Make an initial guess of "Variable J" model parameter values for one curve
initial_guess_c3_variable_j.Rd
Creates a function that makes an initial guess of "variable J" model parameter
values for one curve. This function is used internally by
fit_c3_variable_j
.
Values estimated by this guessing function should be considered inaccurate, and should always be improved upon by an optimizer.
Usage
initial_guess_c3_variable_j(
alpha_g,
alpha_old,
alpha_s,
alpha_t,
Gamma_star_at_25,
Kc_at_25,
Ko_at_25,
cc_threshold_rd = 100,
Wj_coef_C = 4.0,
Wj_coef_Gamma_star = 8.0,
a_column_name = 'A',
ci_column_name = 'Ci',
etr_column_name = 'ETR',
gamma_star_norm_column_name = 'Gamma_star_norm',
j_norm_column_name = 'J_norm',
kc_norm_column_name = 'Kc_norm',
ko_norm_column_name = 'Ko_norm',
oxygen_column_name = 'oxygen',
phips2_column_name = 'PhiPS2',
qin_column_name = 'Qin',
rl_norm_column_name = 'RL_norm',
total_pressure_column_name = 'total_pressure',
tp_norm_column_name = 'Tp_norm',
vcmax_norm_column_name = 'Vcmax_norm'
)
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. Ifalpha_g
is not a number, then there must be a column inrc_exdf
calledalpha_g
with appropriate units. A numeric value supplied here will overwrite the values in thealpha_g
column ofrc_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. Ifalpha_old
is not a number, then there must be a column inrc_exdf
calledalpha_old
with appropriate units. A numeric value supplied here will overwrite the values in thealpha_old
column ofrc_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. Ifalpha_s
is not a number, then there must be a column inrc_exdf
calledalpha_s
with appropriate units. A numeric value supplied here will overwrite the values in thealpha_s
column ofrc_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. Ifalpha_t
is not a number, then there must be a column inrc_exdf
calledalpha_t
with appropriate units. A numeric value supplied here will overwrite the values in thealpha_t
column ofrc_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)
. IfGamma_star_at_25
is not a number, then there must be a column inrc_exdf
calledGamma_star_at_25
with appropriate units. A numeric value supplied here will overwrite the values in theGamma_star_at_25
column ofrc_exdf
if it exists.- Kc_at_25
The Michaelis-Menten constant for Rubisco carboxylation at 25 degrees C, expressed in
micromol mol^(-1)
. IfKc_at_25
is not a number, then there must be a column inrc_exdf
calledKc_at_25
with appropriate units. A numeric value supplied here will overwrite the values in theKc_at_25
column ofrc_exdf
if it exists.- Ko_at_25
The Michaelis-Menten constant for Rubisco oxygenation at 25 degrees C, expressed in
mmol mol^(-1)
. IfKo_at_25
is not a number, then there must be a column inrc_exdf
calledKo_at_25
with appropriate units. A numeric value supplied here will overwrite the values in theKo_at_25
column ofrc_exdf
if it exists.- cc_threshold_rd
An upper cutoff value for the chloroplast CO2 concentration in
micromol mol^(-1)
to be used when estimatingRL
.- 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 inmicromol m^(-2) s^(-1)
.- ci_column_name
The name of the column in
rc_exdf
that contains the intercellular CO2 concentration inmicromol mol^(-1)
.- etr_column_name
The name of the column in
rc_exdf
that contains the electron transport rate as estimated by the measurement system inmicromol m^(-2) s^(-1)
.- gamma_star_norm_column_name
The name of the column in
rc_exdf
that contains the normalizedGamma_star
values (with units ofnormalized to Gamma_star at 25 degrees C
).- j_norm_column_name
The name of the column in
rc_exdf
that contains the normalizedJ
values (with units ofnormalized to J at 25 degrees C
).- kc_norm_column_name
The name of the column in
rc_exdf
that contains the normalizedKc
values (with units ofnormalized to Kc at 25 degrees C
).- ko_norm_column_name
The name of the column in
rc_exdf
that contains the normalizedKo
values (with units ofnormalized to Ko at 25 degrees C
).- oxygen_column_name
The name of the column in
exdf_obj
that contains the concentration of O2 in the ambient air, expressed as a percentage (commonly 21% or 2%); the units must bepercent
.- phips2_column_name
The name of the column in
rc_exdf
that contains values of the operating efficiency of photosystem II (dimensionless).- qin_column_name
The name of the column in
rc_exdf
that contains values of the incident photosynthetically active flux density inmicromol m^(-2) s^(-1)
.- rl_norm_column_name
The name of the column in
rc_exdf
that contains the normalizedRL
values (with units ofnormalized to RL at 25 degrees C
).- total_pressure_column_name
The name of the column in
rc_exdf
that contains the total pressure inbar
.- tp_norm_column_name
The name of the column in
rc_exdf
that contains the normalizedTp
values (with units ofnormalized to Tp at 25 degrees C
).- vcmax_norm_column_name
The name of the column in
rc_exdf
that contains the normalizedVcmax
values (with units ofnormalized to Vcmax at 25 degrees C
).
Details
The variable J method is a fitting procedure for estimating values of
alpha_g
, alpha_old
, alpha_s
, alpha_t
,
Gamma_star_at_25
, J_at_25
, Kc_at_25
, Kc_at_25
,
RL_at_25
, tau
, Tp_at_25
, and Vcmax_at_25
from a
measured C3 CO2 response curve + chlorophyll fluorescence. For more
information about these parameters, see the documentation at
calculate_c3_variable_j
and
calculate_c3_assimilation
.
Here, we make an estimate for tau
by noting that gas exchange
measurement systems equipped with chlorophyll fluorometers typically make an
estimate for the electron transport rate (ETR
), which is essentially
synonymous with the actual RuBP regeneration rate. Thus, tau
can be
estimated by inverting the equation for J_actual
:
tau = ETR / (Qin * PhiPSII)
Estimates of the remaining parameters are calculated by setting Cc = Ci
and then calling initial_guess_c3_aci
.
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
, J_at_25
, Kc_at_25
, Ko_at_25
,
RL_at_25
, tau
, 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
# - Kc_at_25 to 400 micromol / mol
# - Ko_at_25 to 275 mmol / mol
guessing_func <- initial_guess_c3_variable_j(
alpha_g = 0,
alpha_old = 0,
alpha_s = 0,
alpha_t = 0,
Gamma_star = 40,
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))
#> $`soybean - 5a`
#> [1] 0.0000000 0.0000000 0.0000000 0.0000000 40.0000000 207.7214921
#> [7] 400.0000000 275.0000000 0.8878856 0.4202992 14.9438964 164.3471181
#>
#> $`tobacco - 1`
#> [1] 0.0000000 0.0000000 0.0000000 0.0000000 40.0000000 246.8426737
#> [7] 400.0000000 275.0000000 1.3254559 0.4202993 18.3858596 343.0340389
#>
#> $`tobacco - 2`
#> [1] 0.0000000 0.0000000 0.0000000 0.0000000 40.0000000 220.4139634
#> [7] 400.0000000 275.0000000 1.1971928 0.4202992 17.2913781 155.4179616
#>
# 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_variable_j,
fit_options = list(alpha_old = 0),
optim_fun = optimizer_null(),
remove_unreliable_param = 0
))
plot_c3_aci_fit(aci_results, 'species_plot', 'Ci')