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Investigator name: First and last name
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Contact information: Your email / mail addresses
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Site name in full: Your site's identifier / name
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Vegetation type: Mixed forest / grasslands / croplands/ etc
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Soil type: Soil type at your site
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Major species: List of major species at the site
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Sample leaf light environment: The general light environment in which the sampled leaf is (e.g. heavily shaded from above)
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Water stress assessment: Indicate whether there is water stress at the time of sampling
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Instrument used: For example - Licor-6400
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Extra info: Any extra information you feel would be helpful to put the sampled leaf in context
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SiteID,Latitude(Degrees),Longitude(Degrees),Elevation,SampleYear,SampleDayOfYear,GrowSeasonStart,GrowSeasonEnd,StandAge,CanopyHeight,LeafAreaIndex,SpeciesSampled,AveTimeResolution,SampleHeight,LeafAge,SpecificLeafArea,LfNitrogenContent,LfCarbonContent,LfPhosphContent
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NoUnit,NorthPositive,EastPositive,m,NoUnit,DayOfYear,DayOfYear,DayOfYear,Year,m,m2/m2,NoBlankSpace,Minutes,m,days,cm2/g,%,%,%
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<This line contains comma-separated data described in the above two lines>
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Gamma*,Kc,Ko,Alpha,Rd,gi
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Pa,Pa,Pa,NoUnit,umol/m2/s,umol/m2/s/Pa
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<This line contains comma-separated values (if you know) described in the above two lines. If not known fill with -9999>
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Obs,HHMMSS,FTime,Photo,!AdjPhoto,!StomCond,!Ci,!Trmmol,!VpdL,Area,StmRat,BLCond,Tair,!Tleaf,TBlk,CO2R,CO2S,H2OR,H2OS,RH_R,RH_S,Flow,!PARi,PARo,Press,CsMch,HsMch,StableF,Status,PhiPS2,OxygenPress
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NoUnit,HHMMSS,Second,umol/m2/s,umol/m2/s,mol/m2/s,umol/mol,mmol/m2/s,kPa,cm2,NA,mol/m2/s,oC,oC,oC,umol/mol,umol/mol,mmol/mol,mmol/mol,%,%,umol/s,umol/m2/s,umol/m2/s,Kpa,umol/mol,mmol/mol,NA,NA,NA,KPA
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<This line and lines below contain comma-separated data described in the above two lines. Columns started with '!' are 'must-have' data>
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Photosynthetic, Internal and Stomatal Conductance Analyses of Leaves (PISCAL)
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Instruction for setting up the input file for PISCAL
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-----Mentioning a brand name in this document does not constitute support for the brand-------
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General instruction
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- Variables with labels started with '!' must be provided in order for PISCAL to do any analysis.
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For other variables, fill in with -9999 if unavailable.
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- Each input file must contain only data from a single curve. Separate curves may be stored in
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separate input data files and submitted at the same time.
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- Save data in comma separated value format (.csv)
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Line 1 to Line 10: Space provided for descriptive information about the investigator,
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contact information, the site,the sample leaf and its general environmental condition
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Line 11: Complementary data not used by PISCAL but needed for properly interpreting the A/Ci data and for synthesis
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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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Line 12: The units of corresponding variables in Line 11
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Line 13: The values of corresponding variables in Line 11
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Line 14: The photosysnthetic model parameters you want to keep constant at the values you provide,
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fill in -9999 if you want to let PISCAL decide
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Gamma* - (Pa), chloroplastic CO2 photocompensation point (must be positive if provided)
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Kc - (Pa), Michaelis-Menten constant for RuBP carboxylation (must be positive if provided)
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Ko - (Pa), Michaelis-Menten constant for RuBP oxygenation (must be positive if provided)
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Alpha - (Dimensionless), the fraction of glycolate carbon not returned to the chloroplast (must be between 0~1 if provided)
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Rd - (umol/m2/s), dark respiration (must be positive if provided)
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gi - (umol/m2/s/Pa), internal (also known as mesophyll) conductance
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Line 15: The units of corresponding variables in Line 14
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Line 16: The values of corresponding variables in Line 14
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Line 17: A/Ci data for a variety of analyses, including photosynthesis, stomatal conductance,
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internal conductance, water use efficiency. At this stage, we only provide to users parameters
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from A/Ci curve analysis. Results from other analyses will be provided to users once they are
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thoroughly tested. The format used here represents a typical output from a Licor-6400 except
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for the last two columns (PhiPS2 and OxygenPress). Most variables have the same label as those
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in the Licor-6400 guidebook with the same definition. Not all variables are used by PISCAL.
