photobiologyInOut v0.4.16

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Read Spectral and Logged Data from Foreign Files

Functions for reading, and in some cases writing, foreign files containing spectral data from spectrometers and their associated software, output from daylight simulation models in common use, and some spectral data repositories. As well as functions for exchange of spectral data with other R packages. Part of the 'r4photobiology' suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.

Readme

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 ARE AS 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.

Functions in photobiologyInOut

Name Description
as.colorSpec Convert into 'colorSpec::colorSpec' objects
read_ASTER_txt Read File downloaded from ASTER data base.
read_FReD_csv Read '.CSV' FReD database.
read_fmi_cum Read daily cummulated solar spectrum data file(s).
read_uvspec_disort_vesa Read libRadtran's uvspec output file from batch job.
read_yoctopuce_csv Read '.CSV' file(s) dowloaded from YoctoPuce modules.
read_avaspec_csv Read '.csv' File Saved by Avantes' Software for AvaSpec.
read_csi_dat Read '.DAT' file(s) saved by modern Campbell Scientific loggers.
hyperSpec2mspct Convert 'hyperSpec::hyperSpec' objects
photobiologyInOut-package photobiologyInOut: Read Spectral and Logged Data from Foreign Files
read_oo_ssirrad Read File Saved by Ocean Optics' SpectraSuite.
read_qtuv_txt Read Quick TUV output file.
read_oo_jazirrad Read Absolute Irradiance File Saved by Ocean Optics' Jaz spectrometer.
read_oo_pidata Read File Saved by Ocean Optics' Raspberry Pi software.
rspec2mspct Convert "pavo::rspec" objects
as.generic_spct Coerce into generic_spct
colorSpec2mspct Convert 'colorSpec::colorSpec' objects
read_licor_prn Read '.PRN' File(s) Saved by LI-COR's PC1800 Program.
read_macam_dta Read '.DTA' File Saved by Macam's Software.
read_tuv_usrout Read TUV output file.
read_uvspec_disort Read libRadtran's uvspec output file.
as.generic_mspct Convert into generic_mspct
read_fmi2mspct Read multiple solar spectra from a data file.
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