Packages

In the list of packages conforming the photobiology suite I have marked in dark green those packages whose status I consider as release candidates (RC in programmers slang means that they are feature frozen and only bugs will be fixed before public release). I have marked in light green those packages which are at beta stage of development, no major features will be added before release, and existing functionality will not be changed significantly before release, but in most cases additional example data will be added. I have marked in orange those packages which are at alpha stage, in other words for which functionality and to some extent user interface will change before release. I have marked in red those packages on which I have done only minimal work, and which are unlikely to be included in the first release of the suite. I have marked in blue those packages which are “frozen” and no longer updated or actively maintained.

Packages publicly available (under development, but  I aim at new versions being backwards compatible in their use, whenever possible).

  • r4photobiology (convenience package that loads packages ‘photobiology’, ‘photobiologyWavebands’, ‘photobiologyInOut’, and ‘ggspectra’, described below.) (git repo, documentation web site)
  • photobiology (all base functions and class definitions) (CRANgit repo, documentation web site)
  • ggspectra (extensions to package ‘ggplot2‘ version >= 2.2.0 for plotting spectral data) (CRANgit repo, documentation web site)
  • photobiologyInOut (functions for importing data from spectrometers and simulation models, and exchanging data with other packages) (CRANgit repo, documentation web site)
  • photobiologyWavebands (predefined waveband objects) (CRANgit repo, documentation web site)
  • photobiologyPlants (functions and data related to the photobiology of plants) (CRAN, git repo, documentation web site)
  • photobiologyFilters (spectral transmittance data for commonly used filters) (git repo, documentation web site)
  • photobiologyReflectors (spectral reflectance data for common objects and materials) (git repo)
  • photobiologyLamps (spectral data for commonly used lamps) (git repo)
  • photobiologyLEDs (spectral data for commonly used LEDs) (git repo)
  • photobiologySensors (spectral data for common broadband sensors) (git repo)
  • photobiologySun (spectral data for solar radiation) (git repo)
  • lamps (function for simulating the light field under a bank of fluorescent tubes) (git repo)
  • ooacquire (spectral data acquisition with Ocean Optics spectrometers)
  • rOmniDriver (an R wrapper to the OmniDriver SDK of Ocean Optics. Can be used with the free OmniDriver runtime available from the Ocean Optics web site to acquire data and control their array spectrometers) (git repo)
  • ggpmisc (Extensions to package ‘ggplot2‘ version >= 2.2.0 for plotting diverse data types) (CRANgit repo, documentation web site)
  • learnrbook (Datasets used in the book “Learn R …as you learnt your mother tongue” by Pedro J. Aphalo)

Packages planned:

  • photobiologyDaylight (data for sunlight and shadelight, under different weather conditions)

Packages at end-of-life:

  • photobiologygg (replaced by package ‘ggspectra’; functions adding functionality to package ggplot2 version <= 1.01) (git repo)
  • MayaCalc (replaced by package ‘ooacquire’; advanced corrections and calibration protocols for Maya2000 Pro array spectrometers)

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