photon ratios: Calculate photon ratios from spectral irradiance

Description

Photon ratios used in plant photobiology to summarize difference in spectral composition of light. Both historical, current and recently proposed photon ratios are implemented. The denominator is always a photon (= quantum) irradiance for a single waveband. The denominator is the irradiance either in a single waveband or the sum of irradiances in two wavebands.

Usage

R_FR(
  spct,
  std = "Smith20",
  use.cached.mult = FALSE,
  use.hinges = TRUE,
  naming = "short",
  name.tag = "[q:q]",
  ...
)
FR_ePAR(
  spct,
  std = "Smith20",
  use.cached.mult = FALSE,
  use.hinges = TRUE,
  naming = "short",
  name.tag = "[q:q]",
  ...
)
FR_PAR(
  spct,
  std = "Smith20",
  use.cached.mult = FALSE,
  use.hinges = TRUE,
  naming = "short",
  name.tag = "[q:q]",
  ...
)
FR_RpFR(
  spct,
  std = "Smith20",
  use.cached.mult = FALSE,
  use.hinges = TRUE,
  naming = "short",
  name.tag = "[q:q]",
  ...
)
R_RpFR(
  spct,
  std = "Smith20",
  use.cached.mult = FALSE,
  use.hinges = TRUE,
  naming = "short",
  name.tag = "[q:q]",
  ...
)
B_G(
  spct,
  std = "Sellaro",
  use.cached.mult = FALSE,
  use.hinges = TRUE,
  naming = "short",
  name.tag = "[q:q]",
  ...
)
UVB_UV(
  spct,
  std = "ISO",
  use.cached.mult = FALSE,
  use.hinges = TRUE,
  naming = "short",
  name.tag = "[q:q]",
  ...
)
UVB_UVA(
  spct,
  std = "ISO",
  use.cached.mult = FALSE,
  use.hinges = TRUE,
  naming = "short",
  name.tag = "[q:q]",
  ...
)
UVA_UV(
  spct,
  std = "ISO",
  use.cached.mult = FALSE,
  use.hinges = TRUE,
  naming = "short",
  name.tag = "[q:q]",
  ...
)
UVAlw_UV(
  spct,
  std = "plants",
  use.cached.mult = FALSE,
  use.hinges = TRUE,
  naming = "short",
  name.tag = "[q:q]",
  ...
)
UVAsw_UV(
  spct,
  std = "plants",
  use.cached.mult = FALSE,
  use.hinges = TRUE,
  naming = "short",
  name.tag = "[q:q]",
  ...
)
UV_PAR(
  spct,
  std = "ISO",
  use.cached.mult = FALSE,
  use.hinges = TRUE,
  naming = "short",
  name.tag = "[q:q]",
  ...
)
UVB_PAR(
  spct,
  std = "ISO",
  use.cached.mult = FALSE,
  use.hinges = TRUE,
  naming = "short",
  name.tag = "[q:q]",
  ...
)
UVA_PAR(
  spct,
  std = "ISO",
  use.cached.mult = FALSE,
  use.hinges = TRUE,
  naming = "short",
  name.tag = "[q:q]",
  ...
)
UVA1_UV(
  spct,
  std = "CIE",
  use.cached.mult = FALSE,
  use.hinges = TRUE,
  naming = "short",
  name.tag = "[q:q]",
  ...
)
UVA2_UV(
  spct,
  std = "CIE",
  use.cached.mult = FALSE,
  use.hinges = TRUE,
  naming = "short",
  name.tag = "[q:q]",
  ...
)
UVA2_UVA(
  spct,
  std = "CIE",
  use.cached.mult = FALSE,
  use.hinges = TRUE,
  naming = "short",
  name.tag = "[q:q]",
  ...
)
UVA1_UVA(
  spct,
  std = "CIE",
  use.cached.mult = FALSE,
  use.hinges = TRUE,
  naming = "short",
  name.tag = "[q:q]",
  ...
)

Value

When spct contains a single spectrum, a single named numeric dimensionless value giving a photon ratio, with name constructed from the name of the wavebands, with "(q:q)" appended is returned. When spct

contains multiple spectra, either in long form or as a collection of spectral objects, the returned object is a data frame with a factor identifying the spectra and a numeric variable with the numeric values of the ratio.

