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.

Two builds and two repositories

The repositories

I will keep from now on two CRAN-like repositories at this site. The one that has been in use for some time will remain in use, but I will only upload to it the stable and well tested versions of the packages.

I have just created a second repository with address R_test instead of R where I will keep the latest versions. This adds a slight complication, but will allow a smoother update process and give a more clear way of choosing the degree of novelty desired.

Releases at

Previews at (Path to repository updated on 7.01.2016!)

I have just uploaded to the “test” repository the result of recent weeks’ work and in particular the updates I did over the weekend to track the update of ggplot2 to version 2.0.0. Package photobiologygg has been replaced by a new package that I wrote over the weekend. The new is called ggspectra. I have re-implemented quite much of the functionality of the old package but there is still work to do on the waveband annotations which will become ggplot statistics. I have added a few new features to the stats I am re-writing which simplify their use, thanks to the improvements to package ggplot2. There are also quite a few improvements in ggplot2itself to facet labelling and even a couple of new geoms and stats have been added to version 2.0.0 of ggplot2. However, in the days since its release a few bugs have been found, and one of them interferes with the proper testing and to some extent use of the stats that I am writing, so if you can, wait a few days until ggplot2 2.0.1 is released. The problem I had was my own misunderstanding about how to create new ggplot statistics!

Future releases and previews

In posts, the released versions will be shown in blue as earlier, and the preview (=test) versions in orange, like this:

photobiology 0.9.0 (release: bug fix, new features)

Description of changes

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

photobiology 0.9.1 (preview: bug fix, new features)

Description of changes

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