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,
...
)
# Default S3 method
xPAR_irrad(
spct,
w.band,
time.unit,
scale.factor,
use.cached.mult,
use.hinges,
...
)
# S3 method for class '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 class '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
)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_attr2tbfor the syntax forattr2tbpassed as is to formal parametercol.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.
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.
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. 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. 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. doi:10.1111/nph.18375 .
See also
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
#> Q_xPAR Q_ePAR Q_PAR Q_FR.700.750
#> 1 0.001031757 0.001031757 0.0008941483 0.0001376089
xPAR_irrad(sun.spct, scale.factor = 1e6) # umol m-2 s-1
#> Q_xPAR Q_ePAR Q_PAR Q_FR.700.750
#> 1 1031.757 1031.757 894.1483 137.6089
xPAR_irrad(sun.spct, time.unit = "hour") # mol m-2 h-1
#> Q_xPAR Q_ePAR Q_PAR Q_FR.700.750
#> 1 3.714326 3.714326 3.218934 0.4953919
# add irradiances for other wavebands
xPAR_irrad(sun.spct, scale.factor = 1e6, w.band = UVA("CIE"))
#> Q_xPAR Q_ePAR Q_PAR Q_FR.700.750 Q_UVA.CIE
#> 1 1031.757 1031.757 894.1483 137.6089 84.82093
# DLI from a daily spectrum (spectral daily integral)
summary(sun_daily.spct)
#> Summary of source_spct [522 x 3] object: sun_daily.spct
#> Wavelength range 280-800 nm, step 0.9-1 nm
#> Label: sunlight, simulated
#> Measured on 2012-06-01 UTC
#> Measured at 60.20911 N, 24.96474 E; Kumpula, Helsinki, FI
#> Variables:
#> w.length: Wavelength [nm]
#> s.e.irrad: Spectral energy exposure [J d-1 m-2 nm-1]
#> s.q.irrad: Spectral photon exposure [mol d-1 m-2 nm-1]
#> --
#> w.length s.e.irrad s.q.irrad
#> Min. :280.0 Min. : 0 Min. :0.00000
#> 1st Qu.:409.2 1st Qu.:17595 1st Qu.:0.07917
#> Median :539.5 Median :23883 Median :0.12116
#> Mean :539.5 Mean :20948 Mean :0.09856
#> 3rd Qu.:669.8 3rd Qu.:26826 3rd Qu.:0.12923
#> Max. :800.0 Max. :32608 Max. :0.13813
xPAR_irrad(sun_daily.spct) # mol m-2 d-1
#> Q_xPAR Q_ePAR Q_PAR Q_FR.700.750
#> 1 42.32959 42.32959 36.31809 6.011504
# multiple spectra
xPAR_irrad(sun_evening.spct, scale.factor = 1e6)
#> Q_xPAR Q_ePAR Q_PAR Q_FR.700.750 spct.idx when.measured
#> 1 84.33188 84.33188 72.72740 11.60448 time.01 2023-06-12 18:38:00
#> 2 81.60325 81.60325 70.53745 11.06581 time.02 2023-06-12 18:39:00
#> 3 82.29405 82.29405 70.74318 11.55087 time.03 2023-06-12 18:40:00
#> 4 82.98129 82.98129 70.94553 12.03576 time.04 2023-06-12 18:41:00
#> 5 88.30088 88.30088 74.24268 14.05820 time.05 2023-06-12 18:42:00
# multiple spectra as a collection
xPAR_irrad(sun_evening.mspct, scale.factor = 1e6)
#> # A tibble: 5 × 5
#> spct.idx Q_xPAR Q_ePAR Q_PAR Q_FR.700.750
#> <fct> <dbl> <dbl> <dbl> <dbl>
#> 1 time.01 84.3 84.3 72.7 11.6
#> 2 time.02 81.6 81.6 70.5 11.1
#> 3 time.03 82.3 82.3 70.7 11.6
#> 4 time.04 83.0 83.0 70.9 12.0
#> 5 time.05 88.3 88.3 74.2 14.1
# copy metadata from the spectra, see help(q_irrad)
xPAR_irrad(sun_evening.mspct,
scale.factor = 1e6,
attr2tb = c("lon", "lat", "when.measured"))
#> # A tibble: 5 × 8
#> spct.idx Q_xPAR Q_ePAR Q_PAR Q_FR.700.750 lon lat when.measured
#> <fct> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dttm>
#> 1 time.01 84.3 84.3 72.7 11.6 24.0 60.2 2023-06-12 18:38:00
#> 2 time.02 81.6 81.6 70.5 11.1 24.0 60.2 2023-06-12 18:39:00
#> 3 time.03 82.3 82.3 70.7 11.6 24.0 60.2 2023-06-12 18:40:00
#> 4 time.04 83.0 83.0 70.9 12.0 24.0 60.2 2023-06-12 18:41:00
#> 5 time.05 88.3 88.3 74.2 14.1 24.0 60.2 2023-06-12 18:42:00