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By using this format, however, Licor-6400 users don't have to do a lot of data organization
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in order to use PISCAL. Users of other instruments could ignore columns that are not needed
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for A/Ci analyses (fill in those columns with -9999) and just provide the essential variables.
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Again, essential variables have labels started with '!'.
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Obs: (dimensionless), the data point No.
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HHMMSS - (hh:mm:ss), clock time
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FTime - (seconds), number of seconds since file opened
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Photo - (umol/m2/s), photosynthetic rate
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!AdjPhoto - (umol/m2/s), adjusted photosynthetic rate (leakage corrected), must provide
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!StomCond - (mol/m2/s), stomatal conductance, must provide
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!Ci - (umol/mol), intercellular CO2 concentration (umol CO2 / mol moist air), must provide
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!Trmmol - (mmol/m2/s), transpiration rate, must provide
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!VpdL - (KPa), water vapor pressure deficit based on leaf temperature, must provide
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Area - (cm2), leaf area
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StmRat - (NA), estimate of the ratio of stomatal conductances of one side of the leaf to the other
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BLCond - (mol/m2/s), total boundary layer conductance
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Tair - (oC), temperature in sample cell
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!Tleaf - (oC), temperature of leaf thermocouple, must provide
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TBlk - (oC), IRGA Block temperature
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CO2R - (umol/mol), reference CO2 concentration
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CO2S - (umol/mol), Sample CO2 concentration
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H2OR - (mmol/mol), reference cell water vapor concentration
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H2OS - (mmol/mol), sample cell water vapor concentration
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RH_R - (%), Reference cell relative humidity
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RH_S - (%), sample cell relative humidity
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Flow - (umol/s), molar flow rate of air entering the leaf chamber
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!PARi - (umol/m2/s), PAR measured by the in-chamber quantum sensor, must provide
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PARo - (umol/m2/s), PAR measured by the external quantum sensor
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Press - (KPa), atmospheric pressure
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CsMch - (umol/mol), sample CO2 offset
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HsMch - (mmol/mol), sample H2O offset
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StableF - (NA), a stability indicator as a decimal value
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Status -(NA), status flag
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PhiPS2 - (NA), DeltaF/Fm, the fraction of absorbed PSII photons that are used in photochemistry
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OxygenPress - (Pa), atmospheric O2 partial pressure
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Line 18: The units of corresponding variables in Line 17
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Line 19 and below: The actual data body of the A/Ci curve
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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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The file 'cntrlcomparison.csv', which is in comma-separated-value format, contains outputs from PISCAL that
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facilitates examination of how well the fitting is. First model prediction is calculated at each sampling
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point. Then model prediction is calculated at many selected levels of intercelluar CO2 partial pressure
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levels under three limitation states to enable plotting curves. The same structure is then repeated for
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each fitting of the same curve with different parameters to be estimated and with different curves. Note
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that some common information about a curve is repeated for each data point to make the structure of the
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file as regular as possible.
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!The first section compares model calculation at the optimized parameters with measurements
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CurveID - (NA), the curve identifier, repeated for each point
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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, repeated for each point
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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, repeated for each point
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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, repeated for each point
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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. repeated for each point
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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, repeated for each point
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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, repeated for each point
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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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PCO2i - (Pa), intercellular CO2 partial pressure
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PCO2c - (Pa), chloroplastic CO2 partial pressure corresponding to the PCO2i of a point.
