The file 'cntrlparameters.csv' is an extended version of the output file 'cntrlbestparameters.csv' 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) Vcmax25 - (umol/m2/s), the maximal Rubisco carboxylation rate at 25 oC. It is related to vcmax at the leaf temperature TLeaf (K) through the following expression: vcmax=Vcmax25*exp(f3)*(1+exp(f2))/(1+exp(f1)) where f1=(sv_vcmax*TLeaf-hd_vcmax)/(R*TLeaf) f2=(sv_vcmax*TRef-hd_vcmax)/(R*TRef) f3=ha_vcmax*(1-TRef/TLeaf)/(R*TRef) TRef is the reference temperature at 25+273.15 K, R is uiversal gas constant in kJmol-1K-1 ha_vcmax: The activation energy (Ha) in Vcmax temperature response function [kJmol-1] hd_vcmax: The deactivation energy (Hd) in Vcmax temperature response function [kJmol-1] sv_vcmax: The entropy term (Sv) in Vcmax temperature response function [kJmol-1K-1] Jmax25 - (umolm-2s-1), the maximal electron transport rate at the 25 oC. Jmax25 is calculated from the electron transport rate at a given level of light and leaf temperature based on a series of relationships from Bernacchi C.J., Pimentel C. & Long S.P.(2003) In vivo temperature response functions of parameters required to model RuBP-limited photosynthesis. Plant Cell and Environment 26, 1419-1430. ha_jmax: The activation energy (Ha) in jmax temperature response function [kJmol-1] hd_jmax: The deactivation energy (Hd) in jmax temperature response function [kJmol-1] sv_jmax: The entropy term (Sv) in jmax temperature response function [kJmol-1K-1] Rdlight25 - (umolm-2s-1), the dark respiration rate at 25 oC. It is related to Rdlight through the following relationship: Rdlight=Rdlight25*exp((ha_darkresp/R)*(1/298.15-1/templeaf)) R is uiversal gas constant in kJmol-1K-1 ha_darkresp: parameter in the temperature response function of dark respiration [kJmol-1] gmeso25: (umolm-2s-1Pa-1). CO2 internal (mesophyll) transfer conductance at 25 oC. It is related to gmeso through the following relationship: gmeso=gmeso25*exp(f3)*(1+exp(f2))/(1+exp(f1)) where f1=(sv_gmeso*TLeaf-hd_gmeso)/(R*TLeaf) f2=(sv_gmeso*TRef-hd_gmeso)/(R*TRef) f3=ha_gmeso*(1-TRef/TLeaf)/(R*TRef) ha_gmeso: The activation energy (Ha) in gmeso temperature response function [kJmol-1] hd_gmeso: The deactivation energy (Hd) in gmeso temperature response function [kJmol-1] sv_gmeso: The entropy term (Sv) in gmeso temperature response function [kJmol-1K-1] tpu25 - (umolm-2s-1), the Triose Phosphate Utilization (TPU) rate at 25 oC. If there are no tpu limitation points in the A/Ci dataset, it is calculated from the asymptotically estimated tpu. tpu=tpu25*exp(f3)*(1+exp(f2))/(1+exp(f1)) where f1=(sv_tpu*TLeaf-hd_tpu)/(R*TLeaf) f2=(sv_tpu*TRef-hd_tpu)/(R*TRef) f3=ha_tpu*(1-TRef/TLeaf)/(R*TRef) ha_tpu: The activation energy (Ha) in tpu temperature response function [kJmol-1] hd_tpu: The deactivation energy (Hd) in tpu temperature response function [kJmol-1] sv_tpu: The entropy term (Sv) in tpu temperature response function [kJmol-1K-1] gammas*25: (Pa). Chloroplastic CO2 photocompensation point at the reference temperature 25 oC. stargamma=gammas25*dexp((ha_stargamma/R)*(1/298.15-1/TLeaf)) ha_stargamma: parameter in the temperature response function of the co2 compensation point [kJmol-1] fkc25: (Pa), Michaelis - Menten constant for CO2 at 25 oC fkc=fkc25*dexp((ha_kc/R)*(1/298.15-1/TLeaf)) fko25: (Pa), Michaelis - Menten constant for O2 at 25 oC fko=fko25*dexp((ha_ko/R)*(1/298.15-1/TLeaf)) ha_kc: a CO2 Michaelis temp coefficient [kJmol-1] ha_ko: a O2 Michaelis temp coefficient [kJmol-1] alpha: (0-1), the fraction of glycolate carbon not returned to the chloroplat [0-1] numrubisco1cur - (NA), total number of points limited by Rubisco numrubp1curve - (NA), total number of points limited by RuBP regeneration numtpu1curve - (NA), total number of points limited by TPU weitedrms1curve - (umolm-2s-1), the root mean square for the fitting