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