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. Non-weighed derived quantities represent summaries of a given range of wavelengths. All constructors default to ISO standardized definitions when they are available, but other competing definitions are also available though parameter std of the constructors of waveband objects. These constructors are specialized versions of the photobiology::waveband() constructor.

In photobiology, 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.

The definitions cover most non-weighted wavebands in common use, like those corresponding ultraviolet, visible and infrared, the light colours seen by humans, photosynthetically active radiation 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.

Definitions also include many weighting functions used in the calculation of effective irradiances and exposures. Weighting functions included in the package are several biological spectral weighting functions (BSWFs) used to estimate effective UV doses. Except for the definition of the erythemal and vitamin-D action spectra for which definitions standardized by CIE exist, the default formulation is one commonly used. It is important to keep in mind that mathematical formulations and extrapolation rules in use are not unique and that it is important to carefully chose the most appropriate one and report exactly which one was used. We hope this package will make this easier.

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’.

Installation

Installation of the most recent stable version from CRAN:

install.packages("photobiologyWavebands")

Installation of the current unstable version from Bitbucket:

# 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

© 2012-2022 Pedro J. Aphalo (pedro.aphalo@helsinki.fi). Released under the GPL, version 2 or greater. This software carries no warranty of any kind.