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2015-11-11 12:46:50 -05:00
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+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)