,
Titta K. Kotilainen [ctb] | Title: | Waveband Definitions for UV, VIS, and IR Radiation |
|---|---|
| Description: | Constructors of waveband objects for commonly used biological spectral weighting functions (BSWFs) and for different wavebands describing named ranges of wavelengths in the ultraviolet (UV), visible (VIS) and infrared (IR) regions of the electromagnetic spectrum. Part of the 'r4photobiology' suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>. |
| Authors: | Pedro J. Aphalo [aut, cre] ,
Titta K. Kotilainen [ctb] |
| Maintainer: | Pedro J. Aphalo <[email protected]> |
| License: | GPL (>= 2) |
| Version: | 0.5.2.9000 |
| Built: | 2024-08-20 05:30:54 UTC |
| Source: | https://github.com/aphalo/photobiologyWavebands |
Constructors of waveband objects for commonly used biological spectral weighting functions (BSWFs) and for different wavebands describing named ranges of wavelengths in the ultraviolet (UV), visible (VIS) and infrared (IR) regions of the electromagnetic spectrum. Part of the 'r4photobiology' suite, Aphalo P. J. (2015) doi:10.19232/uv4pb.2015.1.14.
Package 'photobiologyWavebands' provides constructors for objects of class
waveband from package 'photobiology'. These contructors are based on
standard definitions or frequently used non-standardized definitions. When
different definitions are in common use for a given named waveband the
constructors accept an argument to chose among them. Whenever an ISO standard
provides a definition, this is used by default. In the infrared (IR) there
are many different definitions and waveband names in use. We have tried to
include most of the commonly used names and definitions.
Definitions "matching" the different bands of Landsat imagers are included. These are simple wavelength ranges for wavelengths at half-maximun response as given in the NASA literature, which in some cases presents small inconsistencies. These definitions cannot exactly reproduce instrument responses as they do not describe the real spectral responsiveness of the satellite imagers.
By necessity we cover only a subset of all definitions in use. These should
be thought as convenience functions, as waveband objects according to any
arbitrary definition can be constructed with the constructor provided by
package photobiology-package.
Maintainer: Pedro J. Aphalo [email protected] (ORCID)
Other contributors:
Titta K. Kotilainen [email protected] (ORCID) [contributor]
Aphalo, Pedro J. (2015) The r4photobiology suite. UV4Plants Bulletin, 2015:1, 21-29. doi:10.19232/uv4pb.2015.1.14.
Aphalo, P. J., Albert, A., Björn, L. O., McLeod, A. R., Robson, T. M., Rosenqvist, E. (Eds.). (2012). Beyond the Visible: A handbook of best practice in plant UV photobiology (1st ed., p. xxx + 174). Helsinki: University of Helsinki, Department of Biosciences, Division of Plant Biology. ISBN 978-952-10-8363-1 (PDF), 978-952-10-8362-4 (paperback). Open access PDF download available at https://hdl.handle.net/10138/37558
Caldwell, M. M. (1971) Solar UV irradiation and the growth and development of higher plants. In Giese, A. C. (Ed.) Photophysiology, Academic Press, 1971, 6, 131-177
Diffey, B. L. 1991. Solar ultraviolet radiation effects on biological systems. Review in Physics in Medicine and Biology 36 (3): 299-328.
Green, A. E. S., Miller, J. H. (1975) Measures of biologically active radiation in the 280-340 nm region. Impacts of climate change on the environment. CIAP Monograph, 5, Part 1, Chapter 2.2.4
Green, A. E. S.; Sawada, T. & Shettle, E. P. (1974) The middle ultraviolet reaching the ground Photochemistry and Photobiology, 1974, 19, 251-259
Ibdah, M., Krins, A., Seidlitz, H. K., Heller, W., Strack, D. & Vogt, T. (2002) Spectral dependence of flavonol and betacyanin accumulation in Mesembryanthemum crystallinum under enhanced ultraviolet radiation. Plant, Cell & Environment, 25, 1145-1154
International Commission on Non-Ionizing Radiation Protection (2004) ICNIRP Guidelines on Limits of Exposure to Ultraviolet Radiation of Wavelengths Between 180 nm and 400 nm (Incoherent Optical Radiation). Health Physics 87(2):171-186. https://www.icnirp.org/cms/upload/publications/ICNIRPUV2004.pdf
ISO (2007) Optics and photonics - Spectral bands. ISO Standard 20473:2007. ISO, Geneva.
ISO (2007) Space environment (natural and artificial) - Process for determining solar irradiances. ISO Standard 21348. ISO, Geneva.
Quaite, F. E., Sutherland, B. M., Sutherland, J. C. Action spectrum for DNA damage in alfalfa lowers predicted impact of ozone depletion. Nature, 1992, 358, 576-578
Leutner, B. and Horning, N. (2016). RStoolbox: Tools for Remote Sensing Data Analysis. R package version 0.1.6. https://CRAN.R-project.org/package=RStoolbox
Micheletti, M. I.; Piacentini, R. D. & Madronich, S. (2003) Sensitivity of Biologically Active UV Radiation to Stratospheric Ozone Changes: Effects of Action Spectrum Shape and Wavelength Range Photochemistry and Photobiology, 78, 456-461
Musil, C. F. (1995) Differential effects of elevated ultraviolet-B radiation on the photochemical and reproductive performances of dicotyledonous and monocotyledonous arid-environment ephemerals. Plant, Cell and Environment, 18, 844-854
Murakami, K., Aiga I. (1994) Red/Far-red photon flux ratio used as an index number for morphological control of plant growth under artificial lighting conditions. Proc. Int. Symp. Artificial Lighting, Acta Horticulturae, 418, ISHS 1997.
NASA (nd) Landsat 7 Science Data Users Handbook. https://landsat.gsfc.nasa.gov/wp-content/uploads/2016/08/Landsat7_Handbook.pdf Visited on 2016-12-26.
Sellaro, R., Crepy, M., Trupkin, S. A., Karayekov, E., Buchovsky, A. S., Rossi, C., & Casal, J. J. (2010). Cryptochrome as a sensor of the blue/green ratio of natural radiation in Arabidopsis. Plant physiology, 154(1), 401-409. doi:10.1104/pp.110.160820
Setlow, R. B. (1974) The Wavelengths in Sunlight Effective in Producing Skin Cancer: A Theoretical Analysis. Proceedings of the National Academy of Sciences, 71, 3363-3366
Smith, H. (1982) Light quality, photoperception and plant strategy. Annual Review of Plant Physiology, 33:481-518.
USGS (nd) Landsat 8 Science Data Users Handbook. https://www.usgs.gov/media/files/landsat-8-data-users-handbook. Visited on 2023-01-07.
Webb, A. R.; Slaper, H.; Koepke, P. & Schmalwieser, A. W. Know your standard: clarifying the CIE erythema action spectrum. Photochemistry and photobiology, 2011, 87, 483-486
Useful links:
Report bugs at https://github.com/aphalo/photobiologywavebands/issues
q_irrad(sun.spct, PAR()) # PAR photon irradiance q_irrad(sun.spct, Blue("ISO")) # blue photon irradiance, ISO definition q_irrad(sun.spct, Blue("Sellaro")) # blue photon irradiance, Sellaro et al.'s definition e_irrad(sun.spct, VIS()) # VIS irradiance, ISO definition q_irrad(sun.spct, VIS()) # VIS photon, ISO definitionq_irrad(sun.spct, PAR()) # PAR photon irradiance q_irrad(sun.spct, Blue("ISO")) # blue photon irradiance, ISO definition q_irrad(sun.spct, Blue("Sellaro")) # blue photon irradiance, Sellaro et al.'s definition e_irrad(sun.spct, VIS()) # VIS irradiance, ISO definition q_irrad(sun.spct, VIS()) # VIS photon, ISO definition
Wavelength-range definitions for blue light according to ISO or as commonly used in plant or remote sensing applications.
Blue(std = "ISO")Blue(std = "ISO")
std |
a character string "ISO", "Sellaro", "Broad", "RS" (remote sensing), or Landsat imagers, "LandsatTM", "LandsatETM", or "LandsatOLI". |
The different arguments passed to formal parameter std
determine the range of wavelengths set as boundaries of the returned
waveband object; "ISO" is standardized
definition based on human colour vision; "Sellaro" and
"Broad" are non-standard but used in plant sciences; "RS" is
non-standard but frequently used in remote sensing; the remaining
definitions are for the published wavelength sensitivity range of imagers
(cameras) in the Landsat satellite missions.
A waveband object defining a wavelength range.
The bands are defined as square windows, these can be applied to spectral data to obtain the "true" values, but they do not simulate the sensitivity of broad-band sensors or the spectral transmittance of ionic filters. Some band-pass interference filters may have very sharp cut-in and cut-off, and their effect can be approximated by a square window, but filters based on light absorption will show gradual tails and bell-shaped wavelength-windows. The Landsat instruments have very steep cut-in and cut-off slopes and are well approximated.
Aphalo, P. J., Albert, A., Björn, L. O., McLeod, A. R., Robson, T. M., Rosenqvist, E. (Eds.). (2012). Beyond the Visible: A handbook of best practice in plant UV photobiology (1st ed., p. xxx + 174). Helsinki: University of Helsinki, Department of Biosciences, Division of Plant Biology. ISBN 978-952-10-8363-1 (PDF), 978-952-10-8362-4 (paperback). Open access PDF download available at doi:10.31885/9789521083631.
ISO (2007) Space environment (natural and artificial) - Process for determining solar irradiances. ISO Standard 21348. ISO, Geneva.
Sellaro, R., Crepy, M., Trupkin, S. A., Karayekov, E., Buchovsky, A. S., Rossi, C., & Casal, J. J. (2010). Cryptochrome as a sensor of the blue/green ratio of natural radiation in Arabidopsis. Plant physiology, 154(1), 401-409. doi:10.1104/pp.110.160820.
