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