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PCO2c=PCO2i-AnetCal/internal conductance
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AnetMeas - (umol/m2/s), measured net assimilation rate
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AnetCal - (umol/m2/s), calculated net assimilation rate
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weitedrms - (umol/m2/s), root mean square error of the fitting (weiting coefficient =1)
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PointLimitType - (1,2,3). 1 = point limited by rubisco
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2 = point limited by RuBP regeneration
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3 = point limited by TPU
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!The second section gives photosynthesis for each of the three limitation states at selected values of intercellular
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!partial pressure. Note that the corresponding values of chloraplastic CO2 partial pressure depend on the limitation state.
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CO2i - (Pa), intercellular CO2 partial pressure
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CO2cc- (Pa), Chloraplastic CO2 partial pressure for Rubisco limited photosynthesis
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Ac- (umol/m2/s), Rubisco-limited net assimilation rate calculated with the optimized parameters
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CO2cj- (Pa), Chloraplastic CO2 partial pressure for RuBP regeneration limited photosynthesis
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Aj- (umol/m2/s), RuBP regeneration-limited net assimilation rate calculated with estimated parameters
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CO2ct- (Pa), Chloraplastic CO2 partial pressure for export limited photosynthesis
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At- (umol/m2/s), TPU-limited net assimilation rate calculated with estimated parameters
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@@ -0,0 +1,155 @@
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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
|
||||
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)
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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]
|
||||
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
|
||||
@@ -0,0 +1,31 @@
|
||||
Investigator name: First and last name
|
||||
Contact information: Your email / mail addresses
|
||||
Site name in full: Your site's identifier / name
|
||||
Vegetation type: Mixed forest / grasslands / croplands/ etc
|
||||
Soil type: Soil type at your site
|
||||
Major species: List of major species at the site
|
||||
Sample leaf light environment: The general light environment in which the leaf is in (e.g. heavily shaded from above)
|
||||
Water stress assessment: Indicate whether there is water stress at the time of sampling
|
||||
Instrument used: For example - Licor-6400
|
||||
Extra info: Any extra information you feel would be helpful to put the sampled leaf in context
|
||||
SiteID,Latitude(Degrees),Longitude(Degrees),Elevation,SampleYear,SampleDayOfYear,GrowSeasonStart,GrowSeasonEnd,StandAge,CanopyHeight,LeafAreaIndex,SpeciesSampled,AveTimeResolution,SampleHeight,LeafAge,SpecificLeafArea,LfNitrogenContent,LfCarbonContent,LfPhosphContent
