Help for package photobiologyWavebands

Type:

Package

Title:

Waveband Definitions for UV, VIS, and IR Radiation

Version:

0.5.2

Date:

2023-10-24

Maintainer:

Pedro J. Aphalo <pedro.aphalo@helsinki.fi>

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>.

License:

GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]

VignetteBuilder:

knitr

Depends:

R (≥ 4.0.0), photobiology (≥ 0.11.0)

Suggests:

knitr (≥ 1.40), rmarkdown (≥ 2.20)

LazyLoad:

yes

LazyData:

yes

ByteCompile:

true

Encoding:

UTF-8

URL:

https://docs.r4photobiology.info/photobiologyWavebands/, https://github.com/aphalo/photobiologywavebands

BugReports:

https://github.com/aphalo/photobiologywavebands/issues

RoxygenNote:

7.2.3

NeedsCompilation:

Packaged:

2023-10-24 14:05:36 UTC; aphalo

Author:

Pedro J. Aphalo

[aut, cre], Titta K. Kotilainen

[ctb]

Repository:

CRAN

Date/Publication:

2023-10-24 14:50:03 UTC

photobiologyWavebands: Waveband Definitions for UV, VIS, and IR Radiation

Description

Details

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.

Author(s)

Maintainer: Pedro J. Aphalo pedro.aphalo@helsinki.fi (ORCID)

Other contributors:

Titta K. Kotilainen titta.kotilainen@helsinki.fi (ORCID) [contributor]

References

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

Examples


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 definition

Constructor of blue waveband

Description

Wavelength-range definitions for blue light according to ISO or as commonly used in plant or remote sensing applications.

Usage

Blue(std = "ISO")

Arguments

std

a character string "ISO", "Sellaro", "Broad", "RS" (remote sensing), or Landsat imagers, "LandsatTM", "LandsatETM", or "LandsatOLI".

Details

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.

Value

A waveband object defining a wavelength range.

Note

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.

References

ISO (2007) Space environment (natural and artificial) - Process for determining solar irradiances. ISO Standard 21348. ISO, Geneva.

Examples

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-2

Constructor of CH4 production from pectin weighted waveband

Description

Methane production from pectin BSWF

Usage

CH4(norm = 300, w.low = 275, w.high = 400)

Arguments

norm

normalization wavelength (nm)

w.low

short-end boundary wavelength (nm)

w.high

long-end boundary wavelength (nm)

Value

a waveband object wavelength defining wavelength range, weighting function and normalization wavelength.

References

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 .

Examples

CH4()
CH4(norm = 400)

Gives values for the CH4 production from pectin BSWF as a function of wavelength

Description

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.

Usage

CH4_e_fun(w.length)

Arguments

w.length

numeric array of wavelengths (nm)

Value

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.

References

Examples

CH4_e_fun(293:400)

Gives values for the CH4 production from pectin BSWF as a function of wavelength

Description

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.

Usage

CH4_q_fun(w.length)

Arguments

w.length

numeric array of wavelengths (nm)

Value

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.

Examples

CH4_q_fun(293:400)

CIE1924 luminous efficiency function (photopic human vision)

Description

A dataset containing the wavelengths at a 1 nm interval. Tabulated values for quantum luminous efficiency according to CIE1924.

Format

A response.spct object with 471 rows and 2 variables

Details

The variables are as follows:

w.length (nm)
s.q.response

Note

This luminous efficiency function understimates the renponse to short wavelengths.

References

http://www.cvrl.org/ downloaded on 2015-01-24

Luminous efficiency function (scotopic human vision)

Description

A dataset containing the wavelengths at a 1 nm interval. Tabulated values for quantum luminous efficiency at low light levels according to CIE1951.

Format

A response.spct object with 401 rows and 2 variables

Details

The variables are as follows:

w.length (nm)
s.q.response

References

http://www.cvrl.org/ downloaded on 2015-01-24

CIE2008 luminous efficiency function (2-deg) (photopic human vision)

Description

A dataset containing the wavelengths at a 1 nm interval. Tabulated values for quantum luminous efficiency according to CIE2008 for 2 degrees.

Format

A response.spct object with 441 rows and 2 variables

Details

The variables are as follows:

w.length (nm)
s.q.response

References

http://www.cvrl.org/ downloaded on 2015-01-24

Gives values for the erythemal BSWF as a function of wavelength

Description

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.

