank_hi); #"tank_hi"; # high tank
TDL_cycle$name_tank_low <- as.character(D$name_tank_low); #"tank_low"; # low tank
TDL_cycle$name_reference <- as.character(D$name_reference); #"reference"; # leaf reference
TDL_cycle$name_chamber <- as.character(D$name_chamber); #"chamber"; # leaf chamber
# blank spreadsheet line
# seconds is time length of measurements to use as data
TDL_cycle$seconds_tank_hi <- as.numeric(D$seconds_tank_hi); # high tank
TDL_cycle$seconds_tank_low <- as.numeric(D$seconds_tank_low); # low tank
TDL_cycle$seconds_reference <- as.numeric(D$seconds_reference); # leaf reference
TDL_cycle$seconds_chamber <- as.numeric(D$seconds_chamber); # leaf chamber
TDL_cycle$Hz <- as.numeric(D$Hz); # sampling rate, output of TDL
TDL_cycle$seconds_exclude_first_chamber <- as.numeric(D$seconds_exclude_first_chamber); # time it takes to equilbrate from reference to leaf chamber
TDL_cycle <- set_TDL_cycle(TDL_cycle); # TDL_cycle variables
# If using Licor file
# blank spreadsheet line
Licor_TDL_time_offset_seconds <- as.numeric(D$Licor_TDL_time_offset_seconds);
# positive indicates Licor is ahead of TDL
# (e.g., 16 has Licor = 12:00:00 matches TDL = 12:00:16)
# (that is, gas takes 16 seconds to get from Licor to TDL)
#if (sw$use_Licor) {
# Licor_TDL_time_offset_seconds <- 0; # positive indicates Licor is ahead of TDL
# # (e.g., 16 has Licor = 12:00:00 matches TDL = 12:00:16)
# # (that is, gas takes 16 seconds to get from Licor to TDL)
#};
# blank spreadsheet line
# blank spreadsheet line
# blank spreadsheet line
##details<<
## CONSTANTS SECTION
##details<<
## True calibration tank values
# blank spreadsheet line
val$const$true_value_hi_12C <- as.numeric(D$true_value_hi_12C); # example tank values
val$const$true_value_hi_13C <- as.numeric(D$true_value_hi_13C);
val$const$true_value_lo_12C <- as.numeric(D$true_value_lo_12C);
val$const$true_value_lo_13C <- as.numeric(D$true_value_lo_13C);
# blank spreadsheet line
val$const$fo_13C <- as.numeric(D$fo_13C); # 0.00474; # if only 12 and 13CO2 are measured, fo means fraction of other isotopologues not measured
val$const$fo_18O <- as.numeric(D$fo_18O); # if 12 and 13CO2, and 12C18O16O are measured (not ususal for Dave's machine)
val$const$Rstd_13C <- as.numeric(D$Rstd_13C); # (Rvpdb)
val$const$Rstd_18O <- as.numeric(D$Rstd_18O); # (Rvsmow) may occaisionally be used with Dave's machine, method not tested yet
# blank spreadsheet line
val$const$Gamma_star <- as.numeric(D$Gamma_star); # CO2 compensation point in absence of day respiration. I will need to specify experiment specific values for these constants in the equations below
val$const$f_photo_respiration <- as.numeric(D$f_photo_respiration); # fractionation associated with photorespiration
val$const$e <- as.numeric(D$e); # fractionation associated with day respiration
val$const$Rd <- as.numeric(D$Rd); # day respiration
val$const$k <- as.numeric(D$k); # carboxylation efficiency, often initial slope of A/Ci, or better A/Cc
val$const$b_gm <- as.numeric(D$b_gm);
val$const$b_modeling <- as.numeric(D$b_modeling);
val$const$b_s <- as.numeric(D$b_s); # per mil fractionation as CO2 enters solution at 25C bs = 1.1
# blank spreadsheet line
val$const$a <- as.numeric(D$a); # per mil fractionation in still air (stomatal pore and substomata) a1 = 0.7
val$const$a_b <- as.numeric(D$a_b); # per mil fractionation in boundary layer (slightly mixed) a = 4.44
val$const$a_l <- as.numeric(D$a_l); # per mil fractionation during diffusion in water
val$const$a_i <- val$const$a_l + val$const$b_s; # al+bs
# blank spreadsheet line
##details<<
