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Introduction

Package ‘photobiologyWavebands’ provides constructors for waveband objects, a class defined in package ‘photobiology’. These constructors are convenience functions that allow definition of ranges of wavelengths and biological spectral weighting functions (BSWFs) following definitions in common use, CIE recommendations and ISO standards.

This User Guide is currently very brief, please, consult the help for the individual functions for the details, including references to the literature where the equations and wavelength ranges used in the calculations have been obtained.

Preliminaries

Package ‘photobiologyWavebands’ depends on package ‘photobiology’. We can load and attach both of them with the following statement.

## Loading required package: photobiology
## News at https://www.r4photobiology.info/

Waveband constructors for ranges

Functions for several colour bands, in some cases according to different optional definitions, are listed in the tables below.

Red("ISO")
## Red.ISO 
## low (nm) 610 
## high (nm) 760 
## weighted none
Red("Smith10")
## Red.Smith10 
## low (nm) 655 
## high (nm) 665 
## weighted none
PhR()
## PhR 
## low (nm) 400 
## high (nm) 700 
## weighted none
UV()
## UV.ISO 
## low (nm) 100 
## high (nm) 400 
## weighted none
IR()
## IR.ISO 
## low (nm) 780 
## high (nm) 1e+06 
## weighted none

Waveband constructors for color-based wavelength ranges

constructor std
ultraviolet
UV() ISO
UVC() ISO, medical, none
UVB() ISO, none
UVA() ISO, CIE, none
UVA1() CIE
UVA2() CIE
visible
VIS() ISO
PhR()
Purple() ISO
Blue() ISO, Sellaro
Green() ISO, Sellaro
Yellow() ISO
Orange() ISO
Red() ISO, Smith10, Smith20, Inada, Warrington, Sellaro
Far_red() Smith10, Smith20, Inada, Warrington, Sellaro, BTV, RedEdge20, RedEdge40
infrared
IR() ISO, CIE
NIR() ISO
MIR() ISO
FIR() ISO
IRA() CIE
IRB() CIE
IRC() CIE
SWIR()

Constructors of lists of waveband definitions frequently used together are also defined in the package.

UV_bands("ISO")
## [[1]]
## UVC.ISO 
## low (nm) 100 
## high (nm) 280 
## weighted none 
## 
## [[2]]
## UVB.ISO 
## low (nm) 280 
## high (nm) 315 
## weighted none 
## 
## [[3]]
## UVA.ISO 
## low (nm) 315 
## high (nm) 400 
## weighted none
UV_bands("CIE")
## [[1]]
## UVC.CIE 
## low (nm) 100 
## high (nm) 280 
## weighted none 
## 
## [[2]]
## UVB.CIE 
## low (nm) 280 
## high (nm) 315 
## weighted none 
## 
## [[3]]
## UVA2.CIE 
## low (nm) 315 
## high (nm) 340 
## weighted none 
## 
## [[4]]
## UVA1.CIE 
## low (nm) 340 
## high (nm) 400 
## weighted none
## [[1]]
## UVB.ISO 
## low (nm) 280 
## high (nm) 315 
## weighted none 
## 
## [[2]]
## UVA2.CIE 
## low (nm) 315 
## high (nm) 340 
## weighted none 
## 
## [[3]]
## UVA1.CIE 
## low (nm) 340 
## high (nm) 400 
## weighted none 
## 
## [[4]]
## Blue.Sellaro 
## low (nm) 420 
## high (nm) 490 
## weighted none 
## 
## [[5]]
## Green.Sellaro 
## low (nm) 500 
## high (nm) 570 
## weighted none 
## 
## [[6]]
## Red.Smith20 
## low (nm) 650 
## high (nm) 670 
## weighted none 
## 
## [[7]]
## FarRed.Smith20 
## low (nm) 720 
## high (nm) 740 
## weighted none
constructor std
UV_bands() ISO, CIE, medical, none
VIS_bands() ISO
IR_bands() ISO, CIE
Plants_bands() sensory, sensory10, sensory20, ISO, CIE, none

Waveband constructors for instrument-based wavelength ranges

constructor std
Remote sensing
VIS() LandsatRBV, LandsatOLI, Landsat7, RS
Blue() LandsatTM, LandsatETM, LandsatOLI
Green() LandsatTM, LandsatETM, LandsatOLI, LandsatMSS, LandsatRBV
Red() LandsatTM, LandsatETM, LandsatOLI, LandsatMSS, LandsatRBV
NIR() LandsatTM, LandsatETM, LandsatOLI, LandsatMSS, LandsatRBV
SWIR1() LandsatTM, LandsatETM, LandsatOLI
SWIR2() LandsatTM, LandsatETM, LandsatOLI
TIR1() LandsatTIRS
TIR2() LandsatTM, LandsatETM, LandsatTIRS

Additional constructors are provided for Landsat missions, for example the list of wavebands used in mission Landsat 1 can be created directly.

