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MD12 algorithm for the computation of fluorescence yield

MD12.Rd

MD12 computes the PSII fluorescence quantum yield from the electron transport rate and a set of first-order rate constants describing the competing de-excitation pathways of PSII (photochemistry, fluorescence, constitutive and regulated thermal dissipation). The yield is evaluated both under CO2-limited and under light-limited conditions, and the smaller (limiting) value is returned, following the model described in Van der Tol et al. (2014, Biogeosciences) building on Magnani et al. (2012).

Usage

MD12(ps, Ja, Jms, kps, kf, kds, kDs)

Arguments

ps

numeric vector. PSII photochemical yield (probability that an absorbed photon leads to charge separation), dimensionless [E/E], range 0-1.

Ja

numeric vector. Actual (CO2-limited) electron transport rate, in the same units as Jms (typically umol electrons m^-2 s^-1).

Jms

numeric vector. Potential (light-limited) electron transport rate, reduced for PSII photodamage, in the same units as Ja.

kps

numeric vector. Rate constant for photochemistry at PSII (steady state), dimensionless relative rate constant.

kf

numeric vector. Rate constant for fluorescence emission, dimensionless relative rate constant.

kds

numeric vector. Rate constant for constitutive (basal, dark-type) thermal dissipation at PSII, steady state, dimensionless relative rate constant.

kDs

numeric vector. Rate constant for regulated (NPQ-type) thermal dissipation at PSII, steady state, dimensionless relative rate constant.

Value

numeric vector. PSII fluorescence quantum yield fs, dimensionless [E/E], computed as the minimum of the CO2-limited and light-limited yields.

Author

Christiaan van der Tol (Original version in Matlab)

Carlos Camino (Ported version into R)

Examples

if (FALSE) { # \dontrun{
fs <- MD12(ps, Ja, Jms, kps, kf, kds, kDs)
} # }