photobiologyInOut

Package ‘photobiologyInOut’ provides functions for importing spectral data from diverse sources including instrument-specific files, as well as spectral data output by 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 “foreign” spectral data as well as reading data saved from data loggers.

Developing a package like this is a never-ending task as I have only a limited sample of output files for testing and formats are quite variable. The functions may not work with different software or firmware versions used for acquiring spectral data from instruments. Even the format of files can depend on the current locale and operating system.

This package is the core of a suite of R packages for photobiological calculations described at the r4photobiology web site.

Warning

The functions in this package work with the example files I have access to for testing, but they may not work with your own files as file formats vary.

PLEASE, BE VERY CAREFUL WHEN USING THIS PACKAGE. DO CHECK THAT UNITS USED IN THE IMPORTED FILE ARE THOSE EXPECTED BY THESE FUNCTIONS AND THAT THE VALUES IN THE RETRIEVED DATA ARE THOSE EXPECTED!

If they do not work with your files, they hopefully will be useful as examples for developing your own functions. If you develop new functions or improve the existing ones, please, do contribute them back to this project.

Installation

Installation of the most recent stable version from CRAN:

install.packages("photobiologyInOut")

Installation of the current unstable version from Bitbucket:

# install.packages("devtools")
devtools::install_bitbucket("aphalo/photobiologyInOut")

Documentation

HTML documentation is available at (http://docs.r4photobiology.info/photobiologyInOut/), including a User Guide.

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

Two articles introduce the basic ideas behind the design of the suite and 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://hdl.handle.net/10138/37558).

Contributing

Pull requests, bug reports, and feature requests are welcome at (http://bitbucket.org/aphalo/photobiologyInOut).

Citation

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

citation("photobiologyInOut")
#> 
#> To cite package 'photobiologyInOut' 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

© 2015-2018 Pedro J. Aphalo (pedro.aphalo@helsinki.fi). Released under the GPL, version 2 or greater. This software carries no warranty of any kind.