R 3.6.0 is coming

A new version of R will be released on 2019-04-26. One significant change is the support of HCL colour definitios and palettes. Some defaults for colour palettes are changing (for the better) but small differences may visible in how plots look compared to earlier R versions. There is a post with a summary at the R blog, and a paper arXiv:1903.0649 describing why better palettes for data plotting can be defined.

Another significant change is that serialization format 3 becomes the default. As this format can be read only by R (>= 3.5.0) when sharing files created with save() or saveRDS(), and when sharing saved workspaces one needs to make sure the recipient is using a recent version of R or override this new default to create the files to be shared using the older serialization format 2.

All the packages I maintain should work correctly under R (= 3.6.0), but if you discover a problem, please, raise an issue at bitbucket within the repository of the affected package.

ggpmisc 0.3.1

After the previous major update to ‘ggpmisc’ (0.3.0), a follow up (0.3.1) with multiple new features and smoothed rough edges for some of the features added in version 3.0.0. Package documentation is available at https://docs.r4photobiology.info/ggpmisc/ as a web site.

The enhancements in this and the previous update to ‘ggpmisc’ are made possible by changes to ‘ggplot2’ (>= 3.0.0) made while adding support for sf (simple features).

The functions in ‘ggpmisc’ (>= 0.3.1) are related to different kinds of annotations and insets in ggplots. Annotations of plots with fitted-model equations, fit diagnosis, ANOVA and summary tables, highlighting and labelling of peaks and valleys in curves, and local density-based highlighting or labelling in scatter plots. Additionally specializations of the ggplot() constructor allow on-the-fly conversion of time-series. Two new geoms join geom_table() added in version 0.3.0, geom_plot() and geom_grob(). These three geoms make it possible to add tables, ggplots and arbitrary graphical objects (grobs) as insets to plots respecting the the Grammar of Graphics paradigm.

Inset plot showing means per group.
Inset grobs

A set of new geometries produce marginal annotations: geom_x_margin_point(), geom_y_margin_point(), geom_x_margin_arrow(), geom_y_margin_arrow(), geom_x_margin_grob() and geom_y_margin_grob().

Marginal “points” showing means per group.

Another novel feature is based on the addition of two new aesthetics npcx and npcy, the corresponding scales scale_npcx_continuous() and scale_npcy_continuous(), and several new geometries that make use of then: geom_text_npc(), geom_label_npc(), geom_table_npc(), geom_plot_npc() and geom_grob_npc(). These allow to position insets and annotations relative to the dimensions of the plotting area instead of using native data units. Using "npc" units is more natural for labels or insets that are not directly related to data but that look better if positioned consistently across multiple panels or multiple separately produced plots. One improvement to the stats from earlier versions of ‘ggpmisc’ is the use of these new geoms to achieve more consistent location for insets and labels.

Quadrant counts with panels.
Fitted equations in panels with free y limits.
Inset tables at different positions in different panels.

As in the announcement of the previous version, I have included some example plots taken from the documentation of the package. In all cases annotations are generated automatically, but formatting is flexible.

NOTE: The new version of ‘ggpmisc’ will be soon submitted to CRAN .

photobiologyWavebands 0.4.3

The main changes from version 0.4.2 the previous CRAN release, are:

  • Add waveband definitions for non-standard split of the UVA band with constructors UVAsw() and UVAlw().
  • Add two new definitions of far-red as used in remote sensing: "RedEdge20" and "RedEdge40".
  • Minor updates to documentation.

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

NOTE: The updated package is available through CRAN.

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

photobiologySun 0.4.1

The main changes from version 0.4.0, the most recent version are:

  • Rebuild data objects with ‘photobiology’ 0.9.26 to fix minor bugs.
  • Replace non-ASCII characters in documentation.

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

NOTE: The updated package is available through CRAN.

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