Category: R packages

ggspectra 0.3.1

Package update / R packagesLeave a comment

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

Package update / R packagesOne Comment
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

photobiology 0.9.24

Package update / R packagesLeave a comment

Changes from version 0.9.23, the most recent CRAN release, are:

  • Fix major bug in internally used method merge_attributes(), accidentally introduced in version 0.9.23, which in certain cases triggered fatal errors when using operators or other methods taking two spectra as arguments. This also affected indirectly package ‘ooacquire’.
  • Add method wls_at_target() implementing search and interpolation of wavelengths at which the spectral quantity matches a target value. This method is implemented for all spectral classes and collections of spectra, except raw_spct, chroma_spct and object_spct and corresponding collections.
  • Add (experimental) support for spectral measurements where the exposure time is dependent on the light source instead of on the integration time settings in the spectrometer such as when measuring the light output from xenon-tube flashes.

If you are using version 0.9.23, please, do update to this new version, to avoid being affected by the now fixed bug.

Documentation web site at http://docs.r4photobiology.info/photobiology/ 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 https://bitbucket.org/aphalo/photobiology/issues

photobiology 0.9.23

Package update / R packagesLeave a comment

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 http://docs.r4photobiology.info/photobiology/ 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 https://bitbucket.org/aphalo/photobiology/issues