photobiologyInOut 0.4.16

The main changes from version 0.4.15 the previous CRAN release, are:

  • Revise read_fmi_dat() to extract date from file header and save the file header to the spectral object as a comment.
  • Add new function read_fmi2mspct() for reading spectral irradiance data.
  • Bug fix: decoding of dates in fmi import functions for daily data not always returned POSIXct objects triggering errors in downstream code.

Documentation web site at

NOTE: The updated package is in CRAN.

Please raise issues concerning bugs or enhancements to this package through Bitbucket at

photobiology 0.9.23

Changes from version 0.9.22, the most recent CRAN release, is:

  • Bug fix: Ensure that getWhenMeasured() always returns an object of class POSIXct. Avoids occasional crashes in ‘PhotobiolgyInOut’.
  • Add scale.factor as formal parameter to methods irrad(), q_irrad(), e_irrad(), response(), q_response() and e_response(). Previous behaviour remains the default.
  • Change default value for parameter idx in the various summary methods for collections of spectra. Also add parameter idx to “add attributes to tibble” methods. The new default argument does not affect the default behaviour of the methods. The change in handling of idx = NULL, the old default might break old code in exceptional cases when idx = NULL was passed explicitly in user code instead of relying on it being the default.
  • Rewrite the “get” methods for attributes using a simpler, and possibly faster approach.
  • Add parameter sep to function convolve_each(). Previous behaviour remains the default.

Documentation web site at includes all help pages, with output from all examples, and vignettes in HTML format.
NOTE: The updated package is in CRAN.

Please raise issues concerning bugs or enhancements to this package through Bitbucket

Using the Quick TUV Calculator

As the latest version (0.4.15) of our package ‘photobiologyInOut’ supports the automatic import of the files returned by the Quick TUV Calculator we show here how to produce such files, and link to an example of their import and plotting in R.

The TUV model is a well known model of atmospheric chemistry that also simulates the solar spectrum within the atmosphere or at ground level using a radiation transfer approach. The model is written in FORTRAN and available for local use. When one needs just to compute a few spectra with no special conditions, it is possible to use the on-line interface provided by the National Centre of Atmospheric Research (NCAR) under the name of Quick TUV Calculator.

This interface is easy to use once one understands the different options and required input data. (This video, authored by Pedro J. Aphalo is published with the express permission of Sasha Madronich, creator of the TUV model.)

An R notebook demonstrating how the solar spectrum is affected by variation in the atmospheric composition, solar elevation and observer elevation is available for reading and/or download. The R code used in embedded in this HTML file. Click on the image below to access the article. (The article is still a draft. Corrections and suggestions for improving it are most welcome.)

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