ooacquire 0.1.6

Improvements aiming at continuing the expansion of the support of different Ocean Optics spectrometers and of  additional measurement methods.

  • Update acq_irrad_interactive() adding alternative user-interface modes, allowing users to set comment and what.measured attributes, and to construct collections of spectra.
  • Add pre-built calibrations and methods for additional FLAME-S instruments.
  • Improve algorithm for automatic tuning of integration time to achieve faster convergence.
  • Fix various minor bugs.
  • Update vignettes.
  • Test against OmniDriver 1.2.56
  • Update read_ooov_files() for compatibility with ‘readr’ >= 1.2.0 which is now required

Add support for measurement of pulsed light sources (under development)

The new features described below are under development, subject to change without previous notice and not yet well tested!! (double-check any results and please report any bugs by raising an issue!)

Implement support for measuring output from xenon flashes, including use of such flashes as light sources for measurement of spectral transmittance and reflectance. Use of multiple exposures per integration is also supported and the number of exposures stored as metadata is used during later processing. In the case of pulsed light sources the first conversion of RAW spectra is into counts per exposure, and instead of spectral irradiance spectral fluence per exposure is computed. All changes are backwards compatible with raw data acquired with earlier versions of ‘ooacquire’ and the user interface remains unaltered for the measurement of continuous light sources.

  • Add function acq_fluence_interactive() for measuring spectral fluence of pulsed light sources.
  • Add acq_fraction_pulsed_interactive() for measuring transmittance and reflectance using a pulsed light source.

Documentation website is at http://docs.r4photobiology.info/ooacquire/.

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

NOTE: This package is NOT available through CRAN.

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


  1. from the binary or source packages from the CRAN-compatible repository at http://r.r4photobiology.info/
  2. from sources retrieved from the Git repository at Bitbucket.


devtools::install_bitbucket("aphalo/ooacquire", ref = "0.1.6")

devtools::install_bitbucket("aphalo/photobiology")  # only if not automatically installed/updated

devtools::install_bitbucket("aphalo/photobiologyWavebands")  # only if not automatically installed/updated

devtools::install_bitbucket("aphalo/ggspectra")  # only if not automatically installed/updated

photobiologyInOut 0.4.18

The main changes from version 0.4.17-1 the previous CRAN release, are:

  • Track code breaking change in ‘readr’ (>= 1.2.0)
  • Fix bug in read_oo_pidata() that was preventing reading of Ocean Optics “Raspberry Pi” Flame files with a sequence header line at the top.
  • Add decoding of file header to extract integration time and number of scans to read_oo_pidata().
  • Improve decoding of file header to extract instrument settings in read_oo_jazdata().

Because of code breaking change in package ‘readr’ this version of ‘photobiologyInOut’ requires ‘readr’ >= 1.2.0 to be installed. Function read_oopi_data() from ‘photobiologyInOut’ < 0.4.18 will not work as expected under ‘readr’ >= 1.2.0. (I thank Jim Hester for making a pull request that solved the problem introduced by the change in ‘readr’.

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://bitbucket.org/aphalo/photobiologyinout/issues

ggspectra 0.3.0


Occasional R crashes when stat_label_peaks() and stat_label_valleys() are used together with ggrepel::geom_label_repel(). This is a bug in ‘ggrepel’ (= 0.8.0) at least under Windows with long vectors of labels. The bug affects these stats and the "label.peaks" and "label.valleys" annotations in all plot() methods. The bug has been reported and the author is working on a fix.

Revise to track changes in ‘photobiology’ version 0.9.24 and ‘ggplot2’ 3.0.0, which are now required.

The changes from version 0.2.4, the current CRAN release, are:

Code breaking change!

Change the names of some the values calculated by the stats defined in ‘ggspectra’ to avoid confusion with the names of ‘ggplot2’ aesthetics. (This breaks old code only if any of the renamed variables has been manually mapped using aes(), which is rather unlikely.)

Other non-code breaking changes

  • stat_label_peaks() and stat_label_valleys() now have a new parameter, label.fill which can be used to set the content of ..x.label.. and ..y.label.. for labels not labelled as peaks or valleys. The earlier default of "" is maintained.
  • Add the new stat_find_wls() and stat_find_qtys(), two new statistics useful for highlighting features in spectra.
  • Add parameter ylim to all plot() methods. By default previous behaviour is preserved.
  • Revise plot() methods to support objects with multiple spectra in long form.
  • Revise plot() methods to NOT display by default calculated numerical summaries in annotations when a plot contains multiple spectra.
  • Revise plot() methods to retrieve and validate the name of the factor used to identify multiple spectra, using as default the value stored in the attribute "idfactor" implemented in ‘photobiology’ 0.9.21 and later.
  • Add autoplot() as an alias of plot() for spectra and collections of spectra.

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

NOTE: The updated package has been submitted to CRAN.

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

photobiologyInOut 0.4.17-1

The main changes from version 0.4.16 the previous CRAN release, are:

  • Add new function read_oo_jazpc() to read transmittance (%) and reflectance (%) from processed data output by Ocean Optics’ Jaz modular spectrometer.
  • Fix bug that made CRAN tests to fail under “oldrel” : decoding of dates in fmi and TUV import functions not always returned POSIXct objects under R (=3.4.4) triggering errors in downstream code. (Possible underlying problem: class of returned values from some functions from package ‘lubridate’ seems to depend on the R version.)

Documentation web site at http://docs.r4photobiology.info/photobiologyinout/.

NOTE: This version of the package is in CRAN.

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