Usage

CIE_e_fun(w.length)

Arguments

w.length

numeric array of wavelengths (nm)

Value

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.

Examples

CIE_e_fun(293:400)

Gives values for the erythemal BSWF as a function of wavelength

Description

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.

Usage

CIE_q_fun(w.length)

Arguments

w.length

numeric array of wavelengths (nm)

Value

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.

Examples

CIE_q_fun(293:400)

Constructor of DNA damage (SETLOW) weighted waveband

Description

Naked DNA damage BSWF, Green and Miller's formulation.

Usage

DNA.GM(norm = 300, w.low = 275, w.high = 400)

Constructor of DNA damage (SETLOW) weighted waveband

Description

Naked DNA damage BSWF

Usage

DNA.N(norm = 300, w.low = 275, w.high = 400)

Constructor of DNA damage (Quaite) weighted waveband

Description

Plant DNA damage BSWF as formulated by Musil.

Usage

DNA.P(norm = 300, w.low = 275, w.high = 400)

Constructor of DNA damage (SETLOW) weighted waveband

Description

Naked DNA damage BSWF, Green and Miller's formulation.

Usage

DNA_GM(norm = 300, w.low = 275, w.high = 400)

Arguments

norm

normalization wavelength (nm)

w.low

short-end boundary wavelength (nm)

w.high

long-end boundary wavelength (nm)

Value

a waveband object wavelength defining wavelength range, weighting function and normalization wavelength.

Examples

DNA_GM()
DNA_GM(300)

Gives values for naked DNA BSWF (SETLOW) as a function of wavelength

Description

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.

Usage

DNA_GM_q_fun(w.length)

Arguments

w.length

numeric array of w.length (nm)

Value

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.

Examples

DNA_GM_q_fun(293:400)

Constructor of DNA damage (SETLOW) weighted waveband

Description

Naked DNA damage BSWF

Usage

DNA_N(norm = 300, w.low = 275, w.high = 400)

Arguments

norm

normalization wavelength (nm)

w.low

short-end boundary wavelength (nm)

w.high

long-end boundary wavelength (nm)

Value

a waveband object wavelength defining wavelength range, weighting function and normalization wavelength.

Examples

DNA_N()
DNA_N(300)

Gives values for naked DNA BSWF (SETLOW) as a function of wavelength

Description

This function gives a set of numeric multipliers that can be used as a weight to calculate effective doses and irradiances.

Usage

DNA_N_q_fun(w.length)

Arguments

w.length

numeric array of w.length (nm)

Value

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.

Note

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.

Examples

DNA_N_q_fun(293:400)

Constructor of DNA damage (Quaite) weighted waveband

Description

Plant DNA damage BSWF as formulated by Musil.

Usage

DNA_P(norm = 300, w.low = 275, w.high = 400)

Arguments

norm

normalization wavelength (nm)

w.low

short-end boundary wavelength (nm)

w.high

long-end boundary wavelength (nm)

Value

a waveband object wavelength defining wavelength range, weighting function and normalization wavelength.

Examples

DNA_P()
DNA_P(300)

Gives values for plant DNA BSWF (Quaite) as a function of wavelength

Description

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.

Usage

DNA_P_q_fun(w.length)

Arguments

w.length

numeric array of w.length (nm)

Value

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.

Examples

DNA_P_q_fun(293:400)

Constructor of FLAV BSWF flavonoids

Description

Mesembryanthin accumulation BSWF, data and formulation from Ibdah et al.

Usage

FLAV(norm = 300, w.low = 275, w.high = 346)

Arguments

norm

normalization wavelength (nm)

w.low

short-end boundary wavelength (nm)

w.high

long-end boundary wavelength (nm)

Value

a waveband object wavelength defining wavelength range, weighting function and normalization wavelength.

References

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

Examples

FLAV()
FLAV(300)

Gives values for FLAV BSWF (flavonoid) as a function of wavelength

Description

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.

Usage

FLAV_q_fun(w.length)

Arguments

w.length

numeric array of w.length (nm)

Value

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.

Examples

FLAV_q_fun(293:400)

Constructor of far-red waveband

Description

Wavelength-range definitions for far-red light according as commonly used in plant or remote sensing applications.

Usage

Far_red(std = "ISO")

Arguments

std

a character string, defaults to "ISO", as for other colour definitions, which in this case returns NA.

Details

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).