Other unweighted wavebands:
Far_red(),
Green(),
IR(),
Orange(),
Purple(),
Red(),
UV(),
UVA(),
UVB(),
UVC(),
VIS(),
Yellow()
Blue() Blue("ISO") Blue("Sellaro") e_irrad(sun.spct, Blue()) # W m-2 q_irrad(sun.spct, Blue()) # mol m-2 q_irrad(sun.spct, Blue(), scale.factor = 1e6) # umol m-2Blue() Blue("ISO") Blue("Sellaro") e_irrad(sun.spct, Blue()) # W m-2 q_irrad(sun.spct, Blue()) # mol m-2 q_irrad(sun.spct, Blue(), scale.factor = 1e6) # umol m-2
Methane production from pectin BSWF
CH4(norm = 300, w.low = 275, w.high = 400)CH4(norm = 300, w.low = 275, w.high = 400)
norm |
normalization wavelength (nm) |
w.low |
short-end boundary wavelength (nm) |
w.high |
long-end boundary wavelength (nm) |
a waveband object wavelength defining wavelength range, weighting function and normalization wavelength.
Bloom, A. A.; Lee-Taylor, J.; Madronich, S.; Messenger, D. J.; Palmer, P. I.; Reay, D. S. & McLeod, A. R. (2010) Global methane emission estimates from ultraviolet irradiation of terrestrial plant foliage. New Phytologist, Blackwell Publishing Ltd, 187, 417–425 .
Other BSWF weighted wavebands:
DNA_GM(),
DNA_N(),
DNA_P(),
FLAV(),
GEN_G(),
GEN_M(),
GEN_T(),
PAR(),
PG(),
UV_health_hazard(),
erythema()
CH4() CH4(norm = 400)CH4() CH4(norm = 400)
This function gives a set of numeric multipliers that can be used as a weight to calculate effective doses and irradiances. The returned values are on quantum based effectiveness relative units.
CH4_e_fun(w.length)CH4_e_fun(w.length)
w.length |
numeric array of wavelengths (nm) |
a numeric array of the same length as w.length with values for the BSWF normalized
as in the original source (300 nm) and based on energy effectiveness.
Bloom, A. A.; Lee-Taylor, J.; Madronich, S.; Messenger, D. J.; Palmer, P. I.; Reay, D. S. & McLeod, A. R. (2010) Global methane emission estimates from ultraviolet irradiation of terrestrial plant foliage. New Phytologist, Blackwell Publishing Ltd, 187, 417–425 .
Other BSWF functions:
CH4_q_fun(),
CIE_e_fun(),
CIE_q_fun(),
DNA_GM_q_fun(),
DNA_P_q_fun(),
FLAV_q_fun(),
GEN_G_q_fun(),
GEN_M_q_fun(),
GEN_T_q_fun(),
ICNIRP_e_fun(),
PG_q_fun()
CH4_e_fun(293:400)CH4_e_fun(293:400)
This function gives a set of numeric multipliers that can be used as a weight to calculate effective doses and irradiances. The returned values are on quantum based effectiveness relative units.
CH4_q_fun(w.length)CH4_q_fun(w.length)
w.length |
numeric array of wavelengths (nm) |
a numeric array of the same length as w.length with values for the BSWF normalized
as in the original source (300 nm) but based on quantum effectiveness.
Other BSWF functions:
CH4_e_fun(),
CIE_e_fun(),
CIE_q_fun(),
DNA_GM_q_fun(),
DNA_P_q_fun(),
FLAV_q_fun(),
GEN_G_q_fun(),
GEN_M_q_fun(),
GEN_T_q_fun(),
ICNIRP_e_fun(),
PG_q_fun()
CH4_q_fun(293:400)CH4_q_fun(293:400)
This function gives a set of numeric multipliers that can be used as a weight to calculate effective doses and irradiances. The returned values are on quantum based effectiveness relative units.
CIE_e_fun(w.length)CIE_e_fun(w.length)
w.length |
numeric array of wavelengths (nm) |
a numeric array of the same length as w.length with values for
the BSWF normalized as in the original source (298 nm) and based on energy
effectiveness.
Other BSWF functions:
CH4_e_fun(),
CH4_q_fun(),
CIE_q_fun(),
DNA_GM_q_fun(),
DNA_P_q_fun(),
FLAV_q_fun(),
GEN_G_q_fun(),
GEN_M_q_fun(),
GEN_T_q_fun(),
ICNIRP_e_fun(),
PG_q_fun()
CIE_e_fun(293:400)CIE_e_fun(293:400)
This function gives a set of numeric multipliers that can be used as a weight to calculate effective doses and irradiances. The returned values are on quantum based effectiveness relative units.
CIE_q_fun(w.length)CIE_q_fun(w.length)
w.length |
numeric array of wavelengths (nm) |
a numeric array of the same length as w.length with values for
the BSWF normalized as in the original source (298 nm) and based on quantum
effectiveness.
Other BSWF functions:
CH4_e_fun(),
CH4_q_fun(),
CIE_e_fun(),
DNA_GM_q_fun(),
DNA_P_q_fun(),
FLAV_q_fun(),
GEN_G_q_fun(),
GEN_M_q_fun(),
GEN_T_q_fun(),
ICNIRP_e_fun(),
PG_q_fun()
CIE_q_fun(293:400)CIE_q_fun(293:400)
A dataset containing the wavelengths at a 1 nm interval. Tabulated values for quantum luminous efficiency according to CIE1924.
A response.spct object with 471 rows and 2 variables
The variables are as follows:
w.length (nm)
s.q.response
This luminous efficiency function understimates the renponse to short wavelengths.
http://www.cvrl.org/ downloaded on 2015-01-24
A dataset containing the wavelengths at a 1 nm interval. Tabulated values for quantum luminous efficiency at low light levels according to CIE1951.
A response.spct object with 401 rows and 2 variables
The variables are as follows:
w.length (nm)
s.q.response
http://www.cvrl.org/ downloaded on 2015-01-24
A dataset containing the wavelengths at a 1 nm interval. Tabulated values for quantum luminous efficiency according to CIE2008 for 2 degrees.
A response.spct object with 441 rows and 2 variables
The variables are as follows:
w.length (nm)
s.q.response
http://www.cvrl.org/ downloaded on 2015-01-24
Naked DNA damage BSWF, Green and Miller's formulation.
DNA_GM(norm = 300, w.low = 275, w.high = 400)DNA_GM(norm = 300, w.low = 275, w.high = 400)
norm |
normalization wavelength (nm) |
w.low |
short-end boundary wavelength (nm) |
w.high |
long-end boundary wavelength (nm) |
a waveband object wavelength defining wavelength range, weighting function and normalization wavelength.
Other BSWF weighted wavebands:
CH4(),
DNA_N(),
DNA_P(),
FLAV(),
GEN_G(),
GEN_M(),
GEN_T(),
PAR(),
PG(),
UV_health_hazard(),
erythema()
DNA_GM() DNA_GM(300)DNA_GM() DNA_GM(300)
This function gives a set of numeric multipliers that can be used as a weight to calculate effective doses and irradiances. It uses the seldom used Green and Miller formulation.
DNA_GM_q_fun(w.length)DNA_GM_q_fun(w.length)
w.length |
numeric array of w.length (nm) |
a numeric array of the same length as w.length with values for
the BSWF normalized as in the original source. The returned values are
based on quantum effectiveness units.
Other BSWF functions:
CH4_e_fun(),
CH4_q_fun(),
CIE_e_fun(),
CIE_q_fun(),
DNA_P_q_fun(),
FLAV_q_fun(),
GEN_G_q_fun(),
GEN_M_q_fun(),
GEN_T_q_fun(),
ICNIRP_e_fun(),
PG_q_fun()
DNA_GM_q_fun(293:400)DNA_GM_q_fun(293:400)
Naked DNA damage BSWF
DNA_N(norm = 300, w.low = 275, w.high = 400)DNA_N(norm = 300, w.low = 275, w.high = 400)
norm |
normalization wavelength (nm) |
w.low |
short-end boundary wavelength (nm) |
w.high |
long-end boundary wavelength (nm) |
a waveband object wavelength defining wavelength range, weighting function and normalization wavelength.
Other BSWF weighted wavebands:
CH4(),
DNA_GM(),
DNA_P(),
FLAV(),
GEN_G(),
GEN_M(),
GEN_T(),
PAR(),
PG(),
UV_health_hazard(),
erythema()
DNA_N() DNA_N(300)DNA_N() DNA_N(300)
This function gives a set of numeric multipliers that can be used as a weight to calculate effective doses and irradiances.
DNA_N_q_fun(w.length)DNA_N_q_fun(w.length)
w.length |
numeric array of w.length (nm) |
a numeric array of the same length as w.length with values for
the BSWF normalized as in the original source. The returned values are
based on quantum effectiveness units.
The digitized data as used in the TUV model covers the wavelength range from 256 nm to 364 nm. For longer wavelengths we set the value to zero, and for shorter wavelengths we extrapolate the value for 256 nm.
DNA_N_q_fun(293:400)DNA_N_q_fun(293:400)
Plant DNA damage BSWF as formulated by Musil.
DNA_P(norm = 300, w.low = 275, w.high = 400)DNA_P(norm = 300, w.low = 275, w.high = 400)
norm |
normalization wavelength (nm) |
w.low |
short-end boundary wavelength (nm) |
w.high |
long-end boundary wavelength (nm) |
a waveband object wavelength defining wavelength range, weighting function and normalization wavelength.
Other BSWF weighted wavebands:
CH4(),
DNA_GM(),
DNA_N(),
FLAV(),
GEN_G(),
GEN_M(),
GEN_T(),
PAR(),
PG(),
UV_health_hazard(),
erythema()
DNA_P() DNA_P(300)DNA_P() DNA_P(300)
This function gives a set of numeric multipliers that can be used as a weight to calculate effective doses and irradiances. It uses the formulation proposed by Musil.
