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