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.
Occasional R crashes when
stat_label_valleys() are used together with
ggrepel::geom_label_repel(). This is a bug in ‘ggrepel’ (= 0.8.0) at least under Windows with long vectors of labels. The bug affects these stats and the
"label.valleys" annotations in all
plot() methods. The bug has been reported and the author is working on a fix.
Revise to track changes in ‘photobiology’ version 0.9.24 and ‘ggplot2’ 3.0.0, which are now required.
The changes from version 0.2.4, the current CRAN release, are:
Code breaking change!
Change the names of some the values calculated by the stats defined in ‘ggspectra’ to avoid confusion with the names of ‘ggplot2’ aesthetics. (This breaks old code only if any of the renamed variables has been manually mapped using
aes(), which is rather unlikely.)
Other non-code breaking changes
stat_label_valleys()now have a new parameter,
label.fillwhich can be used to set the content of
..y.label..for labels not labelled as peaks or valleys. The earlier default of
- Add the new
stat_find_qtys(), two new statistics useful for highlighting features in spectra.
- Add parameter
plot()methods. By default previous behaviour is preserved.
plot()methods to support objects with multiple spectra in long form.
plot()methods to NOT display by default calculated numerical summaries in annotations when a plot contains multiple spectra.
plot()methods to retrieve and validate the name of the factor used to identify multiple spectra, using as default the value stored in the attribute
"idfactor"implemented in ‘photobiology’ 0.9.21 and later.
autoplot()as an alias of
plot()for spectra and collections of spectra.
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
The main changes from version 0.4.16 the previous CRAN release, are:
- Add new function
read_oo_jazpc()to read transmittance (%) and reflectance (%) from processed data output by Ocean Optics’ Jaz modular spectrometer.
- Fix bug that made CRAN tests to fail under “oldrel” : decoding of dates in fmi and TUV import functions not always returned
POSIXctobjects under R (=3.4.4) triggering errors in downstream code. (Possible underlying problem: class of returned values from some functions from package ‘lubridate’ seems to depend on the R version.)
Documentation web site at http://docs.r4photobiology.info/photobiologyinout/.
NOTE: This version of the package is in CRAN.
Please raise issues concerning bugs or enhancements to this package through Bitbucket at https://bitbucket.org/aphalo/photobiologyinout/issues
Changes from version 0.9.23, the most recent CRAN release, is:
- Fix major bug in internally used method
merge_attributes(), accidentally introduced in version 0.9.23, which in certain cases triggered fatal errors when using operators or other methods taking two spectra as arguments. This also affected indirectly package ‘ooacquire’.
- Add method
wls_at_target()implementing search and interpolation of wavelengths at which the spectral quantity matches a target value. This method is implemented for all spectral classes and collections of spectra, except
object_spctand corresponding collections.
- Add (experimental) support for spectral measurements where the exposure time is dependent on the light source instead of on the integration time settings in the spectrometer such as when measuring xenon-tube flashes.
If you are using version 0.9.23, please, do update to this new version, to avoid being affected by the now fixed bug.
Documentation web site at http://docs.r4photobiology.info/photobiology/ includes all help pages, with output from all examples, and vignettes in HTML format.
NOTE: The updated package is in CRAN.
Please raise issues concerning bugs or enhancements to this package through Bitbucket https://bitbucket.org/aphalo/photobiology/issues