DNA_P_q_fun(w.length)DNA_P_q_fun(w.length)
w.length |
numeric array of w.length (nm) |
a numeric array of the same length as w.length with values for
the BSWF normalized as in the original source. The returned values are
based on quantum effectiveness units.
Other BSWF functions:
CH4_e_fun(),
CH4_q_fun(),
CIE_e_fun(),
CIE_q_fun(),
DNA_GM_q_fun(),
FLAV_q_fun(),
GEN_G_q_fun(),
GEN_M_q_fun(),
GEN_T_q_fun(),
ICNIRP_e_fun(),
PG_q_fun()
DNA_P_q_fun(293:400)DNA_P_q_fun(293:400)
Erythema BSWF (1998 update)
erythema(std = "CIE98", norm = 298, w.low = 250, w.high = 400) CIE(norm = 298, w.low = 250, w.high = 400)erythema(std = "CIE98", norm = 298, w.low = 250, w.high = 400) CIE(norm = 298, w.low = 250, w.high = 400)
std |
a character string, currently only "CIE98" supported. |
norm |
normalization wavelength (nm) |
w.low |
short-end boundary wavelength (nm) |
w.high |
long-end boundary wavelength (nm) |
a waveband object wavelength defining wavelength range, weighting function and normalization wavelength.
The erythema BSWF from CIE is specified by a mathematical formula, and this is used directly in the definition of the returned waveband.
Standard DIN 5031-10:2018-03 defines BSWF er as a table of interpolated values derived from CIE's definition from 1998. So, the values computed using this R package do not necessarily exactly match those according to DIN 5031-10:2018-03. The range of wavelengths used, 250 to 400 nm, does agree, with those in the standard.
Webb, A. R.; Slaper, H.; Koepke, P. & Schmalwieser, A. W. (2011) Know your standard: clarifying the CIE erythema action spectrum. Photochemistry and photobiology, 2011, 87, 483-486
DIN (2018) Standard DIN 5031-10:2018-03 Optical radiation physics and illuminating engineering. Part 10: Photobiologically effective radiation, quantities, symbols and action spectra. Beuth Verlag, Berlin 2018.
Other BSWF weighted wavebands:
CH4(),
DNA_GM(),
DNA_N(),
DNA_P(),
FLAV(),
GEN_G(),
GEN_M(),
GEN_T(),
PAR(),
PG(),
UV_health_hazard()
Other BSWF weighted wavebands:
CH4(),
DNA_GM(),
DNA_N(),
DNA_P(),
FLAV(),
GEN_G(),
GEN_M(),
GEN_T(),
PAR(),
PG(),
UV_health_hazard()
erythema() erythema("CIE98") CIE() CIE(norm = 300) erythema(norm = 300)erythema() erythema("CIE98") CIE() CIE(norm = 300) erythema(norm = 300)
Wavelength-range definitions for far-red light according as commonly used in plant or remote sensing applications.
Far_red(std = "ISO")Far_red(std = "ISO")
std |
a character string, defaults to "ISO", as for other colour
definitions, which in this case returns |
The different arguments passed to formal parameter std
determine the range of wavelengths set as boundaries of the returned
waveband object; far-red in not defined by "ISO" standard
definitions based on human colour vision, and included under red;
"Smith10", "Smith20", "Inada", "Warrington",
"Sellaro" and "Broad" are non-standard but used in plant
sciences; "RedEdge40" and "RedEdge40" are non-standard but
frequently used in remote sensing.
In plant photobiology the definitions proposed by Prof. Harry Smith are the most widely used, specially to compute a red to far-red photon ratio relevant to phytochrome photoreceptors. However, other authors have used different definitions in their publications. "Smith10" (725-735 nm), "Smith20" (720-740 nm), "Inada" (700-800 nm), "Warrington" (700-850 nm), and "Sellaro" (700-750 nm).
Other definitions used in remote sensing. For example the "red edge" is to detect the condition of vegetation based on light reflectance by green vegetation. These bands are centred at the reflectance transition in the far-red band (725 nm), and here we define "RedEdge40" (705-745 nm) and "RedEdge20" (715-735 nm).
A waveband object defining a wavelength range.
The bands are defined as square windows, these can be applied to spectral data to obtain the "true" values, but they do not simulate the sensitivity of broad-band sensors or the spectral transmittance of ionic filters. Some band-pass interference filters may have very sharp cut-in and cut-off, and their effect can be approximated by a square window, but filters based on light absorption will show gradual tails and bell-shaped wavelength-windows.
Aphalo, P. J., Albert, A., Björn, L. O., McLeod, A. R., Robson, T. M., Rosenqvist, E. (Eds.). (2012). Beyond the Visible: A handbook of best practice in plant UV photobiology (1st ed., p. xxx + 174). Helsinki: University of Helsinki, Department of Biosciences, Division of Plant Biology. ISBN 978-952-10-8363-1 (PDF), 978-952-10-8362-4 (paperback). Open access PDF download available at doi:10.31885/9789521083631.
ISO (2007) Space environment (natural and artificial) - Process for determining solar irradiances. ISO Standard 21348. ISO, Geneva.
Murakami, K., Aiga I. (1994) Red/Far-red photon flux ratio used as an index number for morphological control of plant growth under artificial lighting conditions. Proc. Int. Symp. Artificial Lighting, Acta Horticulturae, 418, ISHS 1997.
Sellaro, R., Crepy, M., Trupkin, S. A., Karayekov, E., Buchovsky, A. S., Rossi, C., & Casal, J. J. (2010). Cryptochrome as a sensor of the blue/green ratio of natural radiation in Arabidopsis. Plant physiology, 154(1), 401-409. doi:10.1104/pp.110.160820.
Smith, H. (1982) Light quality, photoperception and plant strategy. Annual Review of Plant Physiology, 33:481-518. doi:10.1146/annurev.pp.33.060182.002405
NIR for wavebands close to the boundary between red
and infrared regions.
Other unweighted wavebands:
Blue(),
Green(),
IR(),
Orange(),
Purple(),
Red(),
UV(),
UVA(),
UVB(),
UVC(),
VIS(),
Yellow()
Far_red() # no ISO definition exists Far_red("ISO") # no ISO definition exists Far_red("Smith10") # 10 nm wide Far_red("Smith20") # 20 nm wide Far_red("Inada") Far_red("Warrington") Far_red("Sellaro") Far_red("RedEdge40") Far_red("RedEdge20") e_irrad(sun.spct, Far_red("Smith10")) # W m-2 q_irrad(sun.spct, Far_red("Smith10")) # mol m-2 q_irrad(sun.spct, Far_red("Smith10"), scale.factor = 1e6) # umol m-2Far_red() # no ISO definition exists Far_red("ISO") # no ISO definition exists Far_red("Smith10") # 10 nm wide Far_red("Smith20") # 20 nm wide Far_red("Inada") Far_red("Warrington") Far_red("Sellaro") Far_red("RedEdge40") Far_red("RedEdge20") e_irrad(sun.spct, Far_red("Smith10")) # W m-2 q_irrad(sun.spct, Far_red("Smith10")) # mol m-2 q_irrad(sun.spct, Far_red("Smith10"), scale.factor = 1e6) # umol m-2
Mesembryanthin accumulation BSWF, data and formulation from Ibdah et al.
FLAV(norm = 300, w.low = 275, w.high = 346)FLAV(norm = 300, w.low = 275, w.high = 346)
norm |
normalization wavelength (nm) |
w.low |
short-end boundary wavelength (nm) |
w.high |
long-end boundary wavelength (nm) |
a waveband object wavelength defining wavelength range, weighting function and normalization wavelength.
Ibdah, M.; Krins, A.; Seidlitz, H. K.; Heller, W.; Strack, D. & Vogt, T. (2002) Spectral dependence of flavonol and betacyanin accumulation in Mesembryanthemum crystallinum under enhanced ultraviolet radiation. Plant, Cell & Environment, 25, 1145-1154. doi:10.1046/j.1365-3040.2002.00895.x
Other BSWF weighted wavebands:
CH4(),
DNA_GM(),
DNA_N(),
DNA_P(),
GEN_G(),
GEN_M(),
GEN_T(),
PAR(),
PG(),
UV_health_hazard(),
erythema()
FLAV() FLAV(300)FLAV() FLAV(300)
This function gives a set of numeric multipliers that can be used as a weight to calculate effective doses and irradiances. It is the action spectrum for the accumulation of mesembryanthin.
FLAV_q_fun(w.length)FLAV_q_fun(w.length)
w.length |
numeric array of w.length (nm) |
a numeric array of the same length as w.length with values for
the BSWF normalized as in the original source. The returned values are
based on quantum effectiveness units.
Other BSWF functions:
CH4_e_fun(),
CH4_q_fun(),
CIE_e_fun(),
CIE_q_fun(),
DNA_GM_q_fun(),
DNA_P_q_fun(),
GEN_G_q_fun(),
GEN_M_q_fun(),
GEN_T_q_fun(),
ICNIRP_e_fun(),
PG_q_fun()
FLAV_q_fun(293:400)FLAV_q_fun(293:400)
Generalized Plant Action BSWF of Caldwell as formulated by Green et al.
GEN_G(norm = 300, w.low = 275, w.high = 313.3)GEN_G(norm = 300, w.low = 275, w.high = 313.3)
norm |
normalization wavelength (nm) |
w.low |
short-end boundary wavelength (nm) |
w.high |
long-end boundary wavelength (nm) |
a waveband object wavelength defining wavelength range, weighting function and normalization wavelength.