Value

A waveband object defining a wavelength range.

Note

References

ISO (2007) Space environment (natural and artificial) - Process for determining solar irradiances. ISO Standard 21348. ISO, Geneva.

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

Examples

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-2

Constructor of GPAS (Green) weighted waveband

Description

Generalized Plant Action BSWF of Caldwell as formulated by Green et al.

Usage

GEN.G(norm = 300, w.low = 275, w.high = 313.3)

Constructor of GPAS (Micheletti) weighted waveband

Description

Generalized Plant Action BSWF of Caldwell as formulated by Micheletti et al.

Usage

GEN.M(norm = 300, w.low = 275, w.high = 313.3)

Constructor of GPAS (Timijan) weighted waveband

Description

Generalized Plant Action BSWF of Caldwell as formulated by Timijan et al.

Usage

GEN.T(norm = 300, w.low = 275, w.high = 345)

Constructor of GPAS (Green's formulation) weighted waveband

Description

Generalized Plant Action BSWF of Caldwell as formulated by Green et al.

Usage

GEN_G(norm = 300, w.low = 275, w.high = 313.3)

Arguments

norm

normalization wavelength (nm)

w.low

short-end boundary wavelength (nm)

w.high

long-end boundary wavelength (nm)

Value

a waveband object wavelength defining wavelength range, weighting function and normalization wavelength.

Note

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].

References

[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

Examples

GEN_G()
GEN_G(300)

Gives values for GPAS BSWF (Green's formulation) as a function of wavelength

Description

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.

Usage

GEN_G_q_fun(w.length)

Arguments

w.length

numeric array of w.length (nm)

Value

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.

Note

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].

References

[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

Examples

GEN_G_q_fun(293:400)

Constructor of GPAS (Micheletti's formulation) weighted waveband

Description

Generalized Plant Action BSWF of Caldwell [1] as formulated by Micheletti et al. [2]

Usage

GEN_M(norm = 300, w.low = 275, w.high = 313.3)

Arguments

norm

normalization wavelength (nm)

w.low

short-end boundary wavelength (nm)

w.high

long-end boundary wavelength (nm)

Value

a waveband object wavelength defining wavelength range, weighting function and normalization wavelength.

Note

References

[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

Examples

GEN_M()
GEN_M(300)

Gives values for GPAS BSWF (Micheletti's formulation) as a function of wavelength

Description

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.

Usage

GEN_M_q_fun(w.length)

Arguments

w.length

numeric array of w.length (nm)

Value

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.

Note

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].

References

[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

Examples

GEN_M_q_fun(293:400)

Constructor of GPAS (Thimijan's formulation) weighted waveband

Description

Generalized Plant Action BSWF of Caldwell [1] as formulated by Timijan et al. [2]

Usage

GEN_T(norm = 300, w.low = 275, w.high = 345)

Arguments

norm

normalization wavelength (nm)

w.low

short-end boundary wavelength (nm)

w.high

long-end boundary wavelength (nm)

Value

a waveband object wavelength defining wavelength range, weighting function and normalization wavelength.

References

[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.

Examples

GEN_T()
GEN_T(300)

Gives values for GPAS BSWF (Timijan's formulation) as a function of wavelength

Description

This function gives a set of numeric multipliers that can be used as a weight to calculate effective doses and irradiances.

Usage

GEN_T_q_fun(w.length)

Arguments

w.length

numeric array of w.length (nm)

Value

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.

Note

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.

Examples

GEN_T_q_fun(293:400)

Constructor of green waveband

Description

Wavelength-range definitions for green light according to ISO or as commonly used in plant or remote sensing applications.

Usage

Green(std = "ISO")

Arguments

std

a character string "ISO", "Sellaro", "Broad", "RS", "LandsatOLI", "LandsatRBV", "LandsatTM", "LandsatETM", or "LandsatMSS".

Details

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.

Value

A waveband object defining a wavelength range.

Note

When released, this package will replace the package UVcalc.

References

ISO (2007) Space environment (natural and artificial) - Process for determining solar irradiances. ISO Standard 21348. ISO, Geneva.

Examples

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-2

ICNIRP UV health hazard BSWF as a function of wavelength

Description

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.

Usage

ICNIRP_e_fun(w.length)

Arguments

w.length

numeric array of wavelengths (nm)

Value

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.