## Which values to use
# blank spreadsheet line
sw$Licor_or_TDL_A_photosynthesis <- as.numeric(D$Licor_or_TDL_A_photosynthesis); # 1=use Licor values, 0=use specified values for (val$const$flow_rate, val$const$leaf_area, val$const$boundary_layer_cond_to_water, val$const$H2OS, val$const$StmRat)
# blank spreadsheet line
sw$val_const_override_Licor_flow_rate <- as.numeric(D$override_Licor_flow_rate); # 1=use Licor values, 0=use specified values for (val$const$flow_rate, val$const$leaf_area, val$const$boundary_layer_cond_to_water, val$const$H2OS, val$const$StmRat)
val$const$flow_rate <- as.numeric(D$Licor_flow_rate); # these values will normally come from the LI6400, but occaisonally I may want to specify different constants,
sw$val_const_override_Licor_leaf_area <- as.numeric(D$override_Licor_leaf_area); # 1=use Licor values, 0=use specified values for (val$const$flow_rate, val$const$leaf_area, val$const$boundary_layer_cond_to_water, val$const$H2OS, val$const$StmRat)
val$const$leaf_area <- as.numeric(D$Licor_leaf_area); # so when they are used in equations below,
sw$val_const_override_Licor_boundary_layer_cond_to_water <- as.numeric(D$override_Licor_boundary_layer_cond_to_water); # 1=use Licor values, 0=use specified values for (val$const$flow_rate, val$const$leaf_area, val$const$boundary_layer_cond_to_water, val$const$H2OS, val$const$StmRat)
val$const$boundary_layer_cond_to_water <- as.numeric(D$Licor_boundary_layer_cond_to_water); # I would like to have the option to choose these constants instead of the values in the LI64000 file (gbw)
sw$val_const_override_Licor_H2OS <- as.numeric(D$override_Licor_H2OS); # 1=use Licor values, 0=use specified values for (val$const$flow_rate, val$const$leaf_area, val$const$boundary_layer_cond_to_water, val$const$H2OS, val$const$StmRat)
val$const$H2OS <- as.numeric(D$Licor_H2OS); # Not in calcs below yet
sw$val_const_override_Licor_StmRat <- as.numeric(D$override_Licor_StmRat); # 1=use Licor values, 0=use specified values for (val$const$flow_rate, val$const$leaf_area, val$const$boundary_layer_cond_to_water, val$const$H2OS, val$const$StmRat)
val$const$StmRat <- as.numeric(D$Licor_StmRat); # Not in calcs below yet
##details<<
## constants in formulas not given names
# blank spreadsheet line
val$const$gbc_1.37 <- as.numeric(D$gbc_1_37); # gbc BLcond/1.37 boudary layer conductance for CO2
val$const$gsc_1.6 <- as.numeric(D$gsc_1_6); # gsc gsw/1.6 stomatal conductance for CO2
# blank spreadsheet line
##details<<
## Calculation information
# blank spreadsheet line
sw$calc_pc_to_use <- as.numeric(D$calc_pc_to_use);
# 1 = pc_using_gm
# 2 = pc_using_simple_Delta_for_gm
# 3 = pc_using_simple_Delta_for_modeling
# 4 = pc_using_complex_Delta_no_decarboxylation
# 5 = pc_using_complex_Delta_full_model
# blank spreadsheet line
# blank spreadsheet line
# blank spreadsheet line
# blank spreadsheet line
# NOT USED
# blank spreadsheet line
sw$calc_Delta_i_to_use <- as.numeric(D$calc_Delta_i_to_use);
# 1 = Delta_i_simple_for_gm
# 2 = Delta_i_simple_for_modeling
# 3 = Delta_i_complex_for_gm
# blank spreadsheet line
# blank spreadsheet line
# blank spreadsheet line
sw$calc_gm_to_use <- as.numeric(D$calc_gm_to_use);
# 1 = gm_point_simple
# 2 = gm_point_complex
# blank spreadsheet line
# blank spreadsheet line
##############################################################################
##details<<
## create a list to all returned parameters
PARAM <- list();
PARAM$val <- val ;
PARAM$sw <- sw ;
PARAM$TDL_fn <- TDL_fn ;
PARAM$Licor_fn <- Licor_fn ;
PARAM$plot_format_list <- plot_format_list ;
PARAM$output_fn_prefix <- output_fn_prefix ;
PARAM$output_summary_TDL_fn <- output_summary_TDL_fn ;
PARAM$output_summary_Licor_fn <- output_summary_Licor_fn ;
PARAM$output_summary_Calc_fn <- output_summary_Calc_fn ;
PARAM$output_summary_Calc_last_fn <- output_summary_Calc_last_fn ;
