Update

The new class cps_spct has been added to package photobiology 0.6.2, together with corresponding functions and operators. A suitable plot() method has been added to package photobiologygg 0.3.1. The reason for adding one additional class is that counts-per-second from array spectrometers can be directly used in the calculation of spectral transmittance and spectral reflectance. Objects of this class are expected to be used to hold linearised spectral counts per second with a wavelength calibration applied but no pixel gain calibration applied. The need for this class became apparent during the development of a new version of package MayaCalc for data acquisition from spectrometers, but we think that it could be more generally useful.

Another addition to both packages is the new time.unit attribute value "exposure" with the meaning of the time-integrated response for the whole irradiation or exposure event.

The documentation was tidied-up in both packages, and the User Guides expanded.

NOTE: Sources, and Windows binaries for R 3.2.x, are now available in the repository.

Major update

All packages in the suite have been updated.
This update includes several changes which are not backwards compatible:

  1. S3 classes and methods, and several other functions have been renamed. Dots have been replaced by underscores.
  2. Rescale() has been renamed to fscale().
  3. All dummy packages which have been maintained for backwards compatibility have been removed: photobiologyCry, photobiologyPhy, photobiologyUV, and photobiologyVIS are no longer available and photobiologyPlants and photobiologyWavebands should be used instead.
  4. The code has been fixed so eliminate most warnings during checking.
  5. A new vignette Upgrade Guide has been added to package photobiology.

Being such a major update all version numbers have been increased in the second digit. Current versions are:
photobiology 0.6.1, and version 0.3.0 for all the remaining packages.

Package photobiologyInOut also was modified in several respects, but still cannot be considered stable. The other packages, will not suffer major changes for the first public release of the suite.

NOTE: Please, do upgrade only at a time when you have enough time to upgrade old scripts and old data objects, and solve possible problems!

NOTE: Sources, and Windows binaries for R 3.1.x, and R 3.2.x are now available in the repository.

At the moment the repository at https://www.r4photobiology.info/R is responding very slowly, the mirror at http://www.mv.helsinki.fi/aphalo/R is faster.

Updates

photobiologyInOut 0.2.1
Added function to import spectral irradiance data from files generated by Ocean Optics’ Jaz spectrometer.
Shortened the names of most functions.

Expanded the User Guide.

Not backwards compatible, and interface still subject to change. Not fully tested. Do compare results against software known to work correctly before using these functions for real measurements.

photobiologyWavebands 0.2.6

Edited functions Red(), Far_red() and Plant_bands(), adding additional definitions as found in the plant photobiology scientific literature.

Edited the User Guide to reflect these changes.

NOTE: Sources, and Windows binaries for R 3.1.x, are now available in the repository.