| align_TDL_Licor_times | Find the overlapping time window of the TDL and Licor files... |
| assign_param_variables | Assign PARAM_RAW values from input file to variable names |
| calc_mean_Licor | Calculate the mean for the Licor data based on last... |
| calc_mean_TDL | Calculate the mean and variance for the TDL/Licor data based... |
| calc_mean_TDL_interp_tanks_ref | Summary values for TDL interpolated tanks and reference |
| extract_cycle_timing | Cycle timing |
| f_bs_iter_TDL_Licor | one BS resample of TDL and Licor means |
| f_bs_save_TDL_Licor | save BS resample of TDL and Licor means |
| f_init_bs_matrix | init bs values to zero |
| fix_missing_TDL_values | Replace NA and NAN values in TDL$data by previous value for... |
| f_np_bs_mean | calculate NP BS mean |
| f_par_bs_mean | calculate Par BS mean |
| f_plot_CI_individuals | plot all variables with bs values, mean value, and CI... |
| f_plot_CI_individuals_driver | plot each individual variable |
| f_val_bs_CI | create CI for each calculated value |
| f_val_bs_CI_endpoints | create CI endpoints |
| f_val_bs_matrix | update values for each bs iterate |
| f_val_bs_matrix_check | Helper for 'f_val_bs_matrix', if the vector has zero length,... |
| f_val_calc_all_driver | This function calls all of the 'f_val_calc.*' files |
| f_val_calc_corrected | corrected (Corrected 12C, Corrected 13C) |
| f_val_calc_Cs | Cs, ppm CO2 concentration at the leaf surface, cs calculated... |
| f_val_calc_delta_13C_Assim | delta13C Assimilated, isotopic composition of assimilated... |
| f_val_calc_delta_13C_Resp | delta13C Respired, isotopic composition of respired CO2 |
| f_val_calc_Delta_from_A_ratio | D from A ratio, (Ro/(13A/12A))-1, should be the same as Dobs... |
| f_val_calc_Delta_from_ratios_in_out | Delta from ratios in and out?, (Re/Ro)-1, is this really the... |
| f_val_calc_Delta_i_complex_for_gm | Delta_i complex for gm CHECK DERIVATION predicted... |
| f_val_calc_Delta_i_simple_for_gm | Delta_i simple for gm, predicted discrimination including... |
| f_val_calc_Delta_i_simple_for_modeling | Delta_i simple for modeling a + (b-a) pi/pa predicted... |
| f_val_calc_Delta_obs | Delta, observed discrimination |
| f_val_calc_Delta_obs_permil | Delta per mil, observed discrimination |
| f_val_calc_delta_permil | delta permil (Isotopic composition (d) per mil) |
| f_val_calc_delta_proportion | delta as proportion (Isotopic composition (d) as fraction) |
| f_val_calc_flow_adjusted | Adjusted flow |
| f_val_calc_gain | gain (12C Gain, 13C Gain) |
| f_val_calc_gm_point_complex | gm point complex, internal leaf (mesophyll) conductance... |
| f_val_calc_gm_point_simple | gm point simple, internal leaf (mesophyll) conductance... |
| f_val_calc_gtc | gtc, total (stomatal and boundary layer) conductance for CO2 |
| f_val_calc_isotope_ratio | Isotope ratio |
| f_val_calc_offset | offset (12C Offset, 13C Offset) using hi tank |
| f_val_calc_p | p |
| f_val_calc_pc_using_complex_Delta_full_model | pc using complex D, full model... |
| f_val_calc_pc_using_complex_Delta_no_decarboxylation | pc using complex D, no decarboxylation... |
| f_val_calc_pc_using_gm | pc using gm, total partial pressure of CO2 at the site of... |
| f_val_calc_pc_using_simple_Delta_for_gm | pc using simple D for gm, includes boundary layer |
| f_val_calc_pc_using_simple_Delta_for_modeling | pc using simple D for modeling |
| f_val_calc_pp | pa, partial pressure of CO2 above the leaf, Press is the... |
| f_val_calc_TDL_A_photosynthesis | A, TDL photosynthesis |
| f_val_calc_total_mol_fraction_CO2 | Total mol fraction CO2 |
| f_val_calc_xi | xi |
| get_Licor | get Licor file and format into usable 6400 format |
| interp_TDL_tanks_ref | Interpolate TDL tank and reference values |
| isogasex | Reads TDL and Licor files, aligns them, calculates quantities... |
| isogasex_logo | The isogasex logo, using ASCII or Unicode characters |
| last_TDL_index_for_means | Determine the last index for admissible values to calculate... |
| move_plot_files | move selected plot files to subdirectories |
| my_reg_fit | basic SLR beta fit |
| my_reg_pred | basic SLR y pred |
| plot_A_photosynthesis | Plot A photosynthesis |
| plot_Ca_Cs | Plot Ca Cs, CO2 concentrations above the leaf and at the leaf... |
| plot_Cc_total | Plot Cc, ppm CO2 concentration at the site of carboxylation,... |
| plot_Ci_pi | Plot Ci, pi, CO2 concentration and partial pressure of CO2 in... |
| plot_corrected_total_diff_xi | Plot corrected 12CO2 and 13CO2, total, and difference for... |
| plot_data_cycles | Plot each cycle of TDL measurements (visual diagnostics) |
| plot_delta_Delta_p | Plot delta, Delta, and p |
| plot_Delta_i | Plot Delta_i, predicted discrimination |
| plot_gain_offset | Plot active gains, offsets, and corrected magnitudes |
| plot_gbc_gsc_gtc | Plot gbc, gsc, gtc: boundary layer, stomatal, and total... |
| plot_gm | Plot gm point simple and complex, internal leaf (mesophyll)... |
| plot_Licor_flow_press | Plot Licor uin, xin, La, Atm_press values 7/21/2012 |
| plot_Licor_temp_light | Plot Licor Temp Light values |
| plot_not_na | if no data to plot, plot a dummy box (for when certain Licor... |
| plot_pa_ps | Plot Pa Ps, partial pressure of CO2 above the leaf and at the... |
| plot_pc_simple_complex | Plot pc, simple and complex |
| plot_pc_total | Plot pc, total partial pressure of CO2 at the site of... |
| plot_pi_pa | Plot Totalpi_pa, ratio of substomatal CO2 partial pressure to... |
| plot_val_calc_sum | This function plots all the calculated values |
| progress_time | Calc amount of time since program started |
| read_TDL | read TDL file |
| read_template_param | Read template parameter file |
| read_template_param_table_to_raw | Assign variables from xls template input file to yaml... |
| set_TDL_cycle | TDL_cycle variables |
| s_plot_settings_begin_end | Plot settings for all plots |
| time_window_TDL_Licor_interp | keep only the overlapping time window of TDL and Licor files |
| val_TDL_Licor_variables | Assign TDL and Licor values to val variable names, raw and... |
| write_all_Calc_file | write output section |
| write_CI_Calc_file | write output section |
| write_CI_Licor_file | write output section: Licor file |
| write_CI_TDL_file | write output section: TDL file |
| write_out | write progress to the screen |
| write_progress | write progress to the screen with time elapsed |
| write_summary_Calc_file | write output section |
| write_summary_Licor_file | write output section: Licor file |
| write_summary_TDL_file | write output section: TDL file |
| x_wo_y | x without y |
