R: Farquhar-Ball-Berry coupled leaf gas exchange model
Farquhar
R Documentation
Farquhar-Ball-Berry coupled leaf gas exchange model
Description
Coupled photosynthesis-stomatal conductance model. A full implementation of
the photosynthesis model by Farquhar et al. (1980), as described by Medlyn et
al. (2002) (i.e., following their notation), coupled with a few choices of
Ball-Berry type stomatal conductance models. The default is that of Medlyn et
al. (2011).
Many parameters can be set in this model, including all temperature response
parameters and stomatal conductance parameters. See Details for more
information.
The minimum required parameters are: Vcmax, Jmax, Rd0
and G1. However, the model contains many other parameters, each with
their own default value. To override the default value, for example:
# Use Default values: Farquhar(PAR=1000, Tair=20, Ca=380,
VPD=1, Vcmax=100, Jmax=150, Rd0=1)
# Change the shape of the light response curve: Farquhar(PAR=1000, Tair=20,
Ca=380, VPD=1, Vcmax=100, Jmax=150, Rd0=1, THETA=0.8)
Below is a list and
explanation of all the parameters and their default values.
# Respiration parameters Q10F = 0.67 # logarithm of the Q10
(Equation for respiration : # RESP = RD0 * EXP(Q10F * (TLEAF-RTEMP)/10) *
DAYRESP RTEMP = 25 # Reference temperature (T at which RD0 was measured)
DAYRESP = 1.0 # Respiration in the light as fraction of that in the dark.
TBELOW = -100.0 # No respiration occurs below this temperature (degC).
# Stomatal conductance parameters MODELGS = 4 # model : 4 = Medlyn et al.
2011; 6 = Tuzet et al. 2003. EMAXLEAF = 999 # Only used when considering
soil water stress and MODELGS is not 6. KTOT = 2 # Leaf-specific hydraulic
conductance (mmol m-2 s-1 MPa-1)
G0 = 0.03 # Stomatal leakiness (gs when photosynthesis is zero).
D0L = 5 # Parameter for the Leuning model (MODELGS=3) GAMMA = 0 # Gamma for
all Ball-Berry type models G1 = 7 # Parameter for all Ball-Berry type models
GK = 0.3 # Parameter for three-parameter Medlyn et al. 2011 model (MODELGS=5)
SF = 3.2 # Tuzet model parameters (MODELGS=6) PSIV = -1.9
# Light-response parameters of electron transport rate. THETA = 0.4 # Shape
parameter of the non-rectangular hyperbola. AJQ = 0.324 # Quantum yield of
electron transport. HMSHAPE = 0.999 # Shape of the hyperbolic minimum
function (no need to change)
# Temperature response parameters. # Parameters for Jmax. EAVJ = 37259 # Ha
in Medlyn et al. (2002) EDVJ = 200000 # Hd in Medlyn et al. (2002) DELSJ =
640.02 # DELTAS in Medlyn et al. (2002)
# Parameters for Vcmax. EAVC = 47590 # Ha in Medlyn et al. (2002) EDVC = 0.0
# Hd in Medlyn et al. (2002) DELSC = 0.0 # DELTAS in Medlyn et al. (2002)
Photosynthetically active radiation (mu mol m-2 s-1).
Tair
Air temperature (deg C)
Ca
Atmospheric CO2 (ppm)
VPD
Vapor pressure deficit (kPa)
RH
Relative humidity (ignored unless MODELGS = 2)
Patm
Atmospheric pressure (kPa)
SWP
Soil water potential (MPa)
Vcmax
Required.
Jmax
Required.
Rd0
Dark respiration at 25 deg C (required).
G1
Slope parameter in stomatal conductance model.
...
Other parameters can be set : see Details.
Note
The Farquhar function is really just a wrapper for the
photosyn function in the package GasExchangeR. In that package,
the code is borrowed from the MAESTRA model.
Author(s)
Remko Duursma. Original implementation in FORTRAN by Belinda Medlyn
(in the Maestra model). See : http://maespa.github.io
References
Farquhar, G.D., S. Caemmerer and J.A. Berry. 1980. A biochemical
model of photosynthetic CO2 assimilation in leaves of C3 species. Planta.
149:78-90.
Medlyn, B.E., E. Dreyer, D. Ellsworth, M. Forstreuter, P.C. Harley, M.U.F.
Kirschbaum, X. Le Roux, P. Montpied, J. Strassemeyer, A. Walcroft, K. Wang
and D. Loustau. 2002. Temperature response of parameters of a biochemically
based model of photosynthesis. II. A review of experimental data. Plant Cell
and Environment. 25:1167-1179.
Medlyn, B.E., R.A. Duursma, D. Eamus, D.S. Ellsworth, I.C. Prentice, C.V.M.
Barton, K.Y. Crous, P. De Angelis, M. Freeman and L. Wingate. 2011.
Reconciling the optimal and empirical approaches to modelling stomatal
conductance. Global Change Biology. 17:2134-2144.
See Also
lightresponse,setPhy
Examples
## Not run:
# A ypphy object, using the coupled Farquhar model.
eucphy <- setPhy("Farquhar", leafpars=list(Vcmax=50, Jmax=100, G1=8, G0=0.01, Rd0=1))
# The 'print' method reminds you what it is:
eucphy
## End(Not run)