photobiologyPlants (version 0.6.1-1)

photon irradiances: Constrained extended PAR from spectral irradiance

Description

Compute the constrained extended photosynthetically active radiation (xPAR) photon irradiance and its components ePAR, PAR and FR.700.750.

Usage

xPAR_irrad(
  spct,
  w.band,
  time.unit,
  scale.factor,
  use.cached.mult,
  use.hinges,
  ...
)
# S3 method for default
xPAR_irrad(
  spct,
  w.band,
  time.unit,
  scale.factor,
  use.cached.mult,
  use.hinges,
  ...
)
# S3 method for source_spct
xPAR_irrad(
  spct,
  w.band = list(),
  time.unit = NULL,
  scale.factor = 1,
  use.cached.mult = getOption("photobiology.use.cached.mult", default = FALSE),
  use.hinges = NULL,
  ...
)
# S3 method for source_mspct
xPAR_irrad(
  spct,
  w.band = list(),
  time.unit = NULL,
  scale.factor = 1,
  use.cached.mult = getOption("photobiology.use.cached.mult", default = FALSE),
  use.hinges = NULL,
  ...,
  attr2tb = NULL,
  idx = "spct.idx",
  .parallel = FALSE,
  .paropts = NULL
)

Value

a data.frame with four numeric variables photon irradiances for xPAR, ePAR, PAR, and the far-red with wavelength 700 to 750 nm. expressed in

\(mol m^{-2} s^{-1}\) if scale.factor = 1, and possibly additional ones with metadata copied from the spectra. The data frame has one row for each spectrum in the object passed as argument to formal parameter

spct.

Arguments

spct

an object of class "source.spct".

w.band

a waveband object or a list of waveband objects with additional waveband definitions for which to compute photon irradiance.

time.unit

character or lubridate::duration object.

scale.factor

numeric Multiplier applied to returned value.

use.cached.mult

logical indicating whether multiplier values should be cached between calls.

use.hinges

logical indicating whether to use hinges to reduce interpolation errors.

...

ignored.

attr2tb

character vector, see add_attr2tb for the syntax for attr2tb passed as is to formal parameter col.names.

idx

character Name of the column with the names of the members of the collection of spectra.

.parallel

if TRUE, apply function in parallel, using parallel backend provided by foreach

.paropts

a list of additional options passed into the foreach function when parallel computation is enabled. This is important if (for example) your code relies on external data or packages: use the .export and .packages arguments to supply them so that all cluster nodes have the correct environment set up for computing.

Details

PAR is defined by a very simple biological spectral weighting function (BSWF) giving equal action per photon in the range 400 nm to 700 nm. Radiation in the range 700 to 750 nm has a synergistic effect on the photosynthesis rate as long as it is present in addition to PAR. This synergism is called Emerson's effect. An alternative definition, ePAR, was proposed by Bugbee and Zhen. It uses the same BSWF as PAR but over the range 400 to 750 nm. Apogee, sells nowadays a sensor able to directly measure this photon irradiance, type SQ-610-SS ePAR sensor. The limitation is, as these authors have demonstrated, that when the contribution of FR is more than 40 photosynthesis. This can be assessed by quantifying both components separately, either from spectral data or using a sensor with at least two channels, such as Apogee's S2-141-SS PAR-FAR sensor. This bounded extended PAR is labelled here xPAR.

Under natural illumination and commonly used plant grow lights, a difference between unconstrained (ePAR) and constrained (xPAR) extended PAR is very unlikely to be observed. As xPAR cannot be computed from spectral irradiance using a single waveband definition or measured with a single-channel broadband sensor, this function can be used to check under which conditions ePAR and xPAR irradiances differ.

Methods xPAR_irrad() return four photon irradiances: ePAR (400-750 nm, unconstrained), xPAR(400-750 nm, with FR contribution constrained to a maximum of 40

References

McCree KJ. 1972. Test of current definitions of photosynthetically active radiation against leaf photosynthesis data. Agricultural Meteorology 10, 443-453. tools:::Rd_expr_doi("10.1016/0002-1571(72)90045-3").

McCree KJ. 1976. A Rational Approach to Light Measurements in Plant Ecology. In: Smith H, ed. Commentaries in Plant Science. Oxford: Pergamon Press.

Zhen S, van Iersel M, Bugbee B. 2021. Why Far-Red Photons Should Be Included in the Definition of Photosynthetic Photons and the Measurement of Horticultural Fixture Efficacy. Frontiers in Plant Science 12. tools:::Rd_expr_doi("10.3389/fpls.2021.693445").

Zhen S, van Iersel MW, Bugbee B. 2022. Photosynthesis in sun and shade: the surprising importance of far‐red photons. New Phytologist 236, 538–546. tools:::Rd_expr_doi("10.1111/nph.18375").

See Also

q_irrad() and PAR().

Other photosynthesis-related functions and data: McCree_photosynthesis.mspct, chlorophylls.mspct, chlorophylls_fluorescence.mspct

Examples

# default with a single spectrum (spectral irradiance)
xPAR_irrad(sun.spct) # mol m-2 s-1
xPAR_irrad(sun.spct, scale.factor = 1e6) # umol m-2 s-1
xPAR_irrad(sun.spct, time.unit = "hour") # mol m-2 h-1

# add irradiances for other wavebands
xPAR_irrad(sun.spct, scale.factor = 1e6, w.band = UVA("CIE"))

# DLI from a daily spectrum (spectral daily integral)
summary(sun_daily.spct)
xPAR_irrad(sun_daily.spct) # mol m-2 d-1

# multiple spectra
xPAR_irrad(sun_evening.spct, scale.factor = 1e6)

# multiple spectra as a collection
xPAR_irrad(sun_evening.mspct, scale.factor = 1e6)

# copy metadata from the spectra, see help(q_irrad)
xPAR_irrad(sun_evening.mspct,
           scale.factor = 1e6,
           attr2tb = c("lon", "lat", "when.measured"))