Package ‘r4photobiology’ loads the four most frequently used packages from the “R for Photobiology Suite”. It provides no additional functionality. The four packages are described below and can be also loaded by themselves.
To install the current released versions of these five packages, please use:
To install the latest development version of the package, please use:
To access the documentation website visit http://docs.r4photobiology.info/r4photobiology and to reports problems or bugs please raise an issue at https://bitbucket.org/aphalo/r4photobiology-pkg/issues.
I am writing together with collaborators a book titled “R for Photobiology: Theory and recipes for common calculations”. We are writing it in the open. The PDF file is available through Leanpub at https://leanpub.com/r4photobiology/ and its source is available through Bitbucket at https://bitbucket.org/aphalo/r4photobiology-book.
Package ‘photobiology’ defines a system of classes for storing spectral data and accompanying metadata. For each of these classes specialised summary methods, maths operators and functions are provided. In addition, classes for storing collections of objects of the classes for individual spectra are defined as well as ‘apply’ functions. Extraction and replacement operators are also implemented.
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’.
Package ‘ggspectra extends’ggplot2‘by providing a set of additional statistics, geometries, scales and functions to be used together with package’photobiology‘for plotting radiation-related spectra and annotating the plots with quantities derived from spectral data. Non-weighted derived quantities represent summaries of a given range of wavelengths, which can be expressed either in energy or photon based units. 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 cues. Peaks and valleys present in spectral data can also be annotated. Color-patch charts can be created based on any R color definitions, including those generated from wavelengths and visual response functions with functions in package’photobiology’.
This package uses the new functionality added to ‘ggplot2’ at version 2.2.0 and is not compatible with earlier versions of this package.
Package ‘photobiologyInOut’ provides functions for importing spectral data from diverse sources including instrument-specific files, as well as spectral data output from solar-radiation simulation models. It also includes functions for exchanging spectral data with other R packages. Package ‘photobiologyInOut’ complements other packages in the ‘r4photobiology suite’ by allowing reading and writing of “foreign” spectral data as well as reading data saved from data loggers.
The suite of R packages for photobiological calculations is described at the r4photobiology web site, where documentation is also available as web pages.