Fix “breaking” bug causing fatal errors after package ‘Rcpp’ was updated, and many non-breaking but important bugs.

Several improvements aiming at continuing the expanding the support to different Ocean Optics spectrometers, and to the documentation.

  •  Fix serious bug that triggered a fatal error with current version of ‘Rcpp’.
  • Add functions choose_sr_interactive() and choose_ch_interactive() and revise acq_irrad_interactive() and acq_fraction_interactive() to make use of them.
  •  Add fields to the instrument descriptor to store the numeric coefficients in addition to functions for non-linearity and wavelength calibrations.
  • Add pre-built calibrations and methods for our Jaz instrument.
  • Update and expand the vignettes and examples.

This version of the package is available through the r4photobiology repository  and through Bitbucket.

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

Book and package: Learn R …as you learnt your mother tongue

Book cover

Book cover

Book draft of 2017-05-14 and ‘learnrbook’ package 0.0.2.

My book titled Learn R …as you learnt your mother tongue is gradually approaching completion, but the text is not yet polished. Today’s milestone is that the first version of the companion R package has been accepted for distribution through CRAN.

In the draft version I uploaded today, published as earlier ones through Leanpub, approximately 95% of the book content is included. Today’s version differs from earlier ones in that as now the original datasets and files used in examples are now in package ‘learnrbook’, the example code has been edited to make use of it. The package is since yesterday in CRAN. The updated version of the book also tracks improvements in version 0.2.15 of my package ‘ggpmisc’, which is since today in CRAN.

The PDF of this updated draft of the book is available at http://leanpub.com/learnr for whatever price you would like to pay for it (including for free). However, paying even as little as 1€ for your copy would go a long way towards supporting the expenses of running this web site.

R 3.4.0 released

R 3.4.0 was released some days ago. A compatibility update to RStudio is also available.

The repositories at this site and obviously also at CRAN now contain package binary distributions for R 3.4.x and R 3.3.x.

One major change in this release is that the JIT (just in time) compiler is enabled by default. I have not done any benchmarking yet.

I have written a page explaining how to upgrade your R installation.

The code examples in my book Learn R …as you learnt your mother tongue continue to work as expected. However not all the package updates for R 3.4.0 are yet in CRAN. In package ‘gganimate’ function gg_animate() has been renamed gganimate().

The code examples in our book R for Photobiology: Theory and recipes for common calculations run without problems. Due to recent updates to the packages in my R for Photobiology Suite, used in the book examples, fewer warnings than earlier are triggered.

ooacquire 0.1.2

This is the second release of package ‘ooacquire’. It is an important update as it include bug fixes and enhancements which have some (minor) effect on the calculated spectral values. The update also removes some spurious warnings and has additional documentation, although not yet in final form.This package allows the acquisition of spectral data from spectrometers from Ocean Optics connected through the OmniDriver run-time, which is available at no cost from Ocean Optics. The current version implements several corrections and measuring protocols unavailable elsewhere in a single modular framework. Some of these cannot be used off-the-shelf as they require the characterisation and calibration of each individual spectrometer, so as to obtain usable values for constants. However, once these constants are available they can be passed as data arguments without need to modify the package itself. Functions are provided for spectral irradiance, spectral transmittance and spectral reflectance measurements. As transmittance and reflectance measurements are normally done relative to reference objects the calibration requirements are less involved than for spectral irradiance.

The package is available through r4photobiology repository.

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