PARAM$output_all_Calc_fn <- output_all_Calc_fn ; # "0.1-16" "2012-07-11"
PARAM$output_CI_TDL_fn <- output_CI_TDL_fn ;
PARAM$output_CI_Licor_fn <- output_CI_Licor_fn ;
PARAM$output_CI_Calc_fn <- output_CI_Calc_fn ;
PARAM$output_CI_Calc_last_fn <- output_CI_Calc_last_fn ;
PARAM$R_bootstrap <- R_bootstrap ;
PARAM$sig_CI <- sig_CI ;
PARAM$seed <- seed ;
PARAM$TDL_cycle <- TDL_cycle ;
PARAM$Licor_TDL_time_offset_seconds <- Licor_TDL_time_offset_seconds;
return( PARAM );
### PARAM list of all inputs from template
} # assign_param_variables()
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#' Assign PARAM_RAW values from input file to variable names
#'
#' initialize lists to hold all data/output
#'
#' Template version
#'
#' switches to use and filenames for TDL and Licor files
#'
#' Prefix for output filenames
#'
#' TIME WINDOW SECTION
#'
#' OUTPUT SECTION
#'
#' plot formats
#'
#' interpolation: 1 = smooth_spline() like tanks
#' 2 = use last reference mean until next measurement (horizontal interp) - for abrupt ref gas changes
#'
#' Bootstrap
#'
#' TDL sampling information
#'
#' CONSTANTS SECTION
#'
#' True calibration tank values
#'
#' Which values to use
#'
#' constants in formulas not given names
#'
#' Calculation information
#'
#' create a list to all returned parameters
#'
#' @param D xxxPARAMxxx
#' @param path xxxPARAMxxx
#'
#' @return PARAM list of all inputs from Excel template
#'
assign_param_variables <-
function# Assign variables from input file to variable names
###
(D
###
, path
###
)
{
################################################################################
# Assign variables from input file to variable names
# When making changes to the workbook, need to:
# 1. read_template_param.R define sheet names
# 2. assign_param_variables.R define variables
## DEBUG
# D <- DATA
##details<<
## initialize lists to hold all data/output
sw <- list(); # create a list for option switches
# Conventions, ultimately put everything in val
val <- list();
# Constants prefix: val$const$*
val$const <- list();
## Results (output) are in val$calc variables
# Calculated prefix: val$calc$*
val$calc <- list();
val$calc$obs <- list(); # for calculated observed values to use in NP bootstrap
val$calc$all <- list(); # for all calculated values in time window "0.1-16" "2012-07-11"
val$calc$sum <- list(); # for calculated summarized (mean) values to use as estimates
val$write <- list(); # to create tables to write_out to files
##details<<
## Template version
sw$template_version <- as.numeric(D$Template_version); # Version of template must match isogasex
# blank spreadsheet line
# Parameter
##details<<
## switches to use and filenames for TDL and Licor files
# blank spreadsheet line
sw$use_TDL <- as.numeric(D$sw_use_TDL); # 1 = process TDL data, 0 = do not use TDL data
TDL_fn <- paste(path, "/", as.character(D$TDL_fn), sep="");
sw$use_Licor <- as.numeric(D$sw_use_Licor); # 1 = process Licor data, 0 = do not use Licor data
Licor_fn <- paste(path, "/", as.character(D$Licor_fn), sep="");
# blank spreadsheet line
# blank spreadsheet line
##details<<
## Prefix for output filenames
# blank spreadsheet line
output_fn_prefix <- as.character(D$output_fn_prefix); # this prefix will appear on all output files
##details<<
## TIME WINDOW SECTION
# blank spreadsheet line
# two rows at a time
val$timewindow$start_time <- strptime(paste(D$Start_date,D$Start_time), "%m/%d/%y %H:%M:%S");
# row in start_time
val$timewindow$end_time <- strptime(paste(D$End_date,D$End_time), "%m/%d/%y %H:%M:%S");
# row in end_time
##details<<
## OUTPUT SECTION
# blank spreadsheet line
sw$print_TDL_missing <- as.numeric(D$print_TDL_missing); # high tank