Arguments

spct: an object of class "source.spct" or an object of class "source.mspct" containing one of more spectra.
std: character Name of the variants of the waveband definitions to use (see table below).
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.
naming: character one of "long", "default", "short" or "none". Used to select the type of names to assign to the returned value.
name.tag: character Used to tag the name of the returned values.
...: named arguments to be forwarded to q_ratio or q_irrad methods.

Details

These functions are convenience wrappers on calls to method q_ratio() with specific waveband definitions from package photobiologyWavebands. To compute other photon ratios call method q_ratio() with predefined or ad hoc waveband() definitions.

Many predefined waveband() definitions accept a character string as argument to std used to select among different standardised and ad hoc but frequently used variations in the wavelength ranges. These functions for computing photon ratios forward the arguments received through parameter std to the parameter of the same name of the different waveband constructors as listed in the table below.

The returned value is the ratio between two photon irradiances (identical two photon fluence values) each integrated over the range of wavelengths in a waveband definition, which can differ in wavelength extent. Some ratios are defined for non-overlapping ranges of wavelengths (e.g., R:FR photon ratio) while others are defined for overlapping ranges of wavelengths (e.g., UVB:UV, which will never exceed 1 in value) or for the sum of irradiance in two wavelength ranges (e.g., FR:R+FR).

Function	Numerator	Denominator	Default `std`	Ref.
`R_FR()`	`Red(std)`	`Far_red(std)`	"Smith20"	4,5,6
`R_RpFR()`	`Red(std)`	`Red(std)` + `Far_red(std)`	"Smith20"	2
`FR_RpFR()`	`Far_red(std)`	`Red(std)` + `Far_red(std)`	"Smith20"	2
`FR_ePAR()`	`Far_red(std)`	`PAR("ePAR")`	"Smith20"	3
`FR_PAR()`	`Far_red(std)`	`PAR("McCree")`	"Smith20"	3
`B_G()`	`Blue(std)`	`Green(std)`	"Sellaro"	4
`UVB_UV()`	`UVB(std)`	`UV(std)`	"ISO"	1,7
`UVB_UVA()`	`UVB(std)`	`UVA(std)`	"ISO"	1,7
`UVA_UV()`	`UVA(std)`	`UV(std)`	"ISO"	1,7
`UVAlw_UV()`	`UVAlw(std)`	`UV(std)`	"plants"	7,8
`UVAsw_UV()`	`UVAsw(std)`	`UV(std)`	"plants"	7,8
`UV_PAR()`	`UV(std)`	`PAR("McCree")`	"ISO"	1
`UVB_PAR()`	`UVB(std)`	`PAR("McCree")`	"ISO"	1
`UVA_PAR()`	`UVA(std)`	`PAR("McCree")`	"ISO"	1
`UVA1_UV()`	`UVA1(std)`	`UV(std)`	"CIE"	1,7
`UVA2_UV()`	`UVA2(std)`	`UV(std)`	"CIE"	1,7
`UVA1_UVA()`	`UVA1(std)`	`UVA(std)`	"CIE"	1,7
`UVA2_UVA()`	`UVA2(std)`	`UVA(std)`	"CIE"	1,7

References

[1] Aphalo PJ, Albert A, Björn LO, McLeod AR, Robson TM, Rosenqvist E (Eds.). 2012. Beyond the Visible: A handbook of best practice in plant UV photobiology. Helsinki: University of Helsinki, Department of Biosciences, Division of Plant Biology. tools:::Rd_expr_doi("10.31885/9789521083631").

