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get.biochemical.MD12

get.biochemical.MD12.Rd

get.biochemical.MD12 Calculates:

  • CO2 concentration in intercellular spaces (umol/mol == ppmv)

  • leaf net photosynthesis (umol/m2/s) of C3 or C4 species

  • fluorescence yield of a leaf (fraction of reference fluorescence yield in dark-adapted and un-stressed leaf)

Note: always use the prescribed units. Temperature can be either oC or K Note: input can be single numbers, vectors, or n-dimensional matrices Note: For consistency reasons, in C4 photosynthesis electron transport rates under CO2-limited conditions are computed by inverting the equation applied for light-limited conditions(Ubierna et al 2013). A discontinuity would result when computing J from ATP requirements of Vp and Vco, as a fixed electron transport partitioning is assumed for light-limited conditions

Date: 21 Sep 2012 Update:

  • 28 Jun 2013 Adaptation for use of Farquhar model of C3 photosynthesis (Farquhar et al 1980).

  • 18 Jul 2013 Inclusion of von Caemmerer model of C4 photosynthesis (von Caemmerer 2000, 2013).

  • 15 Aug 2013 Modified computation of CO2-limited electron transport in C4 species for consistency with light-limited value.

  • 22 Oct 2013 Included effect of qLs on Jmax and electron transport value of kNPQs re-scaled in input as NPQs.

  • 08 Jan 2019 (CvdT): minor modification to adjust to SCOPE_lite.

Usage

get.biochemical.MD12(data.leafbio, data.meteo, fV, get.plots)

Arguments

data.leafbio

LUT table

data.meteo

meteo characterisitics with L (Monin-Obukhov length), also carries the absorbed PAR (Q) and leaf temperature used internally.

fV

fraction of Vcmax25 downregulated as function of cumulative absorbed PAR through the canopy (relative activity profile).

get.plots

return plots for gs, assimilation and Jmax, Vcmax rate

Value

the following parameters at eaf level:

  • A in umol/m2/s which is the net assimilation rate of the leaves

  • Ci in umol/mol which is the CO2 concentration in intercellular spaces (assumed to be the same as at carboxylation sites in C3 species)

  • eta in (-) which is the amplification factor to be applied to PSII fluorescence yield spectrum relative to the dark-adapted, un-stressed yield calculated with either Fluspect or FluorMODleaf

Author

Federico Magnani, with contributions from Christiaan van der Tol (Original version in Matlab)

Carlos Camino (Ported version into R)

Examples

if (FALSE) { # \dontrun{
out <- get.biochemical.MD12(data.leafbio, data.meteo, fV = 1, get.plots = FALSE)
} # }