Tag: R

ooacquire 0.1.6

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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

from Data to Viz (external link)

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from data to Viz is a new web site related to data analysis and R. Its aim is to make it easier to choose among different types of data visualisations. It looks beautiful, is easy to navigate, includes “trees” displaying a classification of visualizations and multiple individual examples with the corresponding R code.  Highly recommended!

To access the website and/or to buy the printed poster visit from Data to Viz.

 

R 3.5.0 and spaces in file paths

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The R 3.5.0 update introduced a bug, at least under MS-Windows. File paths containing spaces are truncated at the first space character, leading to errors like:


Fatal error: cannot open file 'C:\Users\<user-name>\AppData\Roaming\WinEdt': No such file or directory

for a file path like 'C:\\Users\\<user-name>\\AppData\\Roaming\\WinEdt Team\\WinEdt 10\\<file-name>' or 'C:/Users/<user-name>/AppData/Roaming/WinEdt Team/WinEdt 10/<file-name>'.

This bug breaks, among other things, the ‘RManager’ extension of the editor WinEdt. I would expect this to cause various other surprising errors after upgrading to R 3.5.0.

This bug is already corrected in the patched version of R 3.5.0 available through CRAN. For Windows, the most recent patched R version can be downloaded from https://cran.r-project.org/bin/windows/base/rpatched.html and installed as usual.

ooacquire 0.1.5

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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