photobiologyInOut 0.4.24

This non-code-breaking update brings a few new features and tracks deprecations in package ‘tidyr’.

The main changes from version 0.4.23 the previous CRAN release, are:

  • Replace use of deprecated tidyr::gather_().
  • Add function read_cid_spectravue_csv() supporting data import from measurements CSV files output by CID Bio-Science’s SpectraVue CI-710s leaf spectrometer.
  • Add function read_foreign2mspct() to apply an import function to a list of files.
  • Add color-related functions spct_CRI(), spct_CCT() and expect_SSI() implemented as wrappers to functions in package ‘colorSpec’. These functions accept source_spct objects as arguments. CRI, CCT and SSI are quantities used to describe light used for illumination, photography, cinematography and video.
  • 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://github.com/aphalo/photobiologyinout/issues

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