ggspectra 0.3.8

Package documentation web site at: https://docs.r4photobiology.info/ggspectra/

Eighteen months from the previous release, this update brings many improvements to autoplot() methods. These include enhanced capabilities for handling of normalized and scaled spectral data, as well as cosmetic tweaks to labels.

This update also includes snaller enhancements and fixes a bug. It tracks changes in packages ‘ggrepel’ (>= 0.9.1), ‘photobiology’ (>= 0.10.10) and ‘ggplot2’ (>= 3.3.3) and deprecation of functions in ‘tidyr’ (>= 1.0.0). The updated code depends on the revised normalize() function in ‘photobiology’ (>= 0.10.10) and on ‘ggrepel’ (>= 0.9.1).

The changes from version 0.3.7, the current CRAN release, are:

  • Revise all autoplot() methods to support on-the-fly normalization internally using photobiology::normalize().
  • Revise autoplot() methods for source_spct, response_spct, filter_spct, reflector_spct, source_mspct, response_mspct, filter_mspct, and reflector_mspct so that if the data are already normalized, by default the normalization is updated according to the arguments passed to unit.out or plot.qty and range. (Update is possible only for objects normalized with ‘photobiology’ (\>= 0.10.7). For objects created with earlier versions, the old behaviour of plotting spectra as is remains unchanged.)
  • Revise autoplot() method for object_mspct to force use of facets when plot.qty = "all" instead of forcing plotting of transmittance only.
  • Revise autoplot() method for object_mspct to correctly handle normalization of collections of spectra, one spectrum at a time, correcting a bug.
  • Revise all autoplot() methods to generate shorter y-axis labels also improving reporting of scaling and normalization when needed.
  • Revise all autoplot() methods to fix bug leading to bad object name in plot title due to delayed evaluation.
  • Add autoplot.cps_mspct(), autoplot.raw_mspct() and autoplot.generic_spct() methods.
  • Add support for faceting to all autoplot() methods for collections of spectra.
  • Revise all autoplot() methods for collections of spectra adding support for sum, prod, var, sd, and se as summaries.
  • Update decoration() to track changes in ‘ggrepel’ (\>= 0.9.1).
  • Update decoration() to use position_nudge() and position_nudge_repel() to displace labels instead of “off-range” justification.
  • Improve handling of multiple spectra in long form by ggplot() methods and by autotitle().
  • Remove direct dependency on ‘dplyr’.
  • Add to the documentation of all autoplot() methods an explanation of how to modify the default plot annotations and tittles using arguments passed to parameter annotations. Also add *see also* links to related help pages.

  • Although this update should not break any code, the y-axis
    labels in plots returned by autoplot() methods have changed, in most cases only cosmetically to shorten them. In a few cases more significant changes correct problems.
  • Although this update should not break any code, the labels for
    peaks and valleys can be at a slightly different position than with
    earlier versions.
  • Although this update does not break any code, plots of collections of object spectra with normalization, will differ from earlier ones as member spectra are now normalized individually (this corrects an earlier bug!).

NOTE: The updated package is on its way to CRAN.

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

ggpp 0.4.4

Version 0.4.4 fixes a bug affecting most of the geometries in the package. Adding multiple layers using the same geom to the same plot would result in only one of these layers being rendered with others silently missing from the graphical output.

Changes compared to version 0.4.3, the previous version in CRAN are:

  • Fix bug caused by repeated grob and grob tree names.

Documentation web site at http://docs.r4photobiology.info/ggpp/ includes all help pages, with output from all examples, vignettes as well as a changelog in HTML format.

NOTE: Version 0.4.4 is on its way to CRAN.

Please raise issues concerning bugs or enhancements to this package through GitHub at https://github.com/aphalo/ggpp/issues. Pull requests are also welcome.

ggpmisc 0.4.6

Version 0.4.6 fixes a significant bug occasionally affecting highlighting and labelling of peaks and valleys. Even though when triggered the problem is easily detectable by looking at the plot, please, update.

Changes compared to version 0.4.5, the previous version in CRAN are:

  • Fix bug in stat_peaks() and stat_valleys(). They could return wrong values for peaks and valleys if the rows in data in the ggplot object were not sorted by the value of x.

Documentation web site at http://docs.r4photobiology.info/ggpmisc/ includes all help pages, with output from all examples, vignettes as well as a changelog in HTML format.

NOTE: Version 0.4.6 is on its way to CRAN.

Please raise issues concerning bugs or enhancements to this package through GitHub https://github.com/aphalo/ggpmisc/issues

photobiology 0.10.10

The package documentation web site is at https://docs.r4photobiology.info/photobiology/ includes a changelog with information for each release since version 0.1.0.

This update concerns mainly methods normalize() and fscale() and the use of attributes to keep a history of these transformations. Some of the reporting enhancements are not operational for objects normalized and re-scaled with previous versions of this package, while all earlier features remain available.

Changes from version 0.10.9 the most recent CRAN release, are:

  • Update normalize() methods to support updating an already present normalization (norm = "update") and skipping the normalization altogether (norm = "skip").
  • Update normalize() methods to store range in the attribute, and getNormalized() to return it.
  • Update normalize() methods to better handle normalization of previously normalized spectra, and add flexibility to the normalization of previously scaled spectra.
  • Add getScaling() and fix minor inconsistency in value returned by getScaled().
  • Fix bug in getNormalization() (wrong named member in returned value from spectra with no normalization data).
  • Fix bug resulting in "normalization" attribute not being copied.
  • Fix bug resulting in not all relevant attributes being copied to the value returned by summary.generic_spct().
  • Improve printing of metadata for normalization and rescaling.
  • Fix bug in shared_member_class() (wrong value returned for empty  collections).
  • Update smooth_spct() to handle bad arguments passed to method without crashing and add support for skipping smoothing (method = "skip").

NOTE: Version 0.10.10 is on its way to CRAN.

Please raise issues concerning bugs or enhancements to this package through GitHub at https://github.com/aphalo/photobiology/issues