Set of functions used in the calculation of photosynthesis.
photo_GammaTemp(Tleaf)
photo_KmTemp(Tleaf, Oi = 209)
photo_VmaxTemp(Vmax298, Tleaf)
photo_JmaxTemp(Jmax298, Tleaf)
photo_electronLimitedPhotosynthesis(Q, Ci, GT, Jmax)
photo_rubiscoLimitedPhotosynthesis(Ci, GT, Km, Vmax)
photo_photosynthesis(Q, Catm, Gc, Tleaf, Vmax298, Jmax298, verbose = FALSE)
photo_leafPhotosynthesisFunction(E, psiLeaf, Catm, Patm, Tair, vpa, u,
absRad, Q, Vmax298, Jmax298,
leafWidth = 1.0, refLeafArea = 1, verbose = FALSE)
photo_leafPhotosynthesisFunction2(E, psiLeaf, Catm, Patm, Tair, vpa, u,
SWRabs, LWRnet, Q, Vmax298, Jmax298,
leafWidth = 1.0, refLeafArea = 1, verbose = FALSE)
photo_sunshadePhotosynthesisFunction(E, psiLeaf, Catm, Patm, Tair, vpa,
SLarea, SHarea, u,
absRadSL, absRadSH, QSL, QSH,
Vmax298SL, Vmax298SH, Jmax298SL, Jmax298SH,
leafWidth = 1.0, verbose = FALSE)
photo_multilayerPhotosynthesisFunction(E, psiLeaf, Catm, Patm, Tair, vpa,
SLarea, SHarea, u,
absRadSL, absRadSH, QSL, QSH,
Vmax298, Jmax298, leafWidth = 1.0,
verbose = FALSE)Values returned for each function are:
photo_GammaTemp: CO2 compensation concentration (micromol * mol-1).
photo_KmTemp: Michaelis-Menten coefficients of Rubisco for Carbon (micromol * mol-1) and Oxigen (mmol * mol-1).
photo_VmaxTemp: Temperature correction of Vmax298.
photo_JmaxTemp: Temperature correction of Jmax298.
photo_electronLimitedPhotosynthesis: Electron-limited photosynthesis (micromol*s-1*m-2) following Farquhar et al. (1980).
photo_rubiscoLimitedPhotosynthesis: Rubisco-limited photosynthesis (micromol*s-1*m-2) following Farquhar et al. (1980).
photo_photosynthesis: Calculates gross photosynthesis (micromol*s-1*m-2) following (Farquhar et al. (1980) and Collatz et al (1991).
photo_leafPhotosynthesisFunction: Returns a data frame with the following columns:
LeafTemperature: Leaf temperature (ºC).
LeafVPD: Leaf vapor pressure deficit (kPa).
LeafCi: Internal CO2 concentration (micromol * mol-1).
Gsw: Leaf stomatal conductance to water vapor (mol * s-1 * m-2).
GrossPhotosynthesis: Gross photosynthesis (micromol*s-1*m-2).
NetPhotosynthesis: Net photosynthesis, after discounting autotrophic respiration (micromol*s-1*m-2).
photo_sunshadePhotosynthesisFunction: Returns a data frame with the following columns:
GrossPhotosynthesis: Gross photosynthesis (micromol*s-1*m-2).
NetPhotosynthesis: Net photosynthesis, after discounting autotrophic respiration (micromol*s-1*m-2).
LeafCiSL: Sunlit leaf internal CO2 concentration (micromol * mol-1).
LeafCiSH: Shade leaf internal CO2 concentration (micromol * mol-1).
LeafTempSL: Sunlit leaf temperature (ºC).
LeafTempSH: Shade leaf temperature (ºC).
LeafVPDSL: Sunlit leaf vapor pressure deficit (kPa).
LeafVPDSH: Shade leaf vapor pressure deficit (kPa).
photo_multilayerPhotosynthesisFunction: Return a data frame with the following columns:
GrossPhotosynthesis: Gross photosynthesis (micromol*s-1*m-2).
NetPhotosynthesis: Net photosynthesis, after discounting autotrophic respiration (micromol*s-1*m-2).
Leaf temperature (in ºC).
Oxigen concentration (mmol*mol-1).
Maximum Rubisco carboxylation rate per leaf area at 298ºK (i.e. 25 ºC) (micromol*s-1*m-2) (for each canopy layer in the case of photo_multilayerPhotosynthesisFunction). 'SH' stands for shade leaves, whereas 'SL' stands for sunlit leaves.
Maximum electron transport rate per leaf area at 298ºK (i.e. 25 ºC) (micromol*s-1*m-2) (for each canopy layer in the case of photo_multilayerPhotosynthesisFunction). 'SH' stands for shade leaves, whereas 'SL' stands for sunlit leaves.
Active photon flux density (micromol * s-1 * m-2).
CO2 internal concentration (micromol * mol-1).
CO2 saturation point corrected by temperature (micromol * mol-1).
Maximum electron transport rate per leaf area (micromol*s-1*m-2).
Km = Kc*(1.0+(Oi/Ko)) - Michaelis-Menten term corrected by temperature (in micromol * mol-1).
Maximum Rubisco carboxylation rate per leaf area (micromol*s-1*m-2).
CO2 air concentration (micromol * mol-1).
CO2 leaf (stomatal) conductance (mol * s-1 * m-2).
Transpiration flow rate per leaf area (mmol*s-1*m-2).
Leaf water potential (MPa).
Atmospheric air pressure (in kPa).
Air temperature (in ºC).
Vapour pressure deficit (in kPa).
Wind speed above the leaf boundary (in m/s) (for each canopy layer in the case of photo_multilayerPhotosynthesisFunction).
Absorbed long- and short-wave radiation (in W*m^-2).
Absorbed short-wave radiation (in W·m-2).
Net long-wave radiation balance (in W·m-2).
Leaf width (in cm).
Leaf reference area.
Boolean flag to indicate console output.
Leaf area index of sunlit/shade leaves (for each canopy layer in the case of photo_multilayerPhotosynthesisFunction).
Instantaneous absorbed radiation (W·m-2) per unit of sunlit/shade leaf area (for each canopy layer in the case of photo_multilayerPhotosynthesisFunction).
Active photon flux density (micromol * s-1 * m-2) per unit of sunlit/shade leaf area (for each canopy layer in the case of photo_multilayerPhotosynthesisFunction).
Miquel De Cáceres Ainsa, CREAF
Details of the photosynthesis submodel are given in a vignette.
Bernacchi, C. J., E. L. Singsaas, C. Pimentel, A. R. Portis, and S. P. Long. 2001. Improved temperature response functions for models of Rubisco-limited photosynthesis. Plant, Cell and Environment 24:253–259.
Collatz, G. J., J. T. Ball, C. Grivet, and J. A. Berry. 1991. Physiological and environmental regulation of stomatal conductance, photosynthesis and transpiration: a model that includes a laminar boundary layer. Agricultural and Forest Meteorology 54:107–136.
Farquhar, G. D., S. von Caemmerer, and J. A. Berry. 1980. A biochemical model of photosynthetic CO2 assimilation in leaves of C3 species. Planta 149:78–90.
Leuning, R. 2002. Temperature dependence of two parameters in a photosynthesis model. Plant, Cell and Environment 25:1205–1210.
Sperry, J. S., M. D. Venturas, W. R. L. Anderegg, M. Mencuccini, D. S. Mackay, Y. Wang, and D. M. Love. 2016. Predicting stomatal responses to the environment from the optimization of photosynthetic gain and hydraulic cost. Plant Cell and Environment.
hydraulics_supplyFunctionNetwork, biophysics_leafTemperature, spwb