The output file 'cntrlbestparameters.csv', which is in comma-separated-value format, contains parameters
estimated for all A/Ci curves that are submitted in the same batch. The values of these parameters are
given at the temperatures of sample leaves (that is, the estiamted parameters are not adjusted to the
same reference temperature). A curve may be fitted for multiple times, depending on what paramters are
fixed and what parameters are estimated. The first and and second partial derivatives of the cost function
with respect to the estimated paramters are also given. A valid estimation has a zero first derivative but
a non-zero second derivative.
Variables contained in the file
CurveID -(NA), the curve ID (the file name of the A/Ci curve)
ChlFlUse? -(0/1), whether or not chlorophyll fluorescence data are used for identifying the limitation states
0 = not used, 1 = used. (Currently this choice is still under evaluation and therefore ChlFlUse? = 0).
FitGi? -(0/1), whether or not the internal conductance (gi) is fitted for.
0 = not fitted and gi is either infinite or fixed at the value provided by the user.
1 = gi is estiamted
FitGamma*? - (0/1), whether or not the chloroplastic CO2 partial pressure photocompensation point is
fitted for. 0= not fitted, a prescribed value is used.
FitKco? - (0/1), whether or not the apparent Michaelis - Menten constant Kco = Kc(1+O/Ko) is fitted for.
0= not fitted, a prescribed value is calculated from Kc, Ko and the oxygen partial pressure.
1= Fitted for.
FitRd? - (0/1), whether the dark respiration is fitted for. 0= not fitted for, a prescribed value is used.
1= fitted for.
FitAlpha? - (0/1), whether alpha (the non-returned fraction of the glycolate carbon
recycled in the photorespiratory cycle) is fitted for.
0= not fitted for and alpha = 0
1= fitted for
LimitCombina - (NA), the combination of limitation states present in the A/Ci dataset. Parameters
are estimated for those limitation states that occur in the measured curve.
Rubisco: Rubisco limitation (Vcmax, Kco)
RuBP: RuBP regeneration limitation (J)
Tpu: export limitation (TPU, alpha)
MeanTleaf - (oC): average leaf temperature
MeanPARi - (umol/m2/s) average PAR inside the sample chamber.
MeanPresAir - (KPa) average atmospheric pressure
MeanPO2i - (KPa) average oxygen partial pressure
gmeso - (umol/m2/s/pa), internal CO2 transfer conductance, also called the mesophyll conductance
stargamma - (Pa), chloroplastic CO2 partial pressure photocompensation point
rdlight - (umol/m2/s), dark respiration
vcmax - (umol/m2/s), the maximal Rubisco carboxylation rate
fkco - (Pa), Kco = Kc(1+O/Ko) the apparent Michaelis-Menton constant
fjelect - (umol/m2/s), the electron transport rate at the measurement light and temperature level
tpu - (umol/m2/s), the export rate. tpu is estimated in two ways. If the dataset contains TPU limitation
points, then tpu is estimated from the regular Farquhar model fitting. If the dataset does not
contain TPU limitation points, then tpu is estimated asymptotically by fitting the A/Ci curve with
a sigmoid function: tpu= (Anet_asymptote+Rd)/3
alpha - (0 to 1), the non-returned fraction of the glycolate carbon recycled in the photorespiratory
cycle. alpha is set to 0 if not estimated.
df_gmeso - the first partial derivative of the cost function with respect to gmeso
df_stargamma - the first partial derivative of the cost function with respect to stargamma
df_rdlight- the first partial derivative of the cost function with respect to rdlight
df_vcmax- the first partial derivative of the cost function with respect to vcmax
df_fkco- the first partial derivative of the cost function with respect to fkco
df_fjelect- the first partial derivative of the cost function with respect to fjelect
df_tpu- the first partial derivative of the cost function with respect to tpu
df_alpha- the first partial derivative of the cost function with respect to alpha
df2_gmeso - the second partial derivative of the cost function with respect to gmeso
df2_stargamma - the second partial derivative of the cost function with respect to stargamma
df2_rdlight- the second partial derivative of the cost function with respect to rdlight
df2_vcmax- the second partial derivative of the cost function with respect to vcmax
df2_fkco- the second partial derivative of the cost function with respect to fkco
df2_fjelect- the second partial derivative of the cost function with respect to fjelect
df2_tpu- the second partial derivative of the cost function with respect to tpu
df2_alpha- the second partial derivative of the cost function with respect to alpha
weitedrms: (umol/m2/s), the root mean square error. For A/Ci fitting, the weighting
factor for each data point is 1 (that is, no weighting)