|
||||
NoUnit,NorthPositive,EastPositive,m,NoUnit,DayOfYear,DayOfYear,DayOfYear,Year,m,m2/m2,NoBlankSpace,Minutes,m,days,cm2/g,%,%,%
|
||||
MOFLUX,38.733,-92.2,237.4,2008,174,105,270,70,17,4.2,WhiteOak,3,0.9144,69,203.72,-9999,-9999,-9999
|
||||
Gamma*,Kc,Ko,Alpha,Rd,gi
|
||||
Pa,Pa,Pa,NoUnit,umol/m2/s,umol/m2/s/Pa
|
||||
-9999,-9999,-9999,-9999,-9999,-9999
|
||||
Obs,HHMMSS,FTime,Photo,!AdjPhoto,!StomCond,!Ci,!Trmmol,!VpdL,Area,StmRat,BLCond,Tair,!Tleaf,TBlk,CO2R,CO2S,H2OR,H2OS,RH_R,RH_S,Flow,!PARi,PARo,Press,CsMch,HsMch,StableF,Status,PhiPS2,OxygenPress
|
||||
NoUnit,HHMMSS,Second,umol/m2/s,umol/m2/s,mol/m2/s,umol/mol,mmol/m2/s,kPa,cm2,NA,mol/m2/s,oC,oC,oC,umol/mol,umol/mol,mmol/mol,mmol/mol,%,%,umol/s,umol/m2/s,umol/m2/s,Kpa,umol/mol,mmol/mol,NA,NA,NA,KPA
|
||||
13,14:44:20,664.5,7.51,7.470041223,0.149,279,2.64,1.74,2,1,9.29,25.02,26.93,23.62,374.86,370.62,17.176,18.471,53.32,57.34,400.7,1201,47,98.83,2.63,0.43,0.2,111115,0.093,-9999
|
||||
19,14:46:49,813.5,5.87,5.855008277,0.155,230,2.74,1.73,2,1,9.29,25.33,26.95,24.22,302.85,299.51,17.244,18.589,52.55,56.64,400.7,1201,48,98.82,2.51,0.416,0.8,111115,0.088,-9999
|
||||
25,14:49:19,962.5,4.98,4.986692181,0.158,192,2.78,1.72,2,1,9.29,25.25,26.95,24.02,251.75,248.92,17.346,18.709,53.13,57.3,400.7,1201,43,98.82,2.54,0.408,0.5,111115,0.081,-9999
|
||||
31,14:51:48,1111.5,3.58,3.613166391,0.167,159,2.9,1.7,2,1,9.29,25.22,26.91,24.02,200.66,198.59,17.405,18.823,53.4,57.75,400.7,1200,41,98.82,2.46,0.403,0.5,111115,0.075,-9999
|
||||
37,14:54:17,1260.5,2.27,2.337349887,0.175,123,3.06,1.71,2,1,9.29,25.26,26.99,24.03,149.71,148.35,17.397,18.895,53.22,57.81,400.7,1199,43,98.82,2.34,0.393,0.5,111115,0.069,-9999
|
||||
43,14:56:46,1410.5,0.887,1.001965238,0.184,88.3,3.2,1.7,2,1,9.29,25.35,26.98,24.22,99.42,98.82,17.373,18.939,52.87,57.64,400.7,1199,44,98.82,2.28,0.383,1,111115,0.061,-9999
|
||||
49,14:59:15,1559.5,-0.542,-0.343159241,0.189,51.6,3.28,1.7,2,1,9.29,25.37,26.98,24.21,48.11,48.31,17.366,18.973,52.79,57.67,400.7,1199,45,98.82,2.14,0.376,0.8,111115,0.052,-9999
|
||||
61,15:07:44,2068.5,7.01,6.969621394,0.134,278,2.41,1.76,2,1,9.29,25.03,27.03,23.63,377.22,371.95,16.919,18.495,52.47,57.36,300.1,1199,49,98.82,2.65,0.438,0.2,111115,0.09,-9999
|
||||
68,15:11:13,2277.5,8.46,8.390629343,0.116,347,2.14,1.78,2,1,9.29,24.93,27.05,23.43,482.66,476.34,16.879,18.276,52.67,57.03,300.1,1198,47,98.81,2.74,0.458,0.8,111115,0.098,-9999
|
||||
75,15:14:42,2486.5,8.98,8.883476363,0.0729,387,1.38,1.83,2,1,9.29,24.64,27.04,23.04,607.06,600.53,16.913,17.813,53.72,56.57,300.1,1198,46,98.81,2.71,0.479,0.8,111115,0.102,-9999
|
||||
82,15:18:10,2694.5,9.64,9.509884017,0.0453,439,0.868,1.85,2,1,9.29,24.48,27.04,22.85,806.75,799.86,16.997,17.565,54.49,56.31,300.1,1198,99,98.81,2.37,0.491,0.5,111115,0.102,-9999
|
||||
89,15:21:36,2900.5,10.4,10.24385533,0.0318,454,0.609,1.85,2,1,9.29,24.13,26.92,22.16,1006.08,998.77,16.958,17.357,55.52,56.83,300.1,1198,64,98.8,1.78,0.512,0.5,111115,0.1,-9999
|
||||
96,15:25:02,3106.5,10.3,10.12230686,0.0259,533,0.501,1.86,2,1,9.29,24.11,26.98,22.26,1207.66,1200.37,16.973,17.301,55.61,56.69,300.1,1202,50,98.8,1.46,0.531,0.8,111115,0.101,-9999
|
||||
|
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Reference in New Issue
Block a user