## [[1]]
## Green.LandsatRBV 
## low (nm) 480 
## high (nm) 580 
## weighted none 
## 
## [[2]]
## Red.LandsatRBV 
## low (nm) 580 
## high (nm) 680 
## weighted none 
## 
## [[3]]
## NIR.LandsatRBV 
## low (nm) 700 
## high (nm) 830 
## weighted none 
## 
## [[4]]
## Green.LandsatMSS 
## low (nm) 500 
## high (nm) 600 
## weighted none 
## 
## [[5]]
## Red.LandsatMSS 
## low (nm) 600 
## high (nm) 700 
## weighted none 
## 
## [[6]]
## NIR.LandsatMSS 
## low (nm) 800 
## high (nm) 1100 
## weighted none
constructor std
Landsat_bands() L1, L2, L3, L4, L5, L6; L7, L8
RBV_bands() LandsatRBV, L1, L2
MSS_bands() LandsatMSS, L1, L2, L3, L4, L5
OLI_bands() LandsatOLI, L8
TIRS_bands() LandsatTIRS, L8
ETM_bands() LandsatETM, L4, L5

Calculating irradiances

An example using sun.pct included in package ‘photobiology’. As the input spectral irradiance is units of Watt m-2 nm-1 the output is in mol m-2 s-1 or W m-2.

e_irrad(sun.spct, UV()) # W m-2
## E_]UV.ISO 
##  28.62872 
## attr(,"time.unit")
## [1] "second"
## attr(,"radiation.unit")
## [1] "total energy irradiance"
q_irrad(sun.spct, UV()) * 1e6 # umol s-1 m-2
## Q_]UV.ISO 
##  86.49506 
## attr(,"time.unit")
## [1] "second"
## attr(,"radiation.unit")
## [1] "total photon irradiance"

Irradiances for different wavebands can be grouped into a list of any length. If the list has named members, then these names are used instead of the default ones in the output.

e_irrad(sun.spct, list(Blue(), VIS()))
## E_Blue.ISO  E_VIS.ISO 
##   37.55207  231.86345 
## attr(,"time.unit")
## [1] "second"
## attr(,"radiation.unit")
## [1] "total energy irradiance"
e_irrad(sun.spct, list(B = Blue(), VIS()))
##       E_B E_VIS.ISO 
##  37.55207 231.86345 
## attr(,"time.unit")
## [1] "second"
## attr(,"radiation.unit")
## [1] "total energy irradiance"

The constructor functions for coherent lists of wavebands described above can be used directly.

e_irrad(sun.spct, VIS_bands())
## E_Purple.ISO   E_Blue.ISO  E_Green.ISO E_Yellow.ISO E_Orange.ISO    E_Red.ISO 
##     47.75529     37.55207     49.26860     13.67971     12.00432     79.38159 
## attr(,"time.unit")
## [1] "second"
## attr(,"radiation.unit")
## [1] "total energy irradiance"

Photon ratios

Photon- and energy ratios can be calculated from any pair of waveband objects. This a convenient and very flexible way of doing this type of calculations.

q_ratio(sun.spct, Blue(), VIS())
## Blue:VIS[q:q] 
##     0.1371157 
## attr(,"radiation.unit")
## [1] "q:q ratio"
e_ratio(sun.spct, Blue(), VIS())
## Blue:VIS[e:e] 
##     0.1619577 
## attr(,"radiation.unit")
## [1] "e:e ratio"

Spectral weighting functions (SWFs)

Currently functions for constructing waveband objects describing several BSWFs are implemented (see Table below). These functions take three arguments in most cases as BSWFs have been used and continue to be used inconsistently in the scientific literature. By supplying these arguments different variations of the BSWFs can be obtained. The defaults used are those values which we consider best, usually the most frequently used ones, except in cases when we consider the use of those values problematic for the reliability of the calculations or simply unjustified.

