photobiology 0.10.2

Package update / R packagesLeave a comment

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

This new update comes on the steps of the two previous ones (0.10.0, 0.10.1) and fixes a few bugs found since.

Changes from version 0.10.1 the most recent CRAN release, are:

Bugs fixed

  • color_of() was failing in some cases when it should not.
  • merge2object_spct(), merge_attributes(), interpolate_spct(), [ ] were in certain cases dropping attributes, in most but not all cases only filter.properties.
  • White LED example spectra may have had attributes inconsistently set.
  • Additional test cases were added (a suite of 4165 automatic test cases is used before release).

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

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

R 4.0.0

Tips on using RLeave a comment

R version 4.0.0 has been released today. In the case of complex ggplots there is a noticeable improvement in performance. As is normal in CRAN, packages are automatically tested. Most of the packages I have developed are in CRAN, and you can easily see their check status at any time in the page where they are listed. At the moment there are warnings under OS-X affecting the building of vignettes for many different packages in addition to several of my own, all with the same message. I suspect this problem is related to ‘knitr’ or ‘roxygen2’.

ggpmisc 0.3.4

Package update / R packagesLeave a comment

This version (0.3.4) adds to stat_poly_eq() the ability to return F-value and P-value in addition to the equation of the polynomial, R2, AIC and BIC available in earlier versions of ‘ggpmisc’. The package code and examples have been updated to avoid the use of functions and methods that have been deprecated in recent updates to ‘ggplot2’.

library(ggpmisc) # version >= 0.3.4 !!
ggplot(mtcars, aes(x = wt, y = mpg, colour = factor(cyl))) +
  geom_smooth(method="lm") +
  geom_point() +
  stat_poly_eq(formula = y ~ x,
               aes(label = paste(stat(f.value.label), stat(p.value.label), 
                                 sep = "*`,`~")),
               parse = TRUE,
               label.x.npc = "right") +
  theme_bw()

The code above produces the plot below.

Acknowlegement: This update as well as the very start of the development of this package has been triggered by some great questions posted at stackoverflow. These questions and answers can be found with a search for the tag [ggpmisc] at stackoverflow. When asking questions or help related to this package, please tag your question.

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.

photobiology 0.10.1

Package update / R packagesLeave a comment

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

Continuing with the work released in version 0.10.0, this version includes significant new functionality as well as bug fixes and the rewriting of some smelly/ugly code previously used for the dispatch of math operators and functions. It also includes performance optimizations in the computations of color definitions from wavelengths.

In brief, this update brings: 1) improved handling of conversions among quantities used to describe filters, which required adding a mechanism to store properties of filters as metadata, and revising the code behind mathematical operations and mathematical functions related to filter_spct objects; 2) Support for use of arbitrary chromaticity definitions for tagging of spectra; 3) Changes to error checking and messages, including changing several earlier warnings into errors; several important bug fixes.

Changes from version 0.10.0 the most recent CRAN release, are:

New

  • setFilterProperties(), getFilterProperties(), filter_properties() and filter_properties<-().
  • print() method for filter properties.
  • convertTfrType(), convertThickness().
  • Example data for filters updated with filter properties.
  • Afr2T(), T2Afr(), any2T(), any2A(), and any2Afr().
  • is_absorptance_based().
  • wls_at_target() method for data frames.
  • rbindspct() now allows control of metadata copying

Bugs fixed

  • Serious bug in T2Afr() was causing wrong values to be returned!!
  • Serious bug in clean.object_spct().
  • Revise find_peaks() so that arguments passed to ignore.threshold and strict are obeyed also when span = NULL.

Defunct

  • T2T(), setAfrType(), getAfrType().

Note

Full functionality of convertThickness() and convertTfrType() requires filter_spct objects to have the new "filter.properties" attribute or contain a column "Rfr" with reflectance data like object_spct objects. This means that until packages ‘photobiologyFilters’ and ‘photobiologyPlants’ are updated, these functions cannot be used with the spectral data they contain.

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

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