A handbook on how to do calculations used in photobiological research with R is under preparation. The handbook will describe the use of our suite of R packages and also of functions from base R and packages from CRAN. Authors are Andreas Albert, Titta Kotilainen and myself. Further details, and possibly an early draft for download will be soon available.
I will give a talk at the UseR! conference describing the packages. This will be the first public announcement of the packages, as I consider that the packages, although still under development are now ready for testing by a broader audience and careful use in research and other non-life- or health-threatening measurements and data analysis.
The abstract is available at: http://user2015.math.aau.dk/contributed_talks#153
The presentation slides will be available for download after the conference.
I have updated all the packages in the suite. This is the result testing and programming during recent weeks.
rescale() for spectra. Both functions set object attributes to flag the spectra that have been modified, and no longer are expressed in absolute units. In addition, tests were added to summary functions to disallow use of rescaled or normalized spectral data as input, with the exception of function
rbindspct() was revised to issue a warning when only some of the spectral objects are rescaled or normalized.
Changes in the code for handling ‘
Tfr.type‘ and ‘
Added new functions
New test cases were added.
photobiology 0.5.14 (not released)
New class and methods added:
object.spct, with the corresponding
check.object.spct() functions. Also functions
transmittance() are implemented. New function
absorptance() is implemented only for
object.spct objects. Objects of this class can be used to store corresponding spectral transmittance and spectral reflectance values. No operators are defined for this class as they would be ambiguous. The class attribute needs to be changed to either filter.spct or
reflector.spct before using operators, however, no data is lost in the process, or written except for the class attribute, so the class can be changed back to
object.spct if needed.
New function added:
merge.generic.spct() is a wrapper on
merge.data.table() that sets the correct class to the returned merged spectra, preserves attributes used with
.spct objects and by default merges by
Revised to use new
getTfrType() functions from package photobiology 0.5.15 which is now required. New annotation type: the string
"title" in the annotations parameter of the
plot() functions adds an automatic title to the plot.
photobiologygg 0.2.7 (not released)
object.spct objects. Updated User Guide accordingly. Added function
multiplot() based on
multiplot() example by Winston Chan in his Cookbook for R.
Added data for Petri dishes.
To avoid problems with conversions from spectral transmittance to spectral absorbance and taking into account that what can be really measured is that transmittance is below the detection limit of the instrument used, the minimum value of fractional transmittance has been forced to be 1E-5, with the meaning of 1E-5, consistently with the earlier encoding used for Schott optical glass filters.
Added data for UVMAX LEDs.
New package combining the functions and data in the old
photobiologyCry packages and adding data on optical properties of plant leaves.
Edits to the other packages are related to documentation and in some cases rebuilding of example data with the current version of package photobiology.
NOTE: Sources, and Windows binaries for R 3.1.x, are now available in the repository.