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)
Package 'photobiologyWavebands' is a set of functions and data to be used together with package 'photobiology' for calculating derived quantities from spectral data. Non-weighed derived quantities represent summaries of a given range of wavelengths, which can be expressed either in energy or photon based units. All constructors default to ISO standardized definitions when they are available, but other competing definitions are available. These additional definitions include the wavelengths ranges used by Landsat satellite imagers, as these may be needed to approximate remote-sensing-related index calculations on spectral data.
Derived biologically effective quantities are used to quantify the effect of radiation on different organisms or processes within organisms. These effects can range from damage to perception of informational light signals. Except for the definition of the erythemal and vitamin-D spectra for which CIE definitions exist, those which we consider the most frequently used formulations are used as default. Weighting functions included in the package are the luminous efficiency functions for human vision and several biological spectral weighting functions (BSWFs) used to estimate effective UV doses.
The definitions cover most non-weighted wavebands in common use, and in addition many weighting functions used in the calculation of effective irradiances and exposures. The current version of the package puts emphasis, in the case of weighting functions, on a subset of those in use, but in the future the package will be expanded to included responses relevant to additional groups of organisms. Colour-response and colour-matching functions for human vision and bee vision are included in package 'photobiology'.
Please, see the web site r4photobiology for details on other packages available as part of the suite, and on how to install them.
Add constructors for frequently used infrared bands, and for lists of infrared bands. Add as additional values recognized as argument for parameter std "RS" for wavelength ranges commonly used in remote sensing to the different existing and new waveband constructors. Add constructors for wavelength-range based waveband definitions for the imagers used in Landsat missions 1 to 8 : "LandsatRBV", "LandsatMSS", "LandsatTM", "LandsatETM", "LandsatOLI", and "LandsatTIRS". Add constructor Landsat_bands() returning lists of waveband objects for the different Landsat missions. Update warning messages and error handling in existing constructors. Update Plant_bands() constructor to support CIE's UVA1 and UVA2 definitions. Update vignette.
Remove all definitions of ratios. Remove vignette with plots of the wavebands. Remove dependency of vignettes on package ggspectra.
Use package ggspectra instead of photobiologygg in vignette for compatibility with ggplot2 version 2.
Minor correction of hinges in definitions to avoid errors at boundaries.
Added function and waveband constructor for ICNIRP BSWF. Rebuilt data and package with photobiology 0.8.0.
R_FR_ratio() now uses "Smith10" giving 10 nm bands.
Rebuilt data and package with photobiology 0.6.0. This required some minor edits to the vignettes.
Edited the definitions of Red() and Far_red() to include additional wavelength limits as used by other authors.
Updated User Guide.
Some edits to vignettes.
Added luminous efficiency functions for human vision, and the constants used in the definition of Lumen. Setlow's BSWF is now stored as a response.spct object using the same variable names as in the rest of the suite. The Setlow data from TUV has already been converted to energy units, but this was not noticed when this data was added to the package. This bug is now corrected. Updated User Guide with some examples of the calculation of luminous flux in lux from spectral irradiance data. Added plots of the luminous efficiency curves to the Data Plots vignette.
Update to documentation and vignettes. UVR8-related data and functions moved to package photobiologyPlants.
Now all constructors of waveband objects for BSWFs, have formal arguments w.low and w.high, with values earlier in use, now set as defaults.
Added some references to the documentation.
User Guide edited to match current versions of packages photobiology and photobiologygg, as well as to update to to the current version.
Changed the definition of SWFs functions not to have any intrinsic wavelength limits, and made this limit a new formal argument on the waveband constructor functions, keeping the same defaults. Returned values should remain unchanged. This bit of flexibility is needed as different authors have used different limits for the same BSWFs.
A new formulation for GPAS has been added. The formulation by Micheletti and Piacentini (2002) is used for example in the TUV model (version 5.0). The new waveband constructor is GEN.M().
Changed the definition of SWFs to not include wavelengths shorter than 280 nm, except for the case of UVR8 absorbance.
Edits to User Guide for compatibility and rebuilt with photobiology 0.5.1, now required.
Merge of photobiologyUV and photobiologyVIS packages. Merged and updated the vignettes. Added functions for calculating UV:PAR photon ratios. Added functions for creating some coherent lists of wavebands (e.g. all ISO defined colours).
Added setting of wb.label in functions defining wavebands.
Added "medical" definitions of UVB and UVB.
Added "methane from pectin" BSWF of McLeod et al. (2008)
Minor changes, with no effect on functionality
Revised User Guide and added Catalogue of plot of BSWFs. No changes to the R code.
Added calculation of UV Index.
Internally modified to work with photobiology (>= 0.2.1) User interface unchanged.
Internally modified to work with photobiology (>= 0.2.0) User interface unchanged.
Added vignettes. Still needs some cleaning of code and improved documentation.
First version. Implements equivalent WBs and SWFs to those in UVcalc. The algorithms are exactly the same as most of the functions were just copied from UVcalc 1.3.1
Added setting of wb.label in functions defining wavebands.
Added missing import directive. Rebuilt vignette under photobiology 0.2.16 as the output of the examples is cosmetically different.
Changed waveband definitions to allow caching. A change in package photobiology adds hinges.
Corrected error in green light wavelength range, and added new optional definitions of wave length ranges.
Added a vignette: a manual.