sw$print_TDL_cycle_timing <- as.numeric(D$print_TDL_cycle_timing); # low tank
sw$write_all_obs_file <- as.numeric(D$write_all_obs_file); # leaf reference
sw$save_RData <- as.numeric(D$save_RData); # leaf reference
# blank spreadsheet line
# blank spreadsheet line
##details<<
## plot formats
# blank spreadsheet line
plot_format_list <- NULL; # 1=png, 2=eps, 3=pdf, 4=bmp, 5=jpeg, 6=tiff
if ( as.numeric(D$
# plot formats
png) ) { plot_format_list <- c(plot_format_list, 1); }; # png
if ( as.numeric(D$eps) ) { plot_format_list <- c(plot_format_list, 2); }; # eps
if ( as.numeric(D$pdf) ) { plot_format_list <- c(plot_format_list, 3); }; # pdf
if ( as.numeric(D$bmp) ) { plot_format_list <- c(plot_format_list, 4); }; # bmp
if ( as.numeric(D$jpeg) ) { plot_format_list <- c(plot_format_list, 5); }; # jpeg
if ( as.numeric(D$tiff) ) { plot_format_list <- c(plot_format_list, 6); }; # tiff
#if (sw$use_TDL ) { output_summary_TDL_fn <- paste(output_fn_prefix, "_summary_TDL.csv", sep=""); };
#if (sw$use_Licor) { output_summary_Licor_fn <- paste(output_fn_prefix, "_summary_Licor.csv", sep=""); };
output_summary_TDL_fn <- paste(output_fn_prefix, "_summary_TDL.csv", sep="");
output_summary_Licor_fn <- paste(output_fn_prefix, "_summary_Licor.csv", sep="");
output_summary_Calc_fn <- paste(output_fn_prefix, "_summary_Calc.csv", sep="");
output_summary_Calc_last_fn <- paste(output_fn_prefix, "_summary_Calc_last.csv", sep="");
output_all_Calc_fn <- paste(output_fn_prefix, "_all_Calc.csv", sep=""); # "0.1-16" "2012-07-11"
output_CI_TDL_fn <- paste(output_fn_prefix, "_CI_TDL.csv", sep="");
output_CI_Licor_fn <- paste(output_fn_prefix, "_CI_Licor.csv", sep="");
output_CI_Calc_fn <- paste(output_fn_prefix, "_CI_Calc.csv", sep="");
output_CI_Calc_last_fn <- paste(output_fn_prefix, "_CI_Calc_last.csv", sep="");
##details<<
## interpolation: 1 = smooth.spline() like tanks
## 2 = use last reference mean until next measurement (horizontal interp) - for abrupt ref gas changes
# blank spreadsheet line
# blank spreadsheet line
sw$interp_tank_hi <- as.numeric(D$interp_tank_hi); # high tank
sw$interp_tank_low <- as.numeric(D$interp_tank_low); # low tank
sw$interp_reference <- as.numeric(D$interp_reference); # leaf reference
##details<<
## Bootstrap
# blank spreadsheet line
R_bootstrap <- as.numeric(D$R_bootstrap); # Number of bootstrap samples to assess uncertainty of estimates
sig_CI <- as.numeric(D$sig_CI); # Confidence level for central confidence interval
seed <- as.numeric(D$seed); # pseudorandom number seed, 0 is random based on clock, set to integer for results to be repeatable
# blank spreadsheet line
# blank spreadsheet line
##details<<
## TDL sampling information
TDL_cycle <- list(); # create a list to return with data
# number.* is TDL field "PrevSite"
TDL_cycle$number_tank_hi <- as.numeric(D$number_tank_hi); # 9; # high tank
TDL_cycle$number_tank_low <- as.numeric(D$number_tank_low); #10; # low tank
TDL_cycle$number_reference <- as.numeric(D$number_reference); # 1; # leaf reference
TDL_cycle$number_chamber <- as.numeric(D$number_chamber); #21; # leaf chamber
TDL_cycle$name_tank_hi <- as.character(D$name_tank_hi); #"tank_hi"; # high tank
TDL_cycle$name_tank_low <- as.character(D$name_tank_low); #"tank_low"; # low tank
TDL_cycle$name_reference <- as.character(D$name_reference); #"reference"; # leaf reference
TDL_cycle$name_chamber <- as.character(D$name_chamber); #"chamber"; # leaf chamber
# blank spreadsheet line
# seconds is time length of measurements to use as data
TDL_cycle$seconds_tank_hi <- as.numeric(D$seconds_tank_hi); # high tank
TDL_cycle$seconds_tank_low <- as.numeric(D$seconds_tank_low); # low tank
TDL_cycle$seconds_reference <- as.numeric(D$seconds_reference); # leaf reference