In the original publication [2] describing the formulation, the long-end wavelength boundary is specified as 313.3 nm. This is the default used here. However, in some cases it is of interest to vary this limit in sensitivity analyses. The effect on the RAF and doses of changing this boundary is substantial, and has been analysed by Micheletti et al. [3].
[1]Caldwell, M. M. (1971) Solar UV irradiation and the growth and development of higher plants. In Giese, A. C. (Ed.) Photophysiology, Academic Press, 1971, 6, 131-177
[2] Green, A. E. S.; Sawada, T. & Shettle, E. P. (1974) The middle ultraviolet reaching the ground Photochemistry and Photobiology, 1974, 19, 251-259
[3] Micheletti, M. I.; Piacentini, R. D. & Madronich, S. (2003) Sensitivity of Biologically Active UV Radiation to Stratospheric Ozone Changes: Effects of Action Spectrum Shape and Wavelength Range Photochemistry and Photobiology, 78, 456-461
Other BSWF weighted wavebands:
CH4(),
DNA_GM(),
DNA_N(),
DNA_P(),
FLAV(),
GEN_M(),
GEN_T(),
PAR(),
PG(),
UV_health_hazard(),
erythema()
GEN_G() GEN_G(300)GEN_G() GEN_G(300)
This function gives a set of numeric multipliers that can be used as a weight to calculate effective doses and irradiances. The BSWF is normalized at 280 nm.
GEN_G_q_fun(w.length)GEN_G_q_fun(w.length)
w.length |
numeric array of w.length (nm) |
a numeric array of the same length as w.length with values for the BSWF normalized
as in the original source. The returned values are based on quantum effectiveness units.
In the original publication [2] describing the formulation, the long-end wavelength boundary is specified as 313.3 nm. The equation is coded here with no such limit so that any limit can be set when defining the waveband. We do so because in some cases it is of interest to vary this limit in sensitivity analyses. The effect on the RAF and doses of changing this boundary is substantial, and has been analysed by Micheletti et al. [3].
[1] Caldwell, M. M. (1971) Solar UV irradiation and the growth and development of higher plants. In Giese, A. C. (Ed.) Photophysiology, Academic Press, 1971, 6, 131-177
[2] Green, A. E. S.; Sawada, T. & Shettle, E. P. (1974) The middle ultraviolet reaching the ground Photochemistry and Photobiology, 1974, 19, 251-259
[3] Micheletti, M. I.; Piacentini, R. D. & Madronich, S. (2003) Sensitivity of Biologically Active UV Radiation to Stratospheric Ozone Changes: Effects of Action Spectrum Shape and Wavelength Range Photochemistry and Photobiology, 78, 456-461
Other BSWF functions:
CH4_e_fun(),
CH4_q_fun(),
CIE_e_fun(),
CIE_q_fun(),
DNA_GM_q_fun(),
DNA_P_q_fun(),
FLAV_q_fun(),
GEN_M_q_fun(),
GEN_T_q_fun(),
ICNIRP_e_fun(),
PG_q_fun()
GEN_G_q_fun(293:400)GEN_G_q_fun(293:400)
Generalized Plant Action BSWF of Caldwell [1] as formulated by Micheletti et al. [2]
GEN_M(norm = 300, w.low = 275, w.high = 313.3)GEN_M(norm = 300, w.low = 275, w.high = 313.3)
norm |
normalization wavelength (nm) |
w.low |
short-end boundary wavelength (nm) |
w.high |
long-end boundary wavelength (nm) |
a waveband object wavelength defining wavelength range, weighting function and normalization wavelength.
In the original publication [2] describing the formulation, the long-end wavelength boundary is specified as 313.3 nm. This is the default used here. However, in some cases it is of interest to vary this limit in sensitivity analyses. The effect on the RAF and doses of changing this boundary is substantial, and has been analysed by Micheletti et al. [3].
[1]Caldwell, M. M. (1971) Solar UV irradiation and the growth and development of higher plants. In Giese, A. C. (Ed.) Photophysiology, Academic Press, 1971, 6, 131-177
[2] Micheletti, M. I.; Piacentini, R. D. & Madronich, S. (2003) Sensitivity of Biologically Active UV Radiation to Stratospheric Ozone Changes: Effects of Action Spectrum Shape and Wavelength Range Photochemistry and Photobiology, 78, 456-461
new_waveband and waveband
Other BSWF weighted wavebands:
CH4(),
DNA_GM(),
DNA_N(),
DNA_P(),
FLAV(),
GEN_G(),
GEN_T(),
PAR(),
PG(),
UV_health_hazard(),
erythema()
GEN_M() GEN_M(300)GEN_M() GEN_M(300)
This function gives a set of numeric multipliers that can be used as a weight to calculate effective doses and irradiances. The BSWF is normalized at 300 nm.
GEN_M_q_fun(w.length)GEN_M_q_fun(w.length)
w.length |
numeric array of w.length (nm) |
a numeric array of the same length as w.length with values for
the BSWF normalized as in the original source. The returned values are
based on quantum effectiveness units.
In the original publication [2] describing the formulation, the long-end wavelength boundary is not specified, but 313.3 nm is usually used. The equation is coded here with the limit at 342 nm as at longer wavelengths the values increase with increasing wavelength. The effect on the RAF and doses of changing this boundary ican be substantial, and has been analysed by Micheletti et al. [3].
[1]Caldwell, M. M. (1971) Solar UV irradiation and the growth and development of higher plants. In Giese, A. C. (Ed.) Photophysiology, Academic Press, 1971, 6, 131-177
[2] Micheletti, M. I. and R. D. Piacentini (2002) Irradiancia espetral solar UV-B y su relación con la efectividad de daño biológico a las plantas. ANALES AFA, 13, 242-248
[3] Micheletti, M. I.; Piacentini, R. D. & Madronich, S. (2003) Sensitivity of Biologically Active UV Radiation to Stratospheric Ozone Changes: Effects of Action Spectrum Shape and Wavelength Range Photochemistry and Photobiology, 78, 456-461
Other BSWF functions:
CH4_e_fun(),
CH4_q_fun(),
CIE_e_fun(),
CIE_q_fun(),
DNA_GM_q_fun(),
DNA_P_q_fun(),
FLAV_q_fun(),
GEN_G_q_fun(),
GEN_T_q_fun(),
ICNIRP_e_fun(),
PG_q_fun()
GEN_M_q_fun(293:400)GEN_M_q_fun(293:400)
Generalized Plant Action BSWF of Caldwell [1] as formulated by Timijan et al. [2]
GEN_T(norm = 300, w.low = 275, w.high = 345)GEN_T(norm = 300, w.low = 275, w.high = 345)
norm |
normalization wavelength (nm) |
w.low |
short-end boundary wavelength (nm) |
w.high |
long-end boundary wavelength (nm) |
a waveband object wavelength defining wavelength range, weighting function and normalization wavelength.
[1] Caldwell, M. M. (1971) Solar UV irradiation and the growth and development of higher plants. In Giese, A. C. (Ed.) Photophysiology, Academic Press, 1971, 6, 131-177
[2] Thimijan RW, Cams HR, Campbell L. (1978) Radiation sources and related environmental control for biological and climatic eflFects of UV research. Final report EPA-IAG-D6-0168. Washington: Environmental Protection Agency.
Other BSWF weighted wavebands:
CH4(),
DNA_GM(),
DNA_N(),
DNA_P(),
FLAV(),
GEN_G(),
GEN_M(),
PAR(),
PG(),
UV_health_hazard(),
erythema()
GEN_T() GEN_T(300)GEN_T() GEN_T(300)
This function gives a set of numeric multipliers that can be used as a weight to calculate effective doses and irradiances.
GEN_T_q_fun(w.length)GEN_T_q_fun(w.length)
w.length |
numeric array of w.length (nm) |
a numeric array of the same length as w.length with values for
the BSWF normalized as in the original source. The returned values are
based on quantum effectiveness units.
For wavelengths shorter than 256 nm the value returned by the equation starts decreasing, but we instead extrapolate this maximum value, obtained at 256 nm, to shorter wavelengths. For wavelengths longer than 345 nm we return zero, as is usual parctice.
Other BSWF functions:
CH4_e_fun(),
CH4_q_fun(),
CIE_e_fun(),
CIE_q_fun(),
DNA_GM_q_fun(),
DNA_P_q_fun(),
FLAV_q_fun(),
GEN_G_q_fun(),
GEN_M_q_fun(),
ICNIRP_e_fun(),
PG_q_fun()
GEN_T_q_fun(293:400)GEN_T_q_fun(293:400)
Wavelength-range definitions for green light according to ISO or as commonly used in plant or remote sensing applications.
Green(std = "ISO")Green(std = "ISO")
std |
a character string "ISO", "Sellaro", "Broad", "RS", "LandsatOLI", "LandsatRBV", "LandsatTM", "LandsatETM", or "LandsatMSS". |
The different arguments passed to formal parameter std
determine the range of wavelengths set as boundaries of the returned
waveband object; "ISO" is an standardized
definition based on human colour vision; "Sellaro" and
"Broad" are non-standard but used in plant sciences; "RS" is
non-standard but frequently used in remote sensing; the remaining
definitions are for the published wavelength sensitivity range of imagers
(cameras) in the Landsat satellite missions.
A waveband object defining a wavelength range.
The bands are defined as square windows, these can be applied to spectral data to obtain the "true" values, but they do not simulate the sensitivity of broad-band sensors or the spectral transmittance of ionic filters. Some band-pass interference filters may have very sharp cut-in and cut-off, and their effect can be approximated by a square window, but filters based on light absorption will show gradual tails and bell-shaped wavelength-windows. The Landsat instruments have very steep cut-in and cut-off slopes and are well approximated.
When released, this package will replace the package UVcalc.
