photo | R Documentation |
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_photosynthesisBaldocchi(
Q,
Catm,
Tleaf,
u,
Vmax298,
Jmax298,
leafWidth,
Gsw_AC_slope,
Gsw_AC_intercept
)
photo_leafPhotosynthesisFunction(
E,
psiLeaf,
Catm,
Patm,
Tair,
vpa,
u,
absRad,
Q,
Vmax298,
Jmax298,
leafWidth = 1,
refLeafArea = 1,
verbose = FALSE
)
photo_leafPhotosynthesisFunction2(
E,
psiLeaf,
Catm,
Patm,
Tair,
vpa,
u,
SWRabs,
LWRnet,
Q,
Vmax298,
Jmax298,
leafWidth = 1,
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,
verbose = FALSE
)
photo_multilayerPhotosynthesisFunction(
E,
psiLeaf,
Catm,
Patm,
Tair,
vpa,
SLarea,
SHarea,
u,
absRadSL,
absRadSH,
QSL,
QSH,
Vmax298,
Jmax298,
leafWidth = 1,
verbose = FALSE
)
Tleaf |
Leaf temperature (in ºC). |
Oi |
Oxigen concentration (mmol*mol-1). |
Vmax298 , Vmax298SL , Vmax298SH |
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 |
Jmax298 , Jmax298SL , Jmax298SH |
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 |
Q |
Active photon flux density (micromol * s-1 * m-2). |
Ci |
CO2 internal concentration (micromol * mol-1). |
GT |
CO2 saturation point corrected by temperature (micromol * mol-1). |
Jmax |
Maximum electron transport rate per leaf area (micromol*s-1*m-2). |
Km |
Km = Kc*(1.0+(Oi/Ko)) - Michaelis-Menten term corrected by temperature (in micromol * mol-1). |
Vmax |
Maximum Rubisco carboxylation rate per leaf area (micromol*s-1*m-2). |
Catm |
CO2 air concentration (micromol * mol-1). |
Gc |
CO2 leaf (stomatal) conductance (mol * s-1 * m-2). |
verbose |
Boolean flag to indicate console output. |
u |
Wind speed above the leaf boundary (in m/s) (for each canopy layer in the case of |
leafWidth |
Leaf width (in cm). |
Gsw_AC_slope |
Slope of the An/C vs Gsw relationship |
Gsw_AC_intercept |
Intercept of the An/C vs Gsw relationship |
E |
Transpiration flow rate per leaf area (mmol*s-1*m-2). |
psiLeaf |
Leaf water potential (MPa). |
Patm |
Atmospheric air pressure (in kPa). |
Tair |
Air temperature (in ºC). |
vpa |
Vapour pressure deficit (in kPa). |
absRad |
Absorbed long- and short-wave radiation (in W*m^-2). |
refLeafArea |
Leaf reference area. |
SWRabs |
Absorbed short-wave radiation (in W·m-2). |
LWRnet |
Net long-wave radiation balance (in W·m-2). |
SLarea , SHarea |
Leaf area index of sunlit/shade leaves (for each canopy layer in the case of |
absRadSL , absRadSH |
Instantaneous absorbed radiation (W·m-2) per unit of sunlit/shade leaf area (for each canopy layer in the case of |
QSL , QSH |
Active photon flux density (micromol * s-1 * m-2) per unit of sunlit/shade leaf area (for each canopy layer in the case of |
Details of the photosynthesis submodel are given in the medfate book
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).
Miquel De Cáceres Ainsa, CREAF
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
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.