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Calculate phytochrome photoequilibrium

Source: R/Pfr-Ptot.R
Pfr_Ptot.Rd

Calculate the phytochrome photoequilibrium for monochromatic light from its wavelength or from a spectrum expressed as spectral irradiance.

Usage

Pfr_Ptot(x, ...)

# Default S3 method
Pfr_Ptot(x, ...)

# S3 method for class 'numeric'
Pfr_Ptot(x, spct.out = length(x) > 20, ...)

# S3 method for class 'source_spct'
Pfr_Ptot(x, ..., na.rm = FALSE)

Arguments

x

an R object

...

not used

spct.out

logical Flag indicating if the returned object should be of class response_spct instead of numeric.

na.rm

logical. If TRUE link[stats]{na.omit} is first called on x.

Value

If x is numeric, giving wavelengths (nm), a vector of numeric values giving the \(P_{fr} / P_{tot}\) at each wavelength or a generic_spct object with the wavelength values sorted in ascending order and the corresponding \(P_{fr} / P_{tot}\) values in column s.q.response.

If x is a source_spct object, a single numeric value giving the \(P_{fr} / P_{tot}\).

Details

The calculations are based on data describing the photochemical constants for the plant photoreceptor phytochrome measured in vitro and available for wavelengths in the range 380 nm to 770 nm as published by Mancinelli (1994). For reliable estimates of \(P_{fr} / P_{tot}\) from spectral irradiance, the spectrum should cover all these wavelengths with reasonably high wavelength resolution.

Methods (by class)

  • Pfr_Ptot(default): Default for generic function

  • Pfr_Ptot(numeric): Specialization for numeric

  • Pfr_Ptot(source_spct): Specialization for source_spct

    Calculate phytochrome photoequilibrium from spectral (photon) irradiance

Note

If you use these data in a publication, please cite also the original source as given under references.

References

Mancinelli, A.L. (1994) The physiology of phytochrome action. In Photomorphogenesis in plants, 2nd edition. R.E. Kendrick and G.H.M. Kronenberg, eds. Kluwer Academic Publishers, Dordrecht, pp. 211-269. ISBN 978-0-7923-2551-2 (print), 978-94-011-1884-2 (on-line). doi:10.1007/978-94-011-1884-2_10

See also

Other phytochrome-related functions and data: PHYs.mspct, Pfr_Ptot_R_FR(), Phy_Sigma(), Phy_Sigma_FR(), Phy_Sigma_R(), Phy_reaction_rates()

Examples

# monochromatic light
Pfr_Ptot(620) # one wavelength in nm
#> [1] 0.8746565
Pfr_Ptot(c(570, 600, 630, 660, 690, 735, 760)) # six wavelengths
#> [1] 0.84842692 0.88805135 0.86463731 0.86964902 0.60819793 0.01749967 0.02079894
Pfr_Ptot(sun.spct) # spectrum of terrestrial sunligth
#> [1] 0.68341