Aphalo, P. J., Albert, A., Björn, L. O., McLeod, A. R., Robson, T. M., Rosenqvist, E. (Eds.). (2012). Beyond the Visible: A handbook of best practice in plant UV photobiology (1st ed., p. xxx + 174). Helsinki: University of Helsinki, Department of Biosciences, Division of Plant Biology. ISBN 978-952-10-8363-1 (PDF), 978-952-10-8362-4 (paperback). Open access PDF download available at doi:10.31885/9789521083631.
ISO (2007) Space environment (natural and artificial) - Process for determining solar irradiances. ISO Standard 21348. ISO, Geneva.
Sellaro, R., Crepy, M., Trupkin, S. A., Karayekov, E., Buchovsky, A. S., Rossi, C., & Casal, J. J. (2010). Cryptochrome as a sensor of the blue/green ratio of natural radiation in Arabidopsis. Plant physiology, 154(1), 401-409. doi:10.1104/pp.110.160820.
Other unweighted wavebands:
Blue(),
Far_red(),
IR(),
Orange(),
Purple(),
Red(),
UV(),
UVA(),
UVB(),
UVC(),
VIS(),
Yellow()
Green() Green("ISO") # 500 to 570 Green("Sellaro") # 500 to 570 nm e_irrad(sun.spct, Green()) # W m-2 q_irrad(sun.spct, Green()) # mol m-2 q_irrad(sun.spct, Green(), scale.factor = 1e6) # umol m-2Green() Green("ISO") # 500 to 570 Green("Sellaro") # 500 to 570 nm e_irrad(sun.spct, Green()) # W m-2 q_irrad(sun.spct, Green()) # mol m-2 q_irrad(sun.spct, Green(), scale.factor = 1e6) # umol m-2
This function returns a vector of numeric multipliers that can be used as a weight to calculate effective doses and irradiances. The returned values are on energy based effectiveness relative units. The BSWF is formulated for the range 210 nm to 400 nm.
ICNIRP_e_fun(w.length)ICNIRP_e_fun(w.length)
w.length |
numeric array of wavelengths (nm) |
a numeric array of the same length as w.length with values for
the BSWF normalized as in the original source (270 nm) and based on energy
effectiveness.
Other BSWF functions:
CH4_e_fun(),
CH4_q_fun(),
CIE_e_fun(),
CIE_q_fun(),
DNA_GM_q_fun(),
DNA_P_q_fun(),
FLAV_q_fun(),
GEN_G_q_fun(),
GEN_M_q_fun(),
GEN_T_q_fun(),
PG_q_fun()
ICNIRP_e_fun(210:400)ICNIRP_e_fun(210:400)
Wavelength-range definitions for infrared radiation according to ISO, CIE or as commonly defined in remote sensing applications.
IR(std = "ISO") NIR(std = "ISO") IRA(std = "CIE") SWIR(std = "CIE") IRB(std = "CIE") SWIR1(std = "RS") SWIR2(std = "RS") MIR(std = "ISO") IRC(std = "CIE") FIR(std = "ISO") TIR1(std = "RS") TIR2(std = "RS")IR(std = "ISO") NIR(std = "ISO") IRA(std = "CIE") SWIR(std = "CIE") IRB(std = "CIE") SWIR1(std = "RS") SWIR2(std = "RS") MIR(std = "ISO") IRC(std = "CIE") FIR(std = "ISO") TIR1(std = "RS") TIR2(std = "RS")
std |
character string, "ISO", "CIE", "RS" or Landsat imagers "LandsatRBV", "LandsatMSS", "LandsatTIRS", "LandsatOLI", "LandsatTM", "LandsatETM", depending on the constructor. |
The values for std = "ISO" are according to ISO 20473. The values for
std = "CIE" are suggested values according to Wikipedia, and need
verification.
The wavelength limits for remote sensing std = "RS" and for
Landsat imagers have been obtained from R package 'RStools' and NASA and USGS
documentation.
The names NIR, SWIR and TIR are abbreviations of near infra-red, short-wave infra-red and thermal infra-red, respectively. The naming conventions are different for "CIE" than "ISO" standards, and the labels of the waveband objects reflect this with "IRA", "IRB", etc., used when appropriate.
A waveband object defining a wavelength range.
Far_red for wavebands close to the boundary between red
and infrared regions.
new_waveband and waveband
Other unweighted wavebands:
Blue(),
Far_red(),
Green(),
Orange(),
Purple(),
Red(),
UV(),
UVA(),
UVB(),
UVC(),
VIS(),
Yellow()
SWIR1() SWIR1("RS") IR() NIR() MIR() IRA() IRB()SWIR1() SWIR1("RS") IR() NIR() MIR() IRA() IRB()
Defined according to "ISO" or "CIE".
IR_bands(std = "ISO")IR_bands(std = "ISO")
std |
a character string "ISO" or "CIE". |
a list of wavebands
Other lists of unweighted wavebands:
Landsat_bands(),
Plant_bands(),
UV_bands(),
VIS_bands()
IR_bands() IR_bands("ISO") IR_bands("CIE")IR_bands() IR_bands("ISO") IR_bands("CIE")
Defined according as ranges of wavelengths according to NASA and USGS manuals. The definitions are as rectangular windows, while the true response functions deviate to some extent from these ideal definitions.
Landsat_bands(std = "L8") RBV_bands(std = "LandsatRBV") MSS_bands(std = "LandsatMSS") OLI_bands(std = "LandsatOLI") TIRS_bands(std = "LandsatTIRS") ETM_bands(std = "LandsatETM")Landsat_bands(std = "L8") RBV_bands(std = "LandsatRBV") MSS_bands(std = "LandsatMSS") OLI_bands(std = "LandsatOLI") TIRS_bands(std = "LandsatTIRS") ETM_bands(std = "LandsatETM")
std |
a character string "L1"..."L9", for missions, "LandsarRBV", "LandsatMSS", etc. for imagers. |
See https://landsat.usgs.gov/spectral-characteristics-viewer for detailed sensitivity spectra for the different bands of the imaginers.
a list of wavebands
Other lists of unweighted wavebands:
IR_bands(),
Plant_bands(),
UV_bands(),
VIS_bands()
Landsat_bands("L1") Landsat_bands("L8") OLI_bands() TIRS_bands()Landsat_bands("L1") Landsat_bands("L8") OLI_bands() TIRS_bands()
Compute the NDVI from spectral reflectance according to waveband definitions from standards or corresponding to satellite imagers.
NDVI(spct, imager = "LandsatOLI", wb.trim = FALSE)NDVI(spct, imager = "LandsatOLI", wb.trim = FALSE)
spct |
reflectance_spct or reflectance_mspct object. |
imager |
character Name of the imager or standard to be used. |
wb.trim |
logical Flag telling if wavebands crossing spectral data boundaries are trimmed or ignored. |
NDVI is used in remote sensing to the diagnose the condition of vegetation, including crops. It is used for Landsat imagery but also at the farm or plot scale using cameras on drones. It is computed as:
NDVI = (NIR - Red) / (NIR + Red)
The waveband ranges used to compute reflectance vary. Even the imagers
in the different Landsat satellites 1 to 8 have had somehow different
wavelength sensitivities. The NDVI() function uses the waveband
constructors Red and NIR defined in this
package. Reflectance is averaged over the wavebands using function
reflectance.
A numeric vector. When the wavelength range of spct does not
fully overlap with both wavebands NA is silently returned.
The value passed as argument to imager must be a valid argument
for both Red and NIR. If the desired return
value is a data frame, function NDxI can be
used to flexibly compute NDVI and any similar index.
Wavelength-range definition for orange radiation according to ISO.
Orange(std = "ISO")Orange(std = "ISO")
std |
a character string "ISO" |
Orange radiation (591...610 nm) as defined in ISO standards based on human colour vision.
A waveband object defining a wavelength range.
ISO (2007) Space environment (natural and artificial) - Process for determining solar irradiances. ISO Standard 21348. ISO, Geneva.
Other unweighted wavebands:
Blue(),
Far_red(),
Green(),
IR(),
Purple(),
Red(),
UV(),
UVA(),
UVB(),
UVC(),
VIS(),
Yellow()
Orange() Orange("ISO") e_irrad(sun.spct, Orange()) # W m-2 q_irrad(sun.spct, Orange()) # mol m-2 q_irrad(sun.spct, Orange(), scale.factor = 1e6) # umol m-2Orange() Orange("ISO") e_irrad(sun.spct, Orange()) # W m-2 q_irrad(sun.spct, Orange()) # mol m-2 q_irrad(sun.spct, Orange(), scale.factor = 1e6) # umol m-2
Waveband definitions for photosynthetic radiation (PhR), photosynthetically active radiation (PAR) and extended photosynthetically active radiation (ePAR) according to different definitions in use for land plants.
PAR(std = "PAR", norm = 550) PhR()PAR(std = "PAR", norm = 550) PhR()
std |
a character string "Plant" (or "range"), "McCree" (or "photon", "PAR"), "Zhen" (or "ePAR"), "Gabrielsen" (or "Gaastra" or "energy") or "Nichiporovich". |
norm |
normalization wavelength (nm) |
Photosynthetically active radiation (400-700 nm) as proposed by McCree (1972), and currently used in plant sciences, gives equal weight to photons within its range, thus weights increase with increasing wavelength when expressed as energy. PAR is normally expressed as photon irradiance or (photosynthetic photon flux density, PPFD) using implicitly 1 as weight for all wavelengths (a BSWF). It is also possible, but very unusual, to express the quantity PAR as defined in McCree (1972) as an energy irradiance, in which case a BSWF with weights different from 1 needs to be used. In this case the default normalization wavelength for the PAR BSWF is set at 550 nm (my own choice).