Waveband constructors for BSWFs

constructor parameters
ultraviolet
PAR() std, norm, w.low, w.high
GEN_G() norm, w.low, w.high
GEN_T() norm, w.low, w.high
GEN_M() norm, w.low, w.high
PG() norm, w.low, w.high
erythema() std, norm, w.low, w.high
CIE() norm, w.low, w.high
ICNIRP() norm, w.low, w.high
DNA_N() norm, w.low, w.high
DNA_GM() norm, w.low, w.high
DNA_P() norm, w.low, w.high
FLAV() norm, w.low, w.high
CH4() norm, w.low, w.high

Effective irradiances and exposures

Both waveband definitions based on a wavelength range and SWFs are stored in waveband objects, that can be created with function .

The same functions used in the examples above for calculation of unweighted irradiances are used to calculate effective irradiances and effective exposures (sometimes called “doses”).

e_irrad(sun.spct, CIE())
## E_]CIE98.298 
##   0.08181583 
## attr(,"time.unit")
## [1] "second"
## attr(,"radiation.unit")
## [1] "total energy irradiance"

BSWFs function definitions

constructor parameters
GEN_G_q_fun() w.length
GEN_T_q_fun() w.length
GEN_M_q_fun() w.length
PG_q_fun() w.length
CIE_e_fun() w.length
CIE_q_fun() w.length
ICNIRP_e_fun() w.length
DNA_N_q_fun() w.length
DNA_GM_q_fun() w.length
DNA_P_q_fun() w.length
FLAV_q_fun() w.length
CH4_e_fun() w.length
CH4_q_fun() w.length

The functions available for calculating action spectra take as argument a vector of wavelengths, and return a vector of effectiveness (either quantum/photon or energy based) depending on how the original source describes them. These functions are listed in the Table above, and an example of their use follows.

# at 1 nm intervals
wavelengths1 <- 285:400
action.spectrum1 <- CIE_e_fun(wavelengths1)

All functions accept a wavelengths vector with variable and arbitrary step sizes, with the condition that the wavelengths are sorted in strictly increasing order.

These functions are used internally by the package, but are also used for the calculation of effective spectral irradiances by multiplication of a source_spct object by a waveband object.

sun.spct * CIE()
## Object: source_spct [122 x 2]
## Wavelength range 280-400 nm, step 0.9230769-1 nm 
## Label: sunlight, simulated 
## Measured on 2010-06-22 09:51:00 UTC 
## Measured at 60.20911 N, 24.96474 E; Kumpula, Helsinki, FI 
## Time unit 1s
## Data weighted using 'CIE98.298' BSWF
## 
## # A tibble: 122 × 2
##    w.length s.e.irrad
##       <dbl>     <dbl>
##  1     280          0
##  2     281.         0
##  3     282.         0
##  4     283.         0
##  5     284.         0
##  6     285.         0
##  7     286.         0
##  8     286.         0
##  9     287.         0
## 10     288.         0
## # ℹ 112 more rows

Luminous flux

The luminous flux per unit area in lux can be calculated as follows using the original luminous efficiency function for the human eye used when the lumen definition was standardized. As we start with spectral irradiance we obtain luminous flux per unit area expressed in lux. The spectra luminous efficiency function data are included in package ‘photobiology’.

e_response(sun.spct * CIE1924_lef.spct) * photopic_sensitivity
## R[/e]_Total 
##    49579.93 
## attr(,"time.unit")
## [1] "second"
## attr(,"radiation.unit")
## [1] "total energy response"

The luminous flux per unit area in lux can be calculated as follows using the latest luminous efficiency function for the human eye.

e_response(sun.spct * CIE2008_lef2deg.spct) * photopic_sensitivity
## R[/e]_Total 
##    53057.78 
## attr(,"time.unit")
## [1] "second"
## attr(,"radiation.unit")
## [1] "total energy response"

As the luminous efficiency functions vary slightly in the wavelength at which the maximum is located, and the wavelength used for the sensitivity constant is fixed by the definition of the Lumen, a small correction is need for exact results (not shown).

An equivalent quantity can be calculated for scotopic vision, using the corresponding function and constant.

e_response(sun.spct * 1e-6 * CIE1951_scotopic_lef.spct) * scotopic_sensitivity
## R[/e]_Total 
##   0.1186256 
## attr(,"time.unit")
## [1] "second"
## attr(,"radiation.unit")
## [1] "total energy response"