[2] Kusuma P, Bugbee B. 2021. Improving the Predictive Value of Phytochrome Photoequilibrium: Consideration of Spectral Distortion Within a Leaf. Frontiers in Plant Science 12. tools:::Rd_expr_doi("10.3389/fpls.2021.596943").

[3] Kusuma P, Bugbee B. 2021. Far-red Fraction: An Improved Metric for Characterizing Phytochrome Effects on Morphology. Journal of the American Society for Horticultural Science 146, 3–13. tools:::Rd_expr_doi("10.21273/jashs05002-20").

[4] Sellaro R, Crepy M, Trupkin SA, Karayekov E, Buchovsky AS, Rossi C, Casal JJ. 2010. Cryptochrome as a sensor of the blue / green ratio of natural radiation in Arabidopsis. Plant Physiology 154, 401–409. tools:::Rd_expr_doi("10.1104/pp.110.160820").

[5] Smith H. 1981. Plants and the Daylight Spectrum. London: Academic Press.

[6] Smith H, Holmes MG. 1984. Techniques in Photomorphogenesis. London: Academic Press.

[7] Rai N, Morales LO, Aphalo PJ. 2021. Perception of solar UV radiation by plants: photoreceptors and mechanisms. Plant Physiology 186, 1382–1396. tools:::Rd_expr_doi("10.1093/plphys/kiab162").

[8] Rai N, Farkas AOD, Safronov O, et al. 2020. The photoreceptor UVR8 mediates the perception of both UV-B and UV-A wavelengths up to 350 nm of sunlight with responsivity moderated by cryptochromes. Plant, Cell & Environment 43, 1513–1527. tools:::Rd_expr_doi("10.1111/pce.13752").

Examples

Run this code

# default, one spectrum
R_FR(sun.spct)

# naming
R_FR(sun.spct, naming = "default")
R_FR(sun.spct, naming = "none")
R_FR(sun.spct, naming = "short")
R_FR(sun.spct, naming = "long")
R_FR(sun.spct, name.tag = "")

# default, multiple spectra
R_FR(sun_evening.spct)
R_FR(sun_evening.mspct)
R_FR(sun_evening.mspct, naming = "long")
R_FR(sun_evening.mspct, name.tag = "")

# different waveband definitions
R_FR(sun.spct, std = "Smith10")
R_FR(sun.spct, std = "Smith20")
R_FR(sun.spct, std = "Sellaro")
R_FR(sun.spct, std = "Apogee")
R_FR(sun.spct, std = "Apogee", naming = "long")

FR_ePAR(sun.spct)
FR_ePAR(sun.spct, "Smith10")
FR_ePAR(sun.spct, "Smith20")
FR_ePAR(sun.spct, "Sellaro")

FR_PAR(sun.spct)
FR_PAR(sun.spct, "Smith10")
FR_PAR(sun.spct, "Smith20")
FR_PAR(sun.spct, "Sellaro")

FR_RpFR(sun.spct)
FR_RpFR(sun.spct, "Smith10")
FR_RpFR(sun.spct, "Smith20")
FR_RpFR(sun.spct, "Sellaro")

R_RpFR(sun.spct)
R_RpFR(sun.spct, "Smith10")
R_RpFR(sun.spct, "Smith20")
R_RpFR(sun.spct, "Sellaro")

B_G(sun.spct)

UVB_UV(sun.spct)

UVB_UVA(sun.spct)

UVA_UV(sun.spct)

UVAlw_UV(sun.spct)

UVAsw_UV(sun.spct)

UV_PAR(sun.spct)

UVB_PAR(sun.spct)

UVA_PAR(sun.spct)

UVA1_UV(sun.spct)

UVA2_UV(sun.spct)

UVA2_UVA(sun.spct)

UVA1_UVA(sun.spct)

Run the code above in your browser using DataLab