A proposal (see Zhen et al., 2021), defines extended photosynthetically
active radiation (400-750 nm) as an alternative to PAR. The need to
consider far-red photons as drivers of photosynthesis has become apparent
with the increased use of LEDs for plant cultivation. WARNING: the proposed
definition limits photon irradiance in the range 700-750 nm to a maximum of
30
larger than 1.4 times PAR even in the presence of far-red photons in
excess, because far-red photons have only a synergistic effect on
photosynthesis in PAR. Ensuring this condition is fulfilled is the
responsibility of the user of PAR(), ePAR() and PhR()
functions. Currently, ePAR can usefully complement PAR, but in my
opinion, it is far too early for it to replace PAR.
Some earlier definitions, described by McCree (1972a) citing Gabrielsen and Gaastra, used this same wavelength range but assuming wavelength-invariant response to energy within this same range, thus weights decrease with increasing wavelength when expressed as photons. McCree (1972a) cites Nichiporovich for a similar energy based quantity but covering a wider range of wavelengths (380-710 nm). McCree's definition from 1972 is currently the one preferred by most researchers and used almost universally in the plant sciences, while others are only of historical interest. Photosynthetic radiation (400-700 nm) is defined as a wavelength range and does not implement the spectral weighting inherent to McCree's (1972) definition of PAR or the earlier energy-based ones described by McCree (1972a).
For PhR, a waveband object defining a wavelength range . For PAR, a waveband object implementing the response curve of PAR as defined by McCree (1972) and thus including a weighting function used in computation of energy-base PAR irradiances. The weights are normalized to 1 at 550 nm. The waveband label is set to "PAR" or "PhR" accordingly.
PAR is sometimes described as a range of wavelengths (e.g., Both et al., 2015), which can be confusing as there is more to McCree's (1972) definition, an spectral response function by which all photons within the range of PAR elicit the same strength of response. As long as PAR is expressed as a photon irradiance or a photon irradiation, this, of course, makes no difference.
ePAR and PAR are meant to be use to quantify light sources with a broad spectrum, i.e., sources giving out white light or pale-coloured light. PAR and ePAR are technical measures of light useful for plants in the same way as illuminance is a measure of how bright light feels to an average human. They were never meant to describe the response to be expected from an individual in particular, be it a plant or human. They are generalizations, that allow us to consistently measure light in different situations.
PAR() and PhR() call the same function definition with
different default arguments.
The default for the normalization wavelength at 550 nm keeps the average weights across the waveband equal to unity, except the special case of ePAR, where the photons in the extension to the range act by synergy.
Standard DIN 5031-10:2018-03 Defines two BSWFs sy1 and sy2 for photosynthesis, none of which are currently implemented in 'photobiologyWavebands'.
McCree, K. J. (1972) The action spectrum, absorptance and quantum yield of photosynthesis in crop plants. Agricultural Meteorology, 9, 191-216. doi:10.1016/0002-1571(71)90022-7
McCree, K. J. (1972a) 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
Both, A. J.; Benjamin, L.; Franklin, J.; Holroyd, G.; Incoll, L. D.; Lefsrud, M. G. & Pitkin, G. (2015) Guidelines for measuring and reporting environmental parameters for experiments in greenhouses. Plant Methods, 11:43. doi:10.1186/s13007-015-0083-5.
DIN (2018) Standard DIN 5031-10:2018-03 Optical radiation physics and illuminating engineering. Part 10: Photobiologically effective radiation, quantities, symbols and action spectra. Beuth Verlag, Berlin 2018
Other BSWF weighted wavebands:
CH4(),
DNA_GM(),
DNA_N(),
DNA_P(),
FLAV(),
GEN_G(),
GEN_M(),
GEN_T(),
PG(),
UV_health_hazard(),
erythema()
PAR() PhR() PAR("Plant") q_irrad(sun.spct, PhR(), scale.factor = 1e6) # umol m-2 s-2 q_irrad(sun.spct, PAR(), scale.factor = 1e6) # umol m-2 s-2 e_irrad(sun.spct, PAR("Gabrielsen")) # W m-2 e_irrad(sun.spct, PhR()) # W m-2 e_irrad(sun.spct, PAR()) # BE W m-2, normalized at 700 nmPAR() PhR() PAR("Plant") q_irrad(sun.spct, PhR(), scale.factor = 1e6) # umol m-2 s-2 q_irrad(sun.spct, PAR(), scale.factor = 1e6) # umol m-2 s-2 e_irrad(sun.spct, PAR("Gabrielsen")) # W m-2 e_irrad(sun.spct, PhR()) # W m-2 e_irrad(sun.spct, PAR()) # BE W m-2, normalized at 700 nm
Plant growth BSWF of Flint and Caldwell
PG(norm = 300, w.low = 275, w.high = 390)PG(norm = 300, w.low = 275, w.high = 390)
norm |
normalization wavelength (nm) |
w.low |
short-end boundary wavelength (nm) |
w.high |
long-end boundary wavelength (nm) |
The mathematical formulation included by Flint and Caldwell (2003) as an appendix is used. While this formulation is consistently used, the range of wavelengths over which it has been applied has varied. We use the approach of the NSF UV network and extrapolate up to 390 nm. The widely used simulation program TUV uses, instead, 366 nm as the boundary, which makes a significant difference to the computed irradiance values in sunlight.
a waveband object wavelength defining wavelength range, weighting function and normalization wavelength.
In the original publication [1], the long-end wavelength boundary is not specified. The longest wavelength at which the plant response was measured is 366 nm. From the data there is no evidence that action would immediately drop to zero at longer wavelengths. We have used in earlier versions the same value as used by the 'NSF Polar Programs UV Monitoring Network' as described in https://web.archive.org/web/20220130091146/http://uv.biospherical.com/Version2/description-Version2-Database3.html.
We use 390 nm as default value for w.high, but make if possible for
the user to set a different wavelength. To reproduce the output of the TUV
simulation model [3] version 5.0 set w.high = 366. The effect on the
RAF and doses of changing this wavelength boundary is substantial, as
discussed by Micheletti et al. [2]. Consequently, the value used must be
always reported to ensure reproducibility. For comparisons with previous
reports one may need to recompute effective irradiances using matching
wavelength boundaries on a case by case basis.
[1] Flint, S. and Caldwell M. M. (2003) A biological spectral weighting function for ozone depletion research with higher plants Physiologia Plantarum, 2003, 117, 137-144
[2] Micheletti, M. I.; Piacentini, R. D. & Madronich, S. (2003) Sensitivity of Biologically Active UV Radiation to Stratospheric Ozone Changes: Effects of Action Spectrum Shape and Wavelength Range Photochemistry and Photobiology, 78, 456-461
[3] https://www2.acom.ucar.edu/modeling/tropospheric-ultraviolet-and-visible-tuv-radiation-model
GEN_G GEN_T GEN_M and
waveband
Other BSWF weighted wavebands:
CH4(),
DNA_GM(),
DNA_N(),
DNA_P(),
FLAV(),
GEN_G(),
GEN_M(),
GEN_T(),
PAR(),
UV_health_hazard(),
erythema()
PG() PG(300)PG() PG(300)
This function gives a set of numeric multipliers that can be used as a weight to calculate effective doses and irradiances. The returned values are on quantum based effectiveness relative units.
PG_q_fun(w.length)PG_q_fun(w.length)
w.length |
numeric array of wavelengths (nm) |
a numeric array of the same length as w.length with values for
the BSWF normalized as in the original source (300 nm)
We follow the original defition here for the equation, with no limtation to the wavelength range. However, be aware that in practice it is not used for long wavelengths (different limits between 366 nm and 400 nm have been used by different authors).
Other BSWF functions:
CH4_e_fun(),
CH4_q_fun(),
CIE_e_fun(),
CIE_q_fun(),
DNA_GM_q_fun(),
DNA_P_q_fun(),
FLAV_q_fun(),
GEN_G_q_fun(),
GEN_M_q_fun(),
GEN_T_q_fun(),
ICNIRP_e_fun()
PG_q_fun(293:400)PG_q_fun(293:400)
Constant value used in the definition of Lumen 1 W is equal to 683 Lumen at 555 nm
photopic_sensitivityphotopic_sensitivity
A single numeric value
A single numeric value
Defined according to different authors.
Plant_bands(std = "sensory20")Plant_bands(std = "sensory20")
std |
a character string "sensory", "sensory10", "sensory20", "Sellaro", "ISO", "CIE", "none" or "", where "ISO", "CIE" and "none" affect only the UV bands. |
a list of wavebands
Other lists of unweighted wavebands:
IR_bands(),
Landsat_bands(),
UV_bands(),
VIS_bands()
Plant_bands() Plant_bands("sensory") Plant_bands("sensory10") Plant_bands("sensory20") Plant_bands("ISO") Plant_bands("CIE")Plant_bands() Plant_bands("sensory") Plant_bands("sensory10") Plant_bands("sensory20") Plant_bands("ISO") Plant_bands("CIE")
Wavelength-range definition for purple radiation according to ISO or imagers in the Landsat satellites.
Purple(std = "ISO")Purple(std = "ISO")
std |
a character string "ISO", or Landsat imager "LandsatOLI". |
Purple (or violet) wavelengths as defined by ISO standards based on human vision overlap the UVA band as defined by a separate ISO standard. In other contexts like plant photobiology purple is included under blue, while some overoptimistic LED sellers call LEDs emitting in the violet region ultraviolet LEDs. In addition to the ISO definition of purple, a purple channel from Landsat imagers is implemented.
A waveband object defining a wavelength range.
Other unweighted wavebands:
Blue(),
Far_red(),
Green(),
IR(),
Orange(),
Red(),
UV(),
UVA(),
UVB(),
UVC(),
VIS(),
Yellow()
Purple() Purple("ISO") e_irrad(sun.spct, Purple()) # W m-2 q_irrad(sun.spct, Purple()) # mol m-2 q_irrad(sun.spct, Purple(), scale.factor = 1e6) # umol m-2Purple() Purple("ISO") e_irrad(sun.spct, Purple()) # W m-2 q_irrad(sun.spct, Purple()) # mol m-2 q_irrad(sun.spct, Purple(), scale.factor = 1e6) # umol m-2
Wavelength-range definitions for red light according to ISO or as commonly used in plant or remote sensing applications.