gamma25: (Pa), the intercellular CO2 partial pressure at which Anet = 0 for leaf temperature at 25 oC. Note that at this point, intercellular CO2 partial pressure = Chloroplastic CO2 fkco25: (Pa), fkco25 = fkc25*(1+O/fko25) leaftemp - (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 Gamma*: (Pa), the chloroplastic CO2 compensation point. CalcedGamma: (Pa), the intercellular CO2 partial pressure at which Anet = 0 for a given leaf temperature. Note that at this point, intercellular CO2 partial pressure = Chloroplastic CO2. Obtained from the fitted Farquhar model. vcmax - (umol/m2/s), the maximal Rubisco carboxylation rate at the measurement leaf temperature fkco - (Pa), Kco = Kc(1+O/Ko) the apparent Michaelis-Menton constant, either estimated from the the A/Ci data or calculated from prescribed Kc and Ko. If it is not estimated from the A/Ci data, then fkco = fkco_mod fkco_mod - (Pa), Kco = Kc(1+O/Ko) the apparent Michaelis-Menton constant, calculated from prescribed Kc and Ko. fjelect: (umolm-2s-1), the electron transport rate at the measurement leaf temperature fjmax: (umolm-2s-1), the maximal electron transport rate the measurement leaf temperature tpu: (umolm-2s-1), the triose phosphaste utilization rate at the measurement leaf temperature. When there are no tpu points in the A/Ci dataset, it is calculated aymptotically. stargamma25_ori: (Pa), the prescribed chloroplastic CO2 photocompensation point at 25 oC. Rdlight: (umolm-2s-1), the dark respiration rate at the measurement leaf temperature. CO2i1Thres25: (Pa), the intercellular CO2 value at the transition between Rubisco limitation and the RuBP regeneration- limitation transition at 25 oC. Anet25_CO2i1: (umolm-2s-1), the Anet at CO2i1Thres25 CO2i2Thres25: (Pa), the intercellular CO2 value at the transition between RuBP regeneration- and TPU- limitation transition at 25 oC Anet25_CO2i2: (umolm-2s-1), Anet at CO2i2Thres25 CO2i1Thres: (Pa), the intercellular CO2 value at the transition between Rubisco limitation and the RuBP regeneration- limitation transition at the measurement leaf temperature. Anet_CO2i1: (umolm-2s-1), Anet at CO2i1Thres CO2i2Thres: (Pa), the intercellular CO2 value at the transition between RuBP regeneration- and TPU- limitation transition at the measurement leaf temperature. Anet_CO2i2: (umolm-2s-1), Anet at CO2i2Thres AsmptoticAnet: (umolm-2s-1), the asymptote of the A/Ci curve 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 !-------------------------------------------------------------------------- The following variables are copied from the A/Ci data files users provide SiteID - (Dimensionless), Site identifier (do not leave blank between letters) Latitude(Degrees) - Site latitude, northern hermisphere positive Longitude(Degrees) - Site longitude, east positive Elevation - (m), site elevation SampleYear - (year), the year when the A/Ci data is taken SampleDayOfYear - (day), the day of year (since 1 Jan) when the A/Ci data is taken GrowSeasonStart - (day), the approximate start day (since 1 Jan) of growing season GrowSeasonEnd - (day), the approximate end day (since 1 Jan) of growing season StandAge - (year), stand age since the last disturbance CanopyHeight - (m), the height of the canopy LeafAreaIndex - (m2/m2), the leaf area index in the middle of growing season SpeciesSampled - (dimensionless), the species of the leaf sample (don't leave blank between letters) AveTimeResolution - (minutes), the average time interval between two consecutive A/Ci data points SampleHeight - (m), the height at which the leaf is located LeafAge - (day), the age of the leaf SpecificLeafArea - (cm2/g), specific leaf area of the sample LfNitrogenContent - (%), dry leaf nitrogen content of the sample LfCarbonContent - (%), dry leaf carbon content of the sample LfPhosphContent - (%), dry leaf phosphorus content of the sample