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.

INSTALLATION:

  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_github("tidyverse/ggplot2")

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

rOmniDriver 0.1.12.9001

This update is an attempt to fix a bug preventing the package from loading under OS X and Linux. Not yet tested, as there seem to be additional problems under OS X at least. The remaining problem seems to be related to some component of OmniDriver being incompatible with OS X.

This is an interim patch which will be replaced in due time with a version tested under multiple OSs rather than only under Windows 10.

This package can be downloaded from the repository at this site, not from CRAN. It has system prerequisites described in the online documentation at http://docs.r4photobiology.info/rOmniDriver.

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

 

ooacquire 0.1.5

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

  • Support use of irradiance calibrations supplied by Ocean Optics
  • Add pre-built calibrations and methods for two Flame-S instruments.

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.  In addition, this version of package ‘ooacquire’ depends on versions of packages ‘photobiology’, ‘photobiologyWavebands’, ‘ggspectra’, and ‘ggplot2’ not yet available through CRAN.

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

INSTALLATION:

  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_github("tidyverse/ggplot2")

devtools::install_bitbucket("aphalo/ooacquire", ref = "0.1.5")

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