TDL_cycle$seconds_chamber <- as.numeric(D$seconds_chamber); # leaf chamber
TDL_cycle$Hz <- as.numeric(D$Hz); # sampling rate, output of TDL
TDL_cycle$seconds_exclude_first_chamber <- as.numeric(D$seconds_exclude_first_chamber); # time it takes to equilbrate from reference to leaf chamber
TDL_cycle <- set_TDL_cycle(TDL_cycle); # TDL_cycle variables
# If using Licor file
# blank spreadsheet line
Licor_TDL_time_offset_seconds <- as.numeric(D$Licor_TDL_time_offset_seconds);
# positive indicates Licor is ahead of TDL
# (e.g., 16 has Licor = 12:00:00 matches TDL = 12:00:16)
# (that is, gas takes 16 seconds to get from Licor to TDL)
#if (sw$use_Licor) {
# Licor_TDL_time_offset_seconds <- 0; # positive indicates Licor is ahead of TDL
# # (e.g., 16 has Licor = 12:00:00 matches TDL = 12:00:16)
# # (that is, gas takes 16 seconds to get from Licor to TDL)
#};
# blank spreadsheet line
# blank spreadsheet line
# blank spreadsheet line
##details<<
## CONSTANTS SECTION
##details<<
## True calibration tank values
# blank spreadsheet line
val$const$true_value_hi_12C <- as.numeric(D$true_value_hi_12C); # example tank values
val$const$true_value_hi_13C <- as.numeric(D$true_value_hi_13C);
val$const$true_value_lo_12C <- as.numeric(D$true_value_lo_12C);
val$const$true_value_lo_13C <- as.numeric(D$true_value_lo_13C);
# blank spreadsheet line
val$const$fo_13C <- as.numeric(D$fo_13C); # 0.00474; # if only 12 and 13CO2 are measured, fo means fraction of other isotopologues not measured
val$const$fo_18O <- as.numeric(D$fo_18O); # if 12 and 13CO2, and 12C18O16O are measured (not ususal for Dave's machine)
val$const$Rstd_13C <- as.numeric(D$Rstd_13C); # (Rvpdb)
val$const$Rstd_18O <- as.numeric(D$Rstd_18O); # (Rvsmow) may occaisionally be used with Dave's machine, method not tested yet
# blank spreadsheet line
val$const$Gamma_star <- as.numeric(D$Gamma_star); # CO2 compensation point in absence of day respiration. I will need to specify experiment specific values for these constants in the equations below
val$const$f_photo_respiration <- as.numeric(D$f_photo_respiration); # fractionation associated with photorespiration
val$const$e <- as.numeric(D$e); # fractionation associated with day respiration
val$const$Rd <- as.numeric(D$Rd); # day respiration
val$const$k <- as.numeric(D$k); # carboxylation efficiency, often initial slope of A/Ci, or better A/Cc
val$const$b_gm <- as.numeric(D$b_gm);
val$const$b_modeling <- as.numeric(D$b_modeling);
val$const$b_s <- as.numeric(D$b_s); # per mil fractionation as CO2 enters solution at 25C bs = 1.1
# blank spreadsheet line
val$const$a <- as.numeric(D$a); # per mil fractionation in still air (stomatal pore and substomata) a1 = 0.7
val$const$a_b <- as.numeric(D$a_b); # per mil fractionation in boundary layer (slightly mixed) a = 4.44
val$const$a_l <- as.numeric(D$a_l); # per mil fractionation during diffusion in water
val$const$a_i <- val$const$a_l + val$const$b_s; # al+bs
# blank spreadsheet line
##details<<
## Which values to use
# blank spreadsheet line
sw$Licor_or_TDL_A_photosynthesis <- as.numeric(D$Licor_or_TDL_A_photosynthesis); # 1=use Licor values, 0=use specified values for (val$const$flow_rate, val$const$leaf_area, val$const$boundary_layer_cond_to_water, val$const$H2OS, val$const$StmRat)
# blank spreadsheet line
sw$val_const_override_Licor_flow_rate <- as.numeric(D$override_Licor_flow_rate); # 1=use Licor values, 0=use specified values for (val$const$flow_rate, val$const$leaf_area, val$const$boundary_layer_cond_to_water, val$const$H2OS, val$const$StmRat)
val$const$flow_rate <- as.numeric(D$Licor_flow_rate); # these values will normally come from the LI6400, but occaisonally I may want to specify different constants,
