As our package ‘photobiologyInOut’ (versions >= 0.4.15) supports the automatic import of the files returned by the Quick TUV Calculator, we show here how to produce such files, and link to an example showing how to import and plot them in R.
Improvements aiming at continuing the expansion of the support of different Ocean Optics spectrometers and of additional measurement methods.
acq_irrad_interactive() adding alternative user-interface modes, allowing users to set comment and what.measured attributes, and to construct collections of spectra.read_ooov_files() for compatibility with ‘readr’ >= 1.2.0 which is now requiredAdd 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.
acq_fluence_interactive() for measuring spectral fluence of pulsed light sources.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:
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
The main changes from version 0.4.17-1 the previous CRAN release, are:
read_oo_pidata() that was preventing reading of Ocean Optics “Raspberry Pi” Flame files with a sequence header line at the top.read_oo_pidata().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
The changes from version 0.3.0, the current CRAN release, are:
plot() and autoplot() methods for classes source_spct and response_spct which prevented plotting of spectra with the time.unit attribute set to any value different from "second".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