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get.biochemical

get.biochemical.Rd

get.biochemical Calculates net assimilation rate A, fluorescence F using biochemical model

This function calculates:

  • stomatal resistance of a leaf or needle (s m-1)

  • photosynthesis of a leaf or needle (umol m-2 s-1)

  • fluorescence of a leaf or needle (fraction of fluor. in the dark)

Usage

get.biochemical(data.leafbio, data.meteo, data.opts, fV, get.plots)

Arguments

data.leafbio

list. Leaf biochemical parameters: Type ('C3' or 'C4'), stressfactor, Vcmax25, BallBerry0, BallBerrySlope, Rdparam, Kn0/Knalpha/Knbeta (NPQ model parameters), optional g_m (mesophyll conductance, mol m^-2 s^-1 bar^-1), and (when temperature correction is enabled) the TDP sub-list of temperature-dependence parameters.

data.meteo

list. Meteorological/leaf micro-environment characteristics: Q (absorbed PAR, umol photons m^-2 s^-1), Cs (CO2 concentration in the leaf boundary layer, ppm), Temp (leaf temperature, deg C or K), eb (vapour pressure in the leaf boundary layer, hPa), Oa (O2 concentration, mmol/mol), p (air pressure, hPa).

data.opts

data.frame. Simulation options; row 7 (tempcor) is a 0/1 flag for whether temperature correction of Vcmax and the rate constants is applied.

fV

numeric. Scaling factor applied to Vcmax25 (e.g. the canopy nitrogen/Vcmax profile factor estimated in the energy balance).

get.plots

logical. If TRUE, returns diagnostic plots for stomatal conductance, assimilation, and Jmax/Vcmax rates.

Value

A list biochem_out with (among others): A (net assimilation rate, umol m^-2 s^-1), Ci/Cc (internal/chloroplast CO2 concentration, ppm), rcw (stomatal resistance, s m^-1), gs (stomatal conductance), Vcmax, Rd, Ja (actual electron transport rate), ps/ps_rel (photochemical yield and degree of light saturation), eta (fluorescence yield relative to dark-adapted), qE/qQ (non-photochemical/photochemical quenching), fs/fo/fm (steady-state/dark/light-saturated fluorescence yields), Kn/NPQ/Kf/Kp/Kd (rate constants), and SIF (solar-induced fluorescence, fs * Q).

References

Farquhar et al. 1980, Collatz et al (1991, 1992), and: Dutta, D., Schimel, D. S., Sun, Y., Tol, C. V. D., & Frankenberg, C. (2019). Optimal inverse estimation of ecosystem parameters from observations of carbon and energy fluxes. Biogeosciences, 16(1), 77-103.

Van der Tol, C., Berry, J. A., Campbell, P. K. E., & Rascher, U. (2014). Models of fluorescence and photosynthesis for interpreting measurements of solar induced chlorophyll fluorescence. Journal of Geophysical Research: Biogeosciences, 119(12), 2312-2327.

Bonan, G. B., Lawrence, P. J., Oleson, K. W., Levis, S., Jung, M., Reichstein, M., ... & Swenson, S. C. (2011). Improving canopy processes in the Community Land Model version 4 (CLM4) using global flux fields empirically inferred from FLUXNET data. Journal of Geophysical Research: Biogeosciences, 116(G2).

Author

Joe Berry and Christiaan van der Tol, Ari Kornfeld (Original version in Matlab)

Carlos Camino (Ported version into R)

last updates Date: 21 Sep 2012.

Update: 20 Feb 2013. Update: Aug 2013: correction of L171: Ci <- Ci*1e6/ p * 1E3

Update: 2016-10 - (JAK) major rewrite to accomodate an iterative solution to the Ball-Berry equation - also allows for g_m to be specified for C3 plants, but only if Ci_input is provided.

Update: 25 Feb 2021: Temperature reponse functions by Dutta et al. implemented

Examples

if (FALSE) { # \dontrun{
biochem_out <- get.biochemical(data.leafbio, data.meteo, data.opts, fV = 1, get.plots = FALSE)
} # }