photobiologyInOut 0.4.18

The main changes from version 0.4.17-1 the previous CRAN release, are:

  • Track code breaking change in ‘readr’ (>= 1.2.0)
  • Fix bug in read_oo_pidata() that was preventing reading of Ocean Optics “Raspberry Pi” Flame files with a sequence header line at the top.
  • Add decoding of file header to extract integration time and number of scans to read_oo_pidata().
  • Improve decoding of file header to extract instrument settings in read_oo_jazdata().

Because of code breaking change in package ‘readr’ this version of ‘photobiologyInOut’ requires ‘readr’ >= 1.2.0 to be installed. Function read_oopi_data() from ‘photobiologyInOut’ < 0.4.18 will not work as expected under ‘readr’ >= 1.2.0. (I thank Jim Hester for making a pull request that solved the problem introduced by the change in ‘readr’.

Documentation web site at http://docs.r4photobiology.info/photobiologyinout/.

NOTE: This version of the package is on its way to CRAN.

Please raise issues concerning bugs or enhancements to this package through Bitbucket at https://bitbucket.org/aphalo/photobiologyinout/issues

ggspectra 0.3.1

The changes from version 0.3.0, the current CRAN release, are:

  • Fix major bug in plot() and autoplot() methods for classes source_spct and response_spct which prevented plotting of spectra with the time.unit attribute set to any value different from "second".

Documentation web site at http://docs.r4photobiology.info/ggspectra/.

NOTE: The updated package has been submitted to CRAN.

Please raise issues concerning bugs or enhancements to this package through Bitbucket at https://bitbucket.org/aphalo/ggspectra/issues

ggspectra 0.3.0


BUG WARNING

Occasional R crashes when stat_label_peaks() and stat_label_valleys() are used together with ggrepel::geom_label_repel(). This is a bug in ‘ggrepel’ (= 0.8.0) at least under Windows with long vectors of labels. The bug affects these stats and the "label.peaks" and "label.valleys" annotations in all plot() methods. The bug has been reported and the author is working on a fix.


Revise to track changes in ‘photobiology’ version 0.9.24 and ‘ggplot2’ 3.0.0, which are now required.

The changes from version 0.2.4, the current CRAN release, are:

Code breaking change!

Change the names of some the values calculated by the stats defined in ‘ggspectra’ to avoid confusion with the names of ‘ggplot2’ aesthetics. (This breaks old code only if any of the renamed variables has been manually mapped using aes(), which is rather unlikely.)

Other non-code breaking changes

  • stat_label_peaks() and stat_label_valleys() now have a new parameter, label.fill which can be used to set the content of ..x.label.. and ..y.label.. for labels not labelled as peaks or valleys. The earlier default of "" is maintained.
  • Add the new stat_find_wls() and stat_find_qtys(), two new statistics useful for highlighting features in spectra.
  • Add parameter ylim to all plot() methods. By default previous behaviour is preserved.
  • Revise plot() methods to support objects with multiple spectra in long form.
  • Revise plot() methods to NOT display by default calculated numerical summaries in annotations when a plot contains multiple spectra.
  • Revise plot() methods to retrieve and validate the name of the factor used to identify multiple spectra, using as default the value stored in the attribute "idfactor" implemented in ‘photobiology’ 0.9.21 and later.
  • Add autoplot() as an alias of plot() for spectra and collections of spectra.

Documentation web site at http://docs.r4photobiology.info/ggspectra/.

NOTE: The updated package has been submitted to CRAN.

Please raise issues concerning bugs or enhancements to this package through Bitbucket at https://bitbucket.org/aphalo/ggspectra/issues