Red(std = "ISO")Red(std = "ISO")
std |
a character string, one of "ISO", "Smith10", "Smith20", "Inada", "Warrington", "Sellaro", "RS", "LandsatOLI", "LandsatTM", "LandsatETM", "LandsatMSS", and "LandsatRBV". |
The different arguments passed to formal parameter std
determine the range of wavelengths set as boundaries of the returned
waveband object; "ISO" is an standardized
definition based on human colour vision; "Smith10",
"Smith20", "Inada", "Warrington", "Sellaro" and
"Broad" are non-standard but used in plant sciences; "RS" is
non-standard but frequently used in remote sensing; the remaining
definitions are for the published wavelength sensitivity range of imagers
(cameras) in the Landsat satellite missions.
In plant photobiology the definitions proposed by Prof. Harry Smith are the most widely used, specially to compute a red to far-red photon ratio relevant to phytochrome photoreceptors. However, other authors have used different definitions in their publications. "Smith10" (655-665 nm), "Smith20" (650-670 nm), "Inada" (600-700 nm), "Warrington" (625-675 nm), and "Sellaro" (620-680 nm).
a waveband object defining a wavelength range.
The bands are defined as square windows, these can be applied to spectral data to obtain the "true" values, but they do not simulate the sensitivity of broad-band sensors or the spectral transmittance of ionic filters. Some band-pass interference filters may have very sharp cut-in and cut-off, and their effect can be approximated by a square window, but filters based on light absorption will show gradual tails and bell-shaped wavelength-windows. The Landsat instruments have very steep cut-in and cut-off slopes and are well approximated.
Aphalo, P. J., Albert, A., Björn, L. O., McLeod, A. R., Robson, T. M., Rosenqvist, E. (Eds.). (2012). Beyond the Visible: A handbook of best practice in plant UV photobiology (1st ed., p. xxx + 174). Helsinki: University of Helsinki, Department of Biosciences, Division of Plant Biology. ISBN 978-952-10-8363-1 (PDF), 978-952-10-8362-4 (paperback). Open access PDF download available at doi:10.31885/9789521083631.
ISO (2007) Space environment (natural and artificial) - Process for determining solar irradiances. ISO Standard 21348. ISO, Geneva.
Murakami, K., Aiga I. (1994) Red/Far-red photon flux ratio used as an index number for morphological control of plant growth under artificial lighting conditions. Proc. Int. Symp. Artificial Lighting, Acta Horticulturae, 418, ISHS 1997.
Sellaro, R., Crepy, M., Trupkin, S. A., Karayekov, E., Buchovsky, A. S., Rossi, C., & Casal, J. J. (2010). Cryptochrome as a sensor of the blue/green ratio of natural radiation in Arabidopsis. Plant physiology, 154(1), 401-409. doi:10.1104/pp.110.160820.
Smith, H. (1982) Light quality, photoperception and plant strategy. Annual Review of Plant Physiology, 33:481-518. doi:10.1146/annurev.pp.33.060182.002405
Other unweighted wavebands:
Blue(),
Far_red(),
Green(),
IR(),
Orange(),
Purple(),
UV(),
UVA(),
UVB(),
UVC(),
VIS(),
Yellow()
Red() Red("ISO") Red("Smith") Red("Sellaro") e_irrad(sun.spct, Red()) # W m-2 q_irrad(sun.spct, Red()) # mol m-2 q_irrad(sun.spct, Red(), scale.factor = 1e6) # umol m-2Red() Red("ISO") Red("Smith") Red("Sellaro") e_irrad(sun.spct, Red()) # W m-2 q_irrad(sun.spct, Red()) # mol m-2 q_irrad(sun.spct, Red(), scale.factor = 1e6) # umol m-2
Constant value for human vision under very weak illumination 1 W is equal to 1699 Lumen at 507 nm
scotopic_sensitivityscotopic_sensitivity
A single numeric value
A single numeric value
A dataset containing the wavelengths at a 0.1 nm interval. Tabulated values for Setlow's naked DNA damage action spectrum as used in the TUV model.
A response.spct object with 1082 rows and 2 variables
The variables are as follows:
w.length (nm)
s.e.response
https://web.archive.org/web/20220130091146/http://uv.biospherical.com/Version2/description-Version2-Database3.html downloaded 2015-02-07
Wavelength-range definition for ultraviolet (UV) radiation according to ISO and CIE standards.
UV(std = "ISO")UV(std = "ISO")
std |
"ISO" or "CIE" |
UV: 100–400 nm. The ranges agree between CIE and ISO standards,
thus, the argument passed to parameter std only affects the labels
in the returned waveband object.
A waveband object defining a wavelength range.
Aphalo, P. J., Albert, A., Björn, L. O., McLeod, A. R., Robson, T. M., Rosenqvist, E. (Eds.). (2012). Beyond the Visible: A handbook of best practice in plant UV photobiology (1st ed., p. xxx + 174). Helsinki: University of Helsinki, Department of Biosciences, Division of Plant Biology. ISBN 978-952-10-8363-1 (PDF), 978-952-10-8362-4 (paperback). Open access PDF download available at doi:10.31885/9789521083631.
Other unweighted wavebands:
Blue(),
Far_red(),
Green(),
IR(),
Orange(),
Purple(),
Red(),
UVA(),
UVB(),
UVC(),
VIS(),
Yellow()
UV() UV("ISO")UV() UV("ISO")
Defined according to "ISO" by default, but other definitions also supported.
UV_bands(std = "ISO")UV_bands(std = "ISO")
std |
a character string "ISO", "CIE", "medical", "plants" or "none". |
a list of wavebands
Other lists of unweighted wavebands:
IR_bands(),
Landsat_bands(),
Plant_bands(),
VIS_bands()
UV_bands() UV_bands("ISO") UV_bands("CIE") UV_bands("medical") UV_bands("plants") UV_bands("none")UV_bands() UV_bands("ISO") UV_bands("CIE") UV_bands("medical") UV_bands("plants") UV_bands("none")
Waveband constructor for ICNIRP UV health hazard 2004 BSWF.
UV_health_hazard(std = "ICNIRP", norm = 270, w.low = 210, w.high = 400) ICNIRP(norm = 270, w.low = 210, w.high = 400)UV_health_hazard(std = "ICNIRP", norm = 270, w.low = 210, w.high = 400) ICNIRP(norm = 270, w.low = 210, w.high = 400)
std |
a character string "ICNIRP". |
norm |
normalization wavelength (nm) |
w.low |
short-end boundary wavelength (nm) |
w.high |
long-end boundary wavelength (nm) |
This BSWF is used for the determination of exposure limits (EL) for workers, and includes a safety margin as it is based on eye and the non-pathologic response of the most sensitive human skin types when not tanned. Values are interpolated according to equations 2a, 2b and 2c in ICNIRP (2004), which cover the range 210 nm to 400 nm.
The program code is provided as is, with no guarantee of suitability for any purpose, and should under no circumstances be used to assess actual health hazards.
a waveband object defining wavelength range, weighting function and normalization wavelength.
The weights at 180, 190, 200 and 205 nm are presented only in tabular in
ICNIRP (2004) and all values at wavelengths < 210 nm taken as NA.
Standard DIN 5031-10:2018-03 defines BSWF uvh as a table of interpolated values derived from ICNIRP UV health hazard. So, the values computed using this R package do not necessarily exactly match those according to DIN 5031-10:2018-03. The range of wavelengths used here, 210 to 400 nm, does not agree, with those in the standard: 180 to 400 nm.
INTERNATIONAL COMMISSION ON NON-IONIZING RADIATION PROTECTION (2004) ICNIRP GUIDELINES ON LIMITS OF EXPOSURE TO ULTRAVIOLET RADIATION OF WAVELENGTHS BETWEEN 180 nm AND 400 nm (INCOHERENT OPTICAL RADIATION). HEALTH PHYSICS 87(2):171-186. https://www.icnirp.org/cms/upload/publications/ICNIRPUV2004.pdf
Other BSWF weighted wavebands:
CH4(),
DNA_GM(),
DNA_N(),
DNA_P(),
FLAV(),
GEN_G(),
GEN_M(),
GEN_T(),
PAR(),
PG(),
erythema()
ICNIRP() UV_health_hazard() UV_health_hazard("ICNIRP")ICNIRP() UV_health_hazard() UV_health_hazard("ICNIRP")
Wavelength-range definitions for ultraviolet-A (UV-A) radiation, by default according to ISO or as commonly used in different application areas.
UVA(std = "ISO") UVA1(std = "CIE") UVA2(std = "CIE") UVAsw(std = "plants") UVAlw(std = "plants") UVAsw(std = "plants")UVA(std = "ISO") UVA1(std = "CIE") UVA2(std = "CIE") UVAsw(std = "plants") UVAlw(std = "plants") UVAsw(std = "plants")
std |
a character string |
Implemented definitions. UV-A according to CIE and ISO standards: 315-400 nm. UV-A according to common non-standard practice: 320-400 nm. UV-A2 according to CIE report 134/1: 315-340 nm. UV-A1 according to CIE report 134/1: 340-400 nm. UV-Asw according to non-standard use possibly suitable for plants: 315-350 nm. UV-Alw according to non-standard use possibly suitable for plants: 350-400 nm.
A waveband object defining a wavelength range.
