photobiology 0.9.22

The only change from version 0.9.21, the most recent CRAN release, is:

  • Remove dependency on package ‘caTools’ which is no longer maintained and is scheduled to be archived in CRAN on 19 July.

After ‘caTools’ stops being available through CRAN, installation of ‘photobiology’ (== 0.9.21) would no longer have been possible as it would also have been archived. This update avoids this.

[update 2018-08-31] ‘caTools’ has been updated and has continued being available through CRAN, so it is to expect that earlier versions of ‘photobiology’ will continue to be available as archived.

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

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

ggplot2 3.0.0

As the updated ‘ggplot2’ 3.0.0 became today available through CRAN, I will soon submit the new package ‘gginnards’ and a new enhanced version of package ‘ggpmisc’. That the first digit of the version of ‘ggplot2’ was increased reflects the fact that this is a major update to ‘ggplot2’ with some code breaking changes. The versions of packages ‘ggpmisc’ and ‘ggspectra’ now in CRAN are compatible with both ‘ggplot2’ 2.2.1 and 3.0.0. See for details on ‘ggplot2’ updates.



I will list here the current preview versions available in the “test repository”. I will just highlight the biggest changes. The new packageggspectra was described in a separate post.

photobiology 0.9.1 (minor bug fixes)

As old programming wisdom tells, usually testing response to input values at a boundary situations is a good way of finding difficult bugs. Such testing revealed some bugs, that could occasionally cause trouble, and almost all edits had to do with fixing such bugs. Some of these could have been called features that did not fit with the normal behaviour of the R language. The main one, has been the way that “empty” results were signalled by means of NA. This is not how R is designed to work, as empty lists and arrays behave in a natural and correct way in loop constructs while NAs need exceptional handling. Still a few additional test cases are missing, and a few additional bugs may show up.

All other packages in the suite (compatibility updates)

photobiologyAll 0.4.2, photobiologyFilters 0.4.1, photobiologyInOut 0.4.0, photobiologyLamps 0.3.3, photobiologyLEDs 0.3.2, photobiologyPlants 0.3.3, photbiologyReflectors 0.3.2, photobiologySensors 0.3.3, photobiologySun 0.3.7, photobiologyWavebands 0.3.4

Because of the update to ggplot2 the vignettes of most packages had to be rebuilt using ggspectra instead of photobiologygg. A few interdependencies of the documentation were also removed. In addition the stricter error checking implemented in photobiology 0.9.x detected a bug in a data build script, which was fixed.

NOTE: Sources, and Windows binaries for R 3.2.x, are now available in the R-test repository.