Examples

ICNIRP_e_fun(210:400)

Constructors of infra-red wavebands

Description

Wavelength-range definitions for infrared radiation according to ISO, CIE or as commonly defined in remote sensing applications.

Usage

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")

Arguments

std

character string, "ISO", "CIE", "RS" or Landsat imagers "LandsatRBV", "LandsatMSS", "LandsatTIRS", "LandsatOLI", "LandsatTM", "LandsatETM", depending on the constructor.

Details

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.

Value

A waveband object defining a wavelength range.

Examples

SWIR1()
SWIR1("RS")
IR()
NIR()
MIR()
IRA()
IRB()

Constructor of lists of infrared wavebands

Description

Defined according to "ISO" or "CIE".

Usage

IR_bands(std = "ISO")

Arguments

std

a character string "ISO" or "CIE".

Value

a list of wavebands

Examples

IR_bands()
IR_bands("ISO")
IR_bands("CIE")

Constructor of lists of wavebands matching Landsat imagers

Description

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.

Usage

Landsat_bands(std = "L8")

RBV_bands(std = "LandsatRBV")

MSS_bands(std = "LandsatMSS")

OLI_bands(std = "LandsatOLI")

TIRS_bands(std = "LandsatTIRS")

ETM_bands(std = "LandsatETM")

Arguments

std

a character string "L1"..."L9", for missions, "LandsarRBV", "LandsatMSS", etc. for imagers.

Details

See https://landsat.usgs.gov/spectral-characteristics-viewer for detailed sensitivity spectra for the different bands of the imaginers.

Value

a list of wavebands

Examples

Landsat_bands("L1")
Landsat_bands("L8")
OLI_bands()
TIRS_bands()

Normalized Vegetation Index

Description

Compute the NDVI from spectral reflectance according to waveband definitions from standards or corresponding to satellite imagers.

Usage

NDVI(spct, imager = "LandsatOLI", wb.trim = FALSE)

Arguments

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.

Details

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.

Value

A numeric vector. When the wavelength range of spct does not fully overlap with both wavebands NA is silently returned.

Note

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.

Constructor of orange waveband

Description

Wavelength-range definition for orange radiation according to ISO.

Usage

Orange(std = "ISO")

Arguments

std

a character string "ISO"

Details

Orange radiation (591...610 nm) as defined in ISO standards based on human colour vision.

Value

A waveband object defining a wavelength range.

References

ISO (2007) Space environment (natural and artificial) - Process for determining solar irradiances. ISO Standard 21348. ISO, Geneva.

Examples

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-2

Constructors of PAR and PhR wavebands

Description

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.

Usage

PAR(std = "PAR", norm = 550)

PhR()

Arguments

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)

Details

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).

Value

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.

Warnings

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.

Note

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'.

References

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

Examples

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 nm

Constructor of PG weighted waveband

Description

Plant growth BSWF of Flint and Caldwell

Usage

PG(norm = 300, w.low = 275, w.high = 390)

Arguments

norm

normalization wavelength (nm)

w.low

short-end boundary wavelength (nm)

w.high

long-end boundary wavelength (nm)

Details

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.

Value

a waveband object wavelength defining wavelength range, weighting function and normalization wavelength.

Note

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.

References

[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

[3] https://www2.acom.ucar.edu/modeling/tropospheric-ultraviolet-and-visible-tuv-radiation-model

Examples

PG()
PG(300)

Gives values for the Plant Growth BSWF as a function of wavelength

Description

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.

Usage

PG_q_fun(w.length)

Arguments

w.length

numeric array of wavelengths (nm)

Value

a numeric array of the same length as w.length with values for the BSWF normalized as in the original source (300 nm)

Note

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).

Examples

PG_q_fun(293:400)

Constructor of lists of wavebands used in plant biology

Description

Defined according to different authors.

Usage

Plant_bands(std = "sensory20")

Arguments

std

a character string "sensory", "sensory10", "sensory20", "Sellaro", "ISO", "CIE", "none" or "", where "ISO", "CIE" and "none" affect only the UV bands.

Value

a list of wavebands

Examples

Plant_bands()
Plant_bands("sensory")
Plant_bands("sensory10")
Plant_bands("sensory20")
Plant_bands("ISO")
Plant_bands("CIE")

Constructor of purple waveband

Description

Wavelength-range definition for purple radiation according to ISO or imagers in the Landsat satellites.

