photobiologyInOut-package: photobiologyInOut: Read Spectral and Logged Data from Foreign...

photobiologyInOut-packageR Documentation

photobiologyInOut: 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.

Data acquisition

The support for Ocean Insight, formerly Ocean Optics, spectrometers in package 'photobiologyInOut' is limited to the import of data acquired with Ocean Optics' software as is. In contrast, package 'ooacquire', part of these same suite, makes it possible to control, modify settings and acquire spectral data from Ocean Optics spectrometers directly from within R. 'ooacquire' also supports the conversion of raw-counts data into physical quantities.


Most of the file formats supported are not standardized, and are a moving target because of changes in instrument firmware and support software. In addition the output format, especially with models, can depend on settings that users can alter. So do check that import is working as expected, and if not, please please raise an issue and upload one example of an incorrectly decoded file.


From version 0.4.4 the time zone (tz) used for decoding dates and times in files imported defaults to "UTC". In most cases you will need to pass the tz (or the locale) where the file was created as an argument to the functions!


Maintainer: Pedro J. Aphalo (ORCID)

Other contributors:


Aphalo, Pedro J. (2015) The r4photobiology suite. UV4Plants Bulletin, 2015:1, 21-29. doi: 10.19232/uv4pb.2015.1.14.

See Also

Useful links:

photobiologyInOut documentation built on Aug. 15, 2022, 9:09 a.m.