initial_guess_c3_aci: Make an initial guess of FvCB model parameter values for one...

In PhotoGEA: Photosynthetic Gas Exchange Analysis

Make an initial guess of FvCB model parameter values for one curve

Description

Creates a function that makes an initial guess of FvCB model parameter values for one curve. This function is used internally by fit_c3_aci.

Values estimated by this guessing function should be considered inaccurate, and should always be improved upon by an optimizer.

Usage

  initial_guess_c3_aci(
    alpha_g,
    alpha_old,
    alpha_s,
    alpha_t,
    Gamma_star_at_25,
    gmc_at_25,
    Kc_at_25,
    Ko_at_25,
    cc_threshold_rl = 100,
    Wj_coef_C = 4.0,
    Wj_coef_Gamma_star = 8.0,
    a_column_name = 'A',
    ci_column_name = 'Ci',
    gamma_star_norm_column_name = 'Gamma_star_norm',
    gmc_norm_column_name = 'gmc_norm',
    j_norm_column_name = 'J_norm',
    kc_norm_column_name = 'Kc_norm',
    ko_norm_column_name = 'Ko_norm',
    oxygen_column_name = 'Oxygen',
    rl_norm_column_name = 'RL_norm',
    total_pressure_column_name = 'total_pressure',
    tp_norm_column_name = 'Tp_norm',
    vcmax_norm_column_name = 'Vcmax_norm',
    debug_mode = FALSE
  )

Arguments

alpha_g	A dimensionless parameter where 0 <= alpha_g <= 1, representing the proportion of glycolate carbon taken out of the photorespiratory pathway as glycine. alpha_g is often assumed to be 0. If alpha_g is not a number, then there must be a column in rc_exdf called alpha_g with appropriate units. A numeric value supplied here will overwrite the values in the alpha_g column of rc_exdf if it exists.
alpha_old	A dimensionless parameter where 0 <= alpha_old <= 1, representing the fraction of remaining glycolate carbon not returned to the chloroplast after accounting for carbon released as CO2. alpha_old is often assumed to be 0. If alpha_old is not a number, then there must be a column in rc_exdf called alpha_old with appropriate units. A numeric value supplied here will overwrite the values in the alpha_old column of rc_exdf if it exists.
alpha_s	A dimensionless parameter where 0 <= alpha_s <= 0.75 * (1 - alpha_g) representing the proportion of glycolate carbon taken out of the photorespiratory pathway as serine. alpha_s is often assumed to be 0. If alpha_s is not a number, then there must be a column in rc_exdf called alpha_s with appropriate units. A numeric value supplied here will overwrite the values in the alpha_s column of rc_exdf if it exists.
alpha_t	A dimensionless parameter where 0 <= alpha_t <= 1 representing the proportion of glycolate carbon taken out of the photorespiratory pathway as CH2-THF. alpha_t is often assumed to be 0. If alpha_t is not a number, then there must be a column in rc_exdf called alpha_t with appropriate units. A numeric value supplied here will overwrite the values in the alpha_t column of rc_exdf if it exists.
Gamma_star_at_25	The chloroplastic CO2 concentration at which CO2 gains from Rubisco carboxylation are exactly balanced by CO2 losses from Rubisco oxygenation, at 25 degrees C, expressed in micromol mol^(-1). If Gamma_star_at_25 is not a number, then there must be a column in rc_exdf called Gamma_star_at_25 with appropriate units. A numeric value supplied here will overwrite the values in the Gamma_star_at_25 column of rc_exdf if it exists.
gmc_at_25	The mesophyll conductance to CO2 diffusion at 25 degrees C, expressed in mol m^(-2) s^(-1) bar^(-1). In the absence of other reliable information, gmc_at_25 is often assumed to be infinitely large. If gmc_at_25 is not a number, then there must be a column in rc_exdf called gmc_at_25 with appropriate units. A numeric value supplied here will overwrite the values in the gmc_at_25 column of rc_exdf if it exists.
Kc_at_25	The Michaelis-Menten constant for Rubisco carboxylation at 25 degrees C, expressed in micromol mol^(-1). If Kc_at_25 is not a number, then there must be a column in rc_exdf called Kc_at_25 with appropriate units. A numeric value supplied here will overwrite the values in the Kc_at_25 column of rc_exdf if it exists.
Ko_at_25	The Michaelis-Menten constant for Rubisco oxygenation at 25 degrees C, expressed in mmol mol^(-1). If Ko_at_25 is not a number, then there must be a column in rc_exdf called Ko_at_25 with appropriate units. A numeric value supplied here will overwrite the values in the Ko_at_25 column of rc_exdf if it exists.
cc_threshold_rl	An upper cutoff value for the chloroplast CO2 concentration in micromol mol^(-1) to be used when estimating RL.
Wj_coef_C	A coefficient in the equation for RuBP-regeneration-limited carboxylation, whose value depends on assumptions about the NADPH and ATP requirements of RuBP regeneration; see calculate_c3_assimilation for more information.
Wj_coef_Gamma_star	A coefficient in the equation for RuBP-regeneration-limited carboxylation, whose value depends on assumptions about the NADPH and ATP requirements of RuBP regeneration; see calculate_c3_assimilation for more information.
a_column_name	The name of the column in rc_exdf that contains the net assimilation in micromol m^(-2) s^(-1).
ci_column_name	The name of the column in rc_exdf that contains the intercellular CO2 concentration in micromol mol^(-1).
gamma_star_norm_column_name	The name of the column in rc_exdf that contains the normalized Gamma_star values (with units of normalized to Gamma_star at 25 degrees C).
gmc_norm_column_name	The name of the column in rc_exdf that contains the normalized mesophyll conductance values (with units of normalized to gmc at 25 degrees C).
j_norm_column_name	The name of the column in rc_exdf that contains the normalized J values (with units of normalized to J at 25 degrees C).
kc_norm_column_name	The name of the column in rc_exdf that contains the normalized Kc values (with units of normalized to Kc at 25 degrees C).
ko_norm_column_name	The name of the column in rc_exdf that contains the normalized Ko values (with units of normalized to Ko at 25 degrees C).
oxygen_column_name	The name of the column in rc_exdf that contains the concentration of O2 in the ambient air, expressed as a percentage (commonly 21% or 2%); the units must be percent.
rl_norm_column_name	The name of the column in rc_exdf that contains the normalized RL values (with units of normalized to RL at 25 degrees C).
total_pressure_column_name	The name of the column in rc_exdf that contains the total pressure in bar.
tp_norm_column_name	The name of the column in rc_exdf that contains the normalized Tp values (with units of normalized to Tp at 25 degrees C).
vcmax_norm_column_name	The name of the column in rc_exdf that contains the normalized Vcmax values (with units of normalized to Vcmax at 25 degrees C).
debug_mode	A logical (TRUE or FALSE) variable indicating whether to operate in debug mode. In debug mode, information about the linear fit used to estimate RL is printed; this can be helpful when troubleshooting issues with a particular curve.

