photobiology 0.9.30

Changes from version 0.9.29 the most recent CRAN release, are:

  • Add function compare_spct() for comparisons between pairs of spectra based on summaries computed over multiple ranges of wavelengths.
  • Add utility method uncollect() for extracting all members of a collection of spectra.
  • Add utility method wl_thin() for reducing the storage size of _spct objects by removing data points in regions with only minor features.
  • Add when_measured() and when_measured<-(), where_measured() and where_measured<-(), what_measured() and what_measured<-(), how_measured() and how_measured<-() as an alternative syntax consistent with base R for setting and querying the attributes when.measured, where.measured, how.measured and what.measured used to store metadata in spectral objects and collections.
  • Add spelling synonyms for all normalization-related methods and functions like normalise() and normalise().
  • Add specialization for collections of spectra and spelling synonyms for normalized_difference_ind().
  • Slightly changed printout: Revise summary.generic_spct() to store the name of the summarized spectrum object and revise print.summary_generic_spct() to display the name of the summarized object.
  • Possibly code breaking: Revise fscale() so that by default it sets the scaled attribute only when the target value for re-scaling is equal to one.
  • Fix bug in get_attributes() methods.
  • Add parameter address to setWhereMeasured(), revise print() methods for spectra to display address when available.
  • Revise getWhereMeasured() to consistently return a data.frame, even when a geocode is missing.
  • Add function na_geocode(), a constructor for a valid geocode data frame with all fields set to NA of correct modes.
  • Revise all logic used for geocodes for consistency in returned and set values.

Some of the intermediate development versions, never submitted to CRAN, did break some code in package ‘ooacquire’. This version of ‘photobiology’ is fully compatible with the current version of ‘ooacquire’.

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

ggpmisc 0.3.3

This version (0.3.3) fixes a bug in stat_poly_eq() introduced in ‘ggpmisc’ 0.3.2 and includes a minor revision to documentation.

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

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

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

ggpmisc 0.3.2

This version (0.3.2) adds as new features scales and statistics that help with the creation of volcano and quadrant plots, such as used with transcriptomics and metabolomics data. A few rough edges remaining in the features added in versions 0.3.0. and 0.3.1 have been polished out. Two issues raised in Bitbucket about the documentation, highlighted some incomplete explanations. These explanations have now been expanded. One important change to the documentation of statistics whose returned values may change depending on arguments is the addition of an example of the use of geom_debug() from package ‘gginnards’ showing how to print to the R console the data returned by statistics, which is the input received by the paired geometries. The User Guide needs still some work, scheduled for the next release. Package documentation is available at https://docs.r4photobiology.info/ggpmisc/ as a web site.

Plots created using the new statistics and scales are shown below. In the quadrant plot, which observations were labelled and highlighted was decided automatically based on local 2D density. Counts for each quadrant are computed on the fly. As the plot is non-the-less created using the grammar of graphics, little if any of the flexibility of ‘ggplot2’ is lost.

Quadrant plot created with packages ‘ggplot2 (3.2.1)’, ‘ggpmisc (0.3.2)’ and ‘ggrepel (0.8.1)’.
Volcano plot created with packages ‘ggplot2’, ‘ggpmisc’ and ‘ggrepel’ (very small p-values have been squished to the top edge of the plotting area).

NOTE: The new version of ‘ggpmisc’ is on its way to CRAN.

ggspectra 0.3.4

The changes from version 0.3.3-1, the current CRAN release, are:

  • Update for compatibility with code-breaking changes in ‘tidyr’ (>= 1.0.0).
  • Minor bug fixes.
  • Make autoplot.object_spct() robust to bad-input data to avoid artefacts on stacked Rfr/Afr/Tfr plots. Data are now sanitized with a warning when off-range.

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

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

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