The non-standard definitions of UV-A and UV-A2 using 320 nm as limit should not be used in any new publications or work as they deviate from the internationally recommended practice. Their continued use leads to confusion. Their inclusion in this package is to allow calculations needed to compare new results and methods against old publications. UV-A1 and UV-A2 definitions are in wide use in medicine, but not yet standardized. Recent research on the plant photoreceptor UVR8 suggests that UV-A1 and UV-A2 bands are also relevant to plants (Rai et al., 2021). UV-Alw and UV-Asw have been used for plants, but UV-A1 and UV-A2 seem now preferable.
Aphalo, P. J., Albert, A., Björn, L. O., McLeod, A. R., Robson, T. M., Rosenqvist, E. (Eds.). (2012). Beyond the Visible: A handbook of best practice in plant UV photobiology (1st ed., p. xxx + 174). Helsinki: University of Helsinki, Department of Biosciences, Division of Plant Biology. ISBN 978-952-10-8363-1 (PDF), 978-952-10-8362-4 (paperback). Open access PDF download available at doi:10.31885/9789521083631.
CIE (1999) 134/1 TC 6-26 report: Standardization of the Terms UV-A1, UV-A2 and UV-B. https://cie.co.at/publications/cie-collection-photobiology-photochemistry-1999
Rai N, Morales LO, Aphalo PJ (2021) Perception of solar UV radiation by plants: photoreceptors and mechanisms. Plant Physiology 186: 1382–1396. doi:10.1093/plphys/kiab162
Other unweighted wavebands:
Blue(),
Far_red(),
Green(),
IR(),
Orange(),
Purple(),
Red(),
UV(),
UVB(),
UVC(),
VIS(),
Yellow()
UVA() UVA("none") UVA("ISO") UVA("CIE") UVA1() UVA1("CIE") UVA2() UVA2("CIE") e_irrad(sun.spct, UVA()) # W m-2 e_irrad(sun.spct, UVA1()) # W m-2 e_irrad(sun.spct, UVA2()) # W m-2UVA() UVA("none") UVA("ISO") UVA("CIE") UVA1() UVA1("CIE") UVA2() UVA2("CIE") e_irrad(sun.spct, UVA()) # W m-2 e_irrad(sun.spct, UVA1()) # W m-2 e_irrad(sun.spct, UVA2()) # W m-2
Wavelength-range definitions for ultraviolet-B, UV-B radiation, by default according to ISO or as commonly used in different application areas.
UVB(std = "ISO")UVB(std = "ISO")
std |
a character string "CIE", "ISO", "medical" or "none" |
Implemented definitions. UV-B according to CIE and ISO standrads: 280–315 nm. UV-B according to common non-standard practice: 280–320 nm. UV-B according to medical or dermatological non-standard practice: 280–320 nm.
a waveband object defining a wavelength range.
The non-standard definition of UV-B using 320 nm as limit should not be used in any new publications or work as it deviates from the internationally accepted standards and its use leads to confusion. Its inclusion in this package is to allow calculations needed to compare new results and methods against old publications.
Aphalo, P. J., Albert, A., Björn, L. O., McLeod, A. R., Robson, T. M., Rosenqvist, E. (Eds.). (2012). Beyond the Visible: A handbook of best practice in plant UV photobiology (1st ed., p. xxx + 174). Helsinki: University of Helsinki, Department of Biosciences, Division of Plant Biology. ISBN 978-952-10-8363-1 (PDF), 978-952-10-8362-4 (paperback). Open access PDF download available at doi:10.31885/9789521083631.
Other unweighted wavebands:
Blue(),
Far_red(),
Green(),
IR(),
Orange(),
Purple(),
Red(),
UV(),
UVA(),
UVC(),
VIS(),
Yellow()
UVB() UVB("ISO") UVB("CIE") UVB("none") UVB("medical") e_irrad(sun.spct, UVB()) # W m-2 q_irrad(sun.spct, UVB()) # mol m-2 q_irrad(sun.spct, UVB(), scale.factor = 1e6) # umol m-2UVB() UVB("ISO") UVB("CIE") UVB("none") UVB("medical") e_irrad(sun.spct, UVB()) # W m-2 q_irrad(sun.spct, UVB()) # mol m-2 q_irrad(sun.spct, UVB(), scale.factor = 1e6) # umol m-2
Wavelength-range definitions for ultraviolet-C (UV-C) radiation, by default according to ISO or as commonly used in different application areas.
UVC(std = "ISO")UVC(std = "ISO")
std |
a character string "CIE", "ISO", "none", or "medical". |
Implemented definitions. UV-C according to CIE and ISO standards: 100–280 nm. UV-c according to common non-standard practice: 200–280 nm. UV-C according to medical or dermatological non-standard practice, e.g. Diffey (1991): 200–290 nm.
a waveband object wavelength defining a wavelength range.
Aphalo, P. J., Albert, A., Björn, L. O., McLeod, A. R., Robson, T. M., Rosenqvist, E. (Eds.). (2012). Beyond the Visible: A handbook of best practice in plant UV photobiology (1st ed., p. xxx + 174). Helsinki: University of Helsinki, Department of Biosciences, Division of Plant Biology. ISBN 978-952-10-8363-1 (PDF), 978-952-10-8362-4 (paperback). Open access PDF download available at doi:10.31885/9789521083631.
Other unweighted wavebands:
Blue(),
Far_red(),
Green(),
IR(),
Orange(),
Purple(),
Red(),
UV(),
UVA(),
UVB(),
VIS(),
Yellow()
UVC() UVC("CIE") UVC("ISO") UVC("none") UVC("medical")UVC() UVC("CIE") UVC("ISO") UVC("none") UVC("medical")
UVI (UV Index) is a unitless quantity based on erythema biological spectral weighting function (BSWF), that gives an easy to interpret UV measure, mainly meant for informing general public about sunburn risk.
UVI(spct, std = "NOAA", integer_UVI = FALSE)UVI(spct, std = "NOAA", integer_UVI = FALSE)
spct |
a |
std |
character One of "WWO", "NOAA". |
integer_UVI |
logical Return a positive integer value according to WWO recommended practice or a numeric value. |
Two different definitions of UV Index are implemented in this package. Setting std="NOAA" follows the definition in Kiedron et al. (2007) but using CIE98 as SWF. NOAA definition discards wavelengths shorter than 286.5 nm as when calculated based on spectral data from Brewer instruments. "WMO" uses the internationally accepted lower limit at 250 nm (see WHO, 2002). "NOAA" is the default as this is safer with noisy data for solar radiation measured at ground level, and in this case the value of UVI should be correct, and almost identical except for errors caused by noise at shorter wavelengths. However, when calculating UVI from radiation spectra from UV lamps, "WMO" should be used, as most UV lamps do emit some radiation between 250 nm and 286.5 nm.
depending on the argument passed to integer_UVI, a numeric
(FALSE) or integer (TRUE) value for the unitless UVI.
The default is to return a numeric value not rounded into a value in the integer-number based recommended UVI scale. This is done to avoid loss of precision in cases when additional operations, such as averaging, are applied to the UVI values.
World Health Organization, World Meteorological Organization, United Nations Environment Programme & International Commission on Non-Ionizing Radiation Protection. (2002) Global Solar UV Index: A Practical Guide. World Health Organization, Geneva. ISBN 9241590076. https://apps.who.int/iris/handle/10665/42459
P. Kiedron, S. Stierle and K. Lantz (2007) Instantaneous UV Index and Daily UV Dose Calculations. NOAA-EPA Brewer Network. https://www.esrl.noaa.gov/gmd/grad/neubrew/docs/UVindex.pdf
UVI(sun.spct) UVI(sun.spct, "WMO") UVI(sun.spct, integer_UVI = TRUE)UVI(sun.spct) UVI(sun.spct, "WMO") UVI(sun.spct, integer_UVI = TRUE)
Visible (to humnas) radiation (380...760 nm) according to ISO standard
definition, no weighting applied. For std = "RS" the returned range is
the same as for PAR(). The panchromatic bands of Landsat missions are
also supported.
VIS(std = "ISO")VIS(std = "ISO")
std |
a character string "ISO" or "RS" (remote sensing). |
A waveband object wavelength defining a wavelength range.
Other unweighted wavebands:
Blue(),
Far_red(),
Green(),
IR(),
Orange(),
Purple(),
Red(),
UV(),
UVA(),
UVB(),
UVC(),
Yellow()
VIS() VIS("ISO") VIS("LandsatOLI") VIS("Landsat7") VIS("Pan.RBV.Landsat3")VIS() VIS("ISO") VIS("LandsatOLI") VIS("Landsat7") VIS("Pan.RBV.Landsat3")
Defined according to "ISO".
VIS_bands(std = "ISO")VIS_bands(std = "ISO")
std |
a character string "ISO". |
a list of wavebands
Other lists of unweighted wavebands:
IR_bands(),
Landsat_bands(),
Plant_bands(),
UV_bands()
VIS_bands() VIS_bands("ISO")VIS_bands() VIS_bands("ISO")
Wavelength-range definition for yellow radiation according to ISO.
Yellow(std = "ISO")Yellow(std = "ISO")
std |
a character string "ISO" |
Yellow radiation (570...591 nm) as defined in ISO standards based on human colour vision.
a waveband object wavelength defining a wavelength range.
Other unweighted wavebands:
Blue(),
Far_red(),
Green(),
IR(),
Orange(),
Purple(),
Red(),
UV(),
UVA(),
UVB(),
UVC(),
VIS()
Yellow() Yellow("ISO") e_irrad(sun.spct, Yellow()) # W m-2 q_irrad(sun.spct, Yellow()) # mol m-2 q_irrad(sun.spct, Yellow(), scale.factor = 1e6) # umol m-2Yellow() Yellow("ISO") e_irrad(sun.spct, Yellow()) # W m-2 q_irrad(sun.spct, Yellow()) # mol m-2 q_irrad(sun.spct, Yellow(), scale.factor = 1e6) # umol m-2