Usage

Purple(std = "ISO")

Arguments

std

a character string "ISO", or Landsat imager "LandsatOLI".

Details

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.

Value

A waveband object defining a wavelength range.

Examples

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-2

Constructor of red waveband

Description

Wavelength-range definitions for red light according to ISO or as commonly used in plant or remote sensing applications.

Usage

Red(std = "ISO")

Arguments

std

a character string, one of "ISO", "Smith10", "Smith20", "Inada", "Warrington", "Sellaro", "RS", "LandsatOLI", "LandsatTM", "LandsatETM", "LandsatMSS", and "LandsatRBV".

Details

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).

Value

a waveband object defining a wavelength range.

Note

References

ISO (2007) Space environment (natural and artificial) - Process for determining solar irradiances. ISO Standard 21348. ISO, Geneva.

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

Examples

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-2

Setlow's action spectrum for DNA damage

Description

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.

Format

A response.spct object with 1082 rows and 2 variables

Details

The variables are as follows:

w.length (nm)
s.e.response

References

https://web.archive.org/web/20220130091146/http://uv.biospherical.com/Version2/description-Version2-Database3.html downloaded 2015-02-07

Constructor of ultraviolet waveband

Description

Wavelength-range definition for ultraviolet (UV) radiation according to ISO and CIE standards.

Usage

UV(std = "ISO")

Arguments

std

"ISO" or "CIE"

Details

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.

Value

A waveband object defining a wavelength range.

References

Examples

UV()
UV("ISO")

Constructor of ultraviolet-A waveband

Description

Wavelength-range definitions for ultraviolet-A (UV-A) radiation, by default according to ISO or as commonly used in different application areas.

Usage

UVA(std = "ISO")

UVA1(std = "CIE")

UVA2(std = "CIE")

UVAsw(std = "plants")

UVAlw(std = "plants")

UVAsw(std = "plants")

Arguments

std

a character string "CIE", "ISO", "none", "medical" or "plants".

Details

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.

Value

A waveband object defining a wavelength range.

Note

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.

References

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

Examples

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-2

Constructor of ultraviolet-B waveband

Description

Wavelength-range definitions for ultraviolet-B, UV-B radiation, by default according to ISO or as commonly used in different application areas.

Usage

UVB(std = "ISO")

Arguments

std

a character string "CIE", "ISO", "medical" or "none"

Details

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.

Value

a waveband object defining a wavelength range.

Note

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.

References

Examples

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-2

Constructor of ultraviolet-C waveband

Description

Wavelength-range definitions for ultraviolet-C (UV-C) radiation, by default according to ISO or as commonly used in different application areas.

Usage

UVC(std = "ISO")

Arguments

std

a character string "CIE", "ISO", "none", or "medical".

Details

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.

Value

a waveband object wavelength defining a wavelength range.

References

Examples

UVC()
UVC("CIE")
UVC("ISO")
UVC("none")
UVC("medical")

Calculate UV Index (UVI) from spectral irradiance

Description

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.

Usage

UVI(spct, std = "NOAA", integer_UVI = FALSE)

Arguments

spct

a source.spct object

std

character One of "WWO", "NOAA".

integer_UVI

logical Return a positive integer value according to WWO recommended practice or a numeric value.

Details

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.

Value

depending on the argument passed to integer_UVI, a numeric (FALSE) or integer (TRUE) value for the unitless UVI.

Note

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.

References

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

Examples

UVI(sun.spct)
UVI(sun.spct, "WMO")
UVI(sun.spct, integer_UVI = TRUE)

Constructor of CIE weighted waveband

Description

This is just a convenience function that returns the same weights as CIE as defined by CIE_e_fun but with no option to change normalization wavelength, and with the wavelength limits adjusted to those used for UVI. Using std="NOAA" follows the definition in https://www.esrl.noaa.gov/gmd/grad/neubrew/docs/UVindex.pdf 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. "NOAA" is the default as this is safer with noisy data for sunlight, and for solar radiation the value of UVI should be correct. When calculating UVI for radiation spectra from UV lamps, "WMO" should be used.

Usage

UVI_wb(std = "NOAA")

Arguments

std

"NOAA" or "WMO"

Details

UVI (UV Index) based on Erythema BSWF

Value

a list defining the wavelength range, weighting and normalization. This is just the CIE98 BSWF but with the wavelength limits adjusted to those used for UVI.

