photobiologyWavebands
Package ‘photobiologyWavebands’ is 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. These additional definitions include the wavelength 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 formulations that we consider the most frequently used are the 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’.
Installation
Installation of the most recent stable version from CRAN:
install.packages("photobiologyWavebands")Installation of the current unstable version from Bitbucket:
# install.packages("devtools")
devtools::install_bitbucket("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 (http://doi.org/10.31885/9789521083631).
Contributing
Pull requests, bug reports, and feature requests are welcome at (https://bitbucket.org/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
© 2012-2020 Pedro J. Aphalo (pedro.aphalo@helsinki.fi). Released under the GPL, version 2 or greater. This software carries no warranty of any kind.