- 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.
- 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).
- etr_column_name
The name of the column in rc_exdf that contains the electron
transport rate as estimated by the measurement system in
micromol m^(-2) s^(-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).
- 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 exdf_obj that contains the concentration
of O2 in the ambient air, expressed as a percentage (commonly 21% or 2%);
the units must be percent.
- 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 in
micromol m^(-2) s^(-1).
- 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
Passed to initial_guess_c3_aci.