References

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

Constructor of lists of UV wavebands

Description

Defined according to "ISO" by default, but other definitions also supported.

Usage

UV_bands(std = "ISO")

Arguments

std

a character string "ISO", "CIE", "medical", "plants" or "none".

Value

a list of wavebands

Examples

UV_bands()
UV_bands("ISO")
UV_bands("CIE")
UV_bands("medical")
UV_bands("plants")
UV_bands("none")

Constructor of UV health hazard weighted waveband

Description

Waveband constructor for ICNIRP UV health hazard 2004 BSWF.

Usage

UV_health_hazard(std = "ICNIRP", norm = 270, w.low = 210, w.high = 400)

ICNIRP(norm = 270, w.low = 210, w.high = 400)

Arguments

std

a character string "ICNIRP".

norm

normalization wavelength (nm)

w.low

short-end boundary wavelength (nm)

w.high

long-end boundary wavelength (nm)

Details

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.

Value

a waveband object defining wavelength range, weighting function and normalization wavelength.

Note

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.

References

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

Examples

ICNIRP()
UV_health_hazard()
UV_health_hazard("ICNIRP")

Constructor of VIS waveband

Description

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.

Usage

VIS(std = "ISO")

Arguments

std

a character string "ISO" or "RS" (remote sensing).

Value

A waveband object wavelength defining a wavelength range.

Examples

VIS()
VIS("ISO")
VIS("LandsatOLI")
VIS("Landsat7")
VIS("Pan.RBV.Landsat3")

Contructor of lists of VIS wavebands

Description

Defined according to "ISO".

Usage

VIS_bands(std = "ISO")

Arguments

std

a character string "ISO".

Value

a list of wavebands

Examples

VIS_bands()
VIS_bands("ISO")

Constructor of yellow waveband

Description

Wavelength-range definition for yellow radiation according to ISO.

Usage

Yellow(std = "ISO")

Arguments

std

a character string "ISO"

Details

Yellow radiation (570...591 nm) as defined in ISO standards based on human colour vision.

Value

a waveband object wavelength defining a wavelength range.

Examples

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-2

Constructor of erythema-weighted waveband

Description

Erythema BSWF (1998 update)

Usage

erythema(std = "CIE98", norm = 298, w.low = 250, w.high = 400)

CIE(norm = 298, w.low = 250, w.high = 400)

Arguments

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)

Value

a waveband object wavelength defining wavelength range, weighting function and normalization wavelength.

Note

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.

References

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

Examples

erythema()
erythema("CIE98")
CIE()
CIE(norm = 300)
erythema(norm = 300)

Photopic sensitivity of the human eye

Description

Constant value used in the definition of Lumen 1 W is equal to 683 Lumen at 555 nm

Usage

photopic_sensitivity

Format

A single numeric value

Details

A single numeric value

Scotopic sensitivity of the human eye

Description

Constant value for human vision under very weak illumination 1 W is equal to 1699 Lumen at 507 nm

Usage

scotopic_sensitivity

Format

A single numeric value

Details

A single numeric value

photobiologyWavebands: Waveband Definitions for UV, VIS, and IR Radiation

Description

Details

Author(s)

References

See Also

Examples

Constructor of blue waveband

Description

Usage

Arguments

Details

Value

Note

References

See Also

Examples

Constructor of CH4 production from pectin weighted waveband

Description

Usage

Arguments

Value

References

See Also

Examples

Gives values for the CH4 production from pectin BSWF as a function of wavelength

Description

Usage

Arguments

Value

References

See Also

Examples

Gives values for the CH4 production from pectin BSWF as a function of wavelength

Description

Usage

Arguments

Value

See Also

Examples

CIE1924 luminous efficiency function (photopic human vision)

Description

Format

Details

Note

References

Luminous efficiency function (scotopic human vision)

Description

Format

Details

References

CIE2008 luminous efficiency function (2-deg) (photopic human vision)

Description

Format

Details

References

Gives values for the erythemal BSWF as a function of wavelength

Description

Usage

Arguments

Value

See Also

Examples

Gives values for the erythemal BSWF as a function of wavelength

Description

Usage

Arguments

Value

See Also

Examples

Constructor of DNA damage (SETLOW) weighted waveband

Description

Usage

See Also

Constructor of DNA damage (SETLOW) weighted waveband

Description

Usage

See Also

Constructor of DNA damage (Quaite) weighted waveband

Description