photobiologyWavebands

Package ‘photobiologyWavebands’ supplies a set of functions and data to be used together with package ‘photobiology’ for calculation of derived quantities from spectral data. Package ‘photobiology’ defines class waveband for storing wavelength ranges or spectral weighting functions plus wavelength ranges and a corresponding constructor function waveband(). Package ‘photobiologyWavebands’ provides specialized contructors so that frequently used wavebands can be created by name instead of directly entering numeric boundaries for wavelength and user-defined functions for weighting as needed when using waveband(). R functions for frequently used to obtain spectral weighting factors from arbitrary wavelengths in nanometres are also exported.

Non-weighted derived quantities represent summaries of a given range of wavelengths, i.e., weight is 1 irrespective of wavelength or use of photon or energy units. In this case constructors of waveband objects default to ISO standardized definitions when they are available, with other competing definitions available by passing character strings as argument to parameter std.

The non-weighted definitions cover most non-weighted wavebands in common use, like those corresponding ultraviolet, visible and infrared, the light colours seen by humans, and some other bands of interest for plants.

Several wavebands corresponding to remote sensing instruments are also provided, including all those for the LANDSAT missions, as non-weighted definitions. The Landsat imagers do have a specific responsiveness at each wavelength, and would in principle have to be defined using response-dependent weighting functions. The calibrations and definitions provided by NASA are based on average response per band. For example, in the OLI instrument several of the bands are relatively narrow, while the wider ones seem to have a response that is flatter on a per photon basis than on an energy basis. If Landsat response bands are to be simulated using spectral data from other instruments these approximations need special consideration.

The definition of photosyntheticaly active radiation (PAR) is non-weighted on a photon basis but spectrally weighted on an energy based. In some cases the same range of wavelengths as in the definition of PAR is used to compute a non-weighted energy irradiance, which should probably not be called PAR because of the different weighting!

Both PAR and illuminance are based on biological spectral weighting functions, approximating the spectral response of photosynthesis and the human-perceived light brightness, respectively. Several other 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 including vision. Weighting function definitions represent measurable or expected biological or photocheminal responses, and consequently they differ if used to compute effective spectral energy- and photon irradiances. Thus, two versions of weighting functions are stored in waveband objects.

Exports from ‘photobiologyWavebands’ also include several weighting functions used in the calculation of effective irradiances and exposures. These are the same functions used by the constructors of waveband objects. These Weighting functions are mostly biological spectral weighting functions (BSWFs) used to estimate effective UV doses. Except for the definition the erythema (human skin reddening) and vitamin-D3 BSWFs for which definitions standardized by CIE exist, the default formulation is one commonly used and preferred by the author of the package. It should be kept in mind that mathematical formulations and extrapolation rules in use are not unique and that it is important to carefully chose the most appropriate ones and report which one was used. We hope this package will make this easier. The estimated summary values depend strongly on the choice of BSWF, its formulation and the extrapolation rules used. These choices remain in the hands of users, expected to have the necessary knowledge.

Colour-response and colour-matching functions for human vision and bee vision are included in package ‘photobiology’. Absorbance spectra for plant photoreceptors and some common plant pigments, as well as action spectra for photosynthesis are included in package ‘photobiologyPlants’. Package ‘colorSpec’ provides tools for working with colours, including colour spaces for devices like cameras. Package ‘photobiologyInOut’ facilitates translation of spectral data stored in classes defined in package ‘photobiology’ and other packages such as ‘colorSpec’.

Installation

Installation of the most recent stable version from CRAN:

install.packages("photobiologyWavebands")

Installation of the current unstable version from GitHub:

# install.packages("remotes")
remotes::install_github("aphalo/photobiologyWavebands")

Documentation

HTML documentation is available at (https://docs.r4photobiology.info/photobiologyWavebands/), including an User Guide.

News on updates to the different packages of the ‘r4photobiology’ suite are regularly posted at (https://www.r4photobiology.info/).

Two articles introduce the basic ideas behind the design of the suite and describe its use: Aphalo P. J. (2015) (https://doi.org/10.19232/uv4pb.2015.1.14) and Aphalo P. J. (2016) (https://doi.org/10.19232/uv4pb.2016.1.15).

A book is under preparation, and the draft is currently available at (https://leanpub.com/r4photobiology/).

A handbook written before the suite was developed contains useful information on the quantification and manipulation of ultraviolet and visible radiation: 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). PDF file available from (https://doi.org/10.31885/9789521083631).

Contributing

Pull requests, bug reports, and feature requests are welcome at (https://github.com/aphalo/photobiologyWavebands).

Citation

If you use this package to produce scientific or commercial publications, please cite according to:

citation("photobiologyWavebands")
#> To cite package 'photobiologyWavebands' in publications, please use:
#> 
#>   Aphalo, Pedro J. (2015) The r4photobiology suite. UV4Plants Bulletin,
#>   2015:1, 21-29. DOI:10.19232/uv4pb.2015.1.14
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Article{,
#>     author = {Pedro J. Aphalo},
#>     title = {The r4photobiology suite},
#>     journal = {UV4Plants Bulletin},
#>     volume = {2015},
#>     number = {1},
#>     pages = {21-29},
#>     year = {2015},
#>     doi = {10.19232/uv4pb.2015.1.14},
#>   }

License

© 2012-2023 Pedro J. Aphalo (pedro.aphalo@helsinki.fi). Released under the GPL, version 2 or greater. This software carries no warranty of any kind.