Details

Here we estimate values of J_at_25, RL_at_25, Tp_at_25, and Vcmax_at_25 from a measured C3 CO2 response curve. It is difficult to estimate values of alpha_g, alpha_old, alpha_s, alpha_t, Gamma_star_at_25, gmc_at_25, Kc_at_25, Ko_at_25 from a curve, so they must be supplied beforehand. For more information about these parameters, see the documentation for calculate_c3_assimilation.

• Estimating RL: Regardless of which process is limiting at low Cc, it is always true that An = -RL when Cc = Gamma_star_agt. Here we make a linear fit of the measured An vs. Cc values where Cc is below cc_threshold_rl, and evaluate it at at Cc = Gamma_star_agt to estimate RL. If there are fewer than two points with Cc <= cc_threshold_rl, the fit cannot be made, and we use a typical value instead (1.0 micromol m^(-2) s^(-1)). Likewise, if the linear fit predicts a negative or NA value for RL, we use the same typical value instead.

• Estimating Vc: Once an estimate for RL has been found, the RuBP carboxylation rate Vc can be estimated using Vc = (An + RL) / (1 - Gamma_star_agt / Cc). This is useful for the remaining parameter estimates.

• Estimating Vcmax: An estimate for Vcmax can be obtained by solving the equation for Wc for Vcmax, and evaluating it with Wc = Vc as estimated above. In the rubisco-limited part of the curve, Vc = Wc and the estimated values of Vcmax should be reasonable. In other parts of the curve, Wc is not the limiting rate, so Vc < Wc. Consequently, the estimated values of Vcmax in these parts of the curve will be smaller. So, to make an overall estimate, we choose the the largest estimated Vcmax value.

• Estimating J and Tp: Estimates for these parameters can be made using the equations for Wj and Wp, similar to the approach followed for Vcmax.

For the parameter values estimated above, the values of RL_norm, Vcmax_norm, and J_norm are used to convert the values at leaf temperature to the values at 25 degrees C.

Value

A function with one input argument rc_exdf, which should be an exdf object representing one C3 CO2 response curve. The return value of this function will be a numeric vector with twelve elements, representing the values of alpha_g, alpha_old, alpha_s, alpha_t, Gamma_star_at_25, gmc_at_25, J_at_25, Kc_at_25, Ko_at_25, RL_at_25, Tp_at_25, and Vcmax_at_25 (in that order).

Examples

# Read an example Licor file included in the PhotoGEA package
licor_file <- read_gasex_file(
  PhotoGEA_example_file_path('c3_aci_1.xlsx')
)

# Define a new column that uniquely identifies each curve
licor_file[, 'species_plot'] <-
  paste(licor_file[, 'species'], '-', licor_file[, 'plot'] )

# Organize the data
licor_file <- organize_response_curve_data(
    licor_file,
    'species_plot',
    c(9, 10, 16),
    'CO2_r_sp'
)

# Calculate the total pressure in the Licor chamber
licor_file <- calculate_total_pressure(licor_file)

# Calculate temperature-dependent values of C3 photosynthetic parameters
licor_file <- calculate_temperature_response(licor_file, c3_temperature_param_bernacchi)

# Create the guessing function; here we set:
# - All alpha values to 0
# - Gamma_star_at_25 to 40 micromol / mol
# - gmc to infinity
# - Kc_at_25 to 400 micromol / mol
# - Ko_at_25 to 275 mmol / mol
guessing_func <- initial_guess_c3_aci(
  alpha_g = 0,
  alpha_old = 0,
  alpha_s = 0,
  alpha_t = 0,
  Gamma_star = 40,
  gmc_at_25 = Inf,
  Kc_at_25 = 400,
  Ko_at_25 = 275
)

# Apply it and see the initial guesses for each curve
print(by(licor_file, licor_file[, 'species_plot'], guessing_func))

# A simple way to visualize the guesses is to "fit" the curves using the null
# optimizer, which simply returns the initial guess
aci_results <- consolidate(by(
  licor_file,
  licor_file[, 'species_plot'],
  fit_c3_aci,
  fit_options = list(alpha_old = 0),
  optim_fun = optimizer_null(),
  remove_unreliable_param = 0
))

plot_c3_aci_fit(aci_results, 'species_plot', 'Ci')

PhotoGEA documentation built on Aug. 25, 2025, 5:13 p.m.