sw$val_const_override_Licor_leaf_area <- as.numeric(D$override_Licor_leaf_area); # 1=use Licor values, 0=use specified values for (val$const$flow_rate, val$const$leaf_area, val$const$boundary_layer_cond_to_water, val$const$H2OS, val$const$StmRat)
val$const$leaf_area <- as.numeric(D$Licor_leaf_area); # so when they are used in equations below,
sw$val_const_override_Licor_boundary_layer_cond_to_water <- as.numeric(D$override_Licor_boundary_layer_cond_to_water); # 1=use Licor values, 0=use specified values for (val$const$flow_rate, val$const$leaf_area, val$const$boundary_layer_cond_to_water, val$const$H2OS, val$const$StmRat)
val$const$boundary_layer_cond_to_water <- as.numeric(D$Licor_boundary_layer_cond_to_water); # I would like to have the option to choose these constants instead of the values in the LI64000 file (gbw)
sw$val_const_override_Licor_H2OS <- as.numeric(D$override_Licor_H2OS); # 1=use Licor values, 0=use specified values for (val$const$flow_rate, val$const$leaf_area, val$const$boundary_layer_cond_to_water, val$const$H2OS, val$const$StmRat)
val$const$H2OS <- as.numeric(D$Licor_H2OS); # Not in calcs below yet
sw$val_const_override_Licor_StmRat <- as.numeric(D$override_Licor_StmRat); # 1=use Licor values, 0=use specified values for (val$const$flow_rate, val$const$leaf_area, val$const$boundary_layer_cond_to_water, val$const$H2OS, val$const$StmRat)
val$const$StmRat <- as.numeric(D$Licor_StmRat); # Not in calcs below yet
##details<<
## constants in formulas not given names
# blank spreadsheet line
val$const$gbc_1.37 <- as.numeric(D$gbc_1_37); # gbc BLcond/1.37 boudary layer conductance for CO2
val$const$gsc_1.6 <- as.numeric(D$gsc_1_6); # gsc gsw/1.6 stomatal conductance for CO2
# blank spreadsheet line
##details<<
## Calculation information
# blank spreadsheet line
sw$calc_pc_to_use <- as.numeric(D$calc_pc_to_use);
# 1 = pc_using_gm
# 2 = pc_using_simple_Delta_for_gm
# 3 = pc_using_simple_Delta_for_modeling
# 4 = pc_using_complex_Delta_no_decarboxylation
# 5 = pc_using_complex_Delta_full_model
# blank spreadsheet line
# blank spreadsheet line
# blank spreadsheet line
# blank spreadsheet line
# NOT USED
# blank spreadsheet line
sw$calc_Delta_i_to_use <- as.numeric(D$calc_Delta_i_to_use);
# 1 = Delta_i_simple_for_gm
# 2 = Delta_i_simple_for_modeling
# 3 = Delta_i_complex_for_gm
# blank spreadsheet line
# blank spreadsheet line
# blank spreadsheet line
sw$calc_gm_to_use <- as.numeric(D$calc_gm_to_use);
# 1 = gm_point_simple
# 2 = gm_point_complex
# blank spreadsheet line
# blank spreadsheet line
##############################################################################
##details<<
## create a list to all returned parameters
PARAM <- list();
PARAM$val <- val ;
PARAM$sw <- sw ;
PARAM$TDL_fn <- TDL_fn ;
PARAM$Licor_fn <- Licor_fn ;
PARAM$plot_format_list <- plot_format_list ;
PARAM$output_fn_prefix <- output_fn_prefix ;
PARAM$output_summary_TDL_fn <- output_summary_TDL_fn ;
PARAM$output_summary_Licor_fn <- output_summary_Licor_fn ;
PARAM$output_summary_Calc_fn <- output_summary_Calc_fn ;
PARAM$output_summary_Calc_last_fn <- output_summary_Calc_last_fn ;
PARAM$output_all_Calc_fn <- output_all_Calc_fn ; # "0.1-16" "2012-07-11"
PARAM$output_CI_TDL_fn <- output_CI_TDL_fn ;
PARAM$output_CI_Licor_fn <- output_CI_Licor_fn ;
PARAM$output_CI_Calc_fn <- output_CI_Calc_fn ;
PARAM$output_CI_Calc_last_fn <- output_CI_Calc_last_fn ;
PARAM$R_bootstrap <- R_bootstrap ;
PARAM$sig_CI <- sig_CI ;
PARAM$seed <- seed ;
PARAM$TDL_cycle <- TDL_cycle ;
PARAM$Licor_TDL_time_offset_seconds <- Licor_TDL_time_offset_seconds;
return( PARAM );
### PARAM list of all inputs from template
} # assign_param_variables()
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