photobiology 0.9.20.9002

The main changes from version 0.9.20, the most recent CRAN release, are:

  • Fix bugs in copy_attributes() function (some attributes were not copied).
  • Add copying of attributes to conversion functions cps2irrad(), cps2Tfr() and cps2Rfr().
  • Add merge_attributes() function and fix bugs in handling of metadata attributes in maths operators, affecting operations between two spectral objects.
  • Implement copy of attributes and automatic _adjustment_ of the "multiple.wl" attribute in the Extraction operator [] for spectral objects.
  • Improve handling of attributes in objects containing multiple spectra in tidy (longitudinal) form. Revise setMultipleWl() to guess number of spectra when multiple.wl argument is NULL.
  • Add setIdFactor() and getIdFactor(), and add parameter idfactor to setGenericSpct() and equivalent functions.
  • Handle gracefully attempts to apply smooth_spct() method to spectra containing NA values. (Warn and return as is.)
  • Add parameter na.rm to peaks(), valleys() and related methods and functions.
  • Add parameter na.rm to normalize() methods.
  • Option "photobiology.verbose" is initialized to the value of R’s option "verbose" at the time the package is attached.
  • If option photobiology.verbose == TRUE, the presence of NA values in spectral data triggers warnings.

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 can be installed from the CRAN-like repository at https://r.r4ohotobiology.info.

Please raise issues concerning bugs or enhancements to this package through Bitbucket https://bitbucket.org/aphalo/photobiology/issues

ggpmisc 0.2.17.9903

While waiting for the release of ‘ggplot2’ 2.3.0 I am keeping two parallel branches of  ‘ggpmisc’ under development.

‘ggpmisc’ 0.2.17 is in CRAN and remains unchanged. It requires the CRAN version of ‘ggplot2’.


‘ggpmisc’ 0.2.17.9903 is in the CRAN-like repository at this site. It is as thoroughly tested as the CRAN version but contains geom_table and the stats that use this geometry, which make use of the development version of ‘ggplot2’ from Github.  ‘ggplot2’ at commit #2620 (2018-05-17) or later is needed for ‘ggpmisc’ 0.2.17.9903, while 0.2.17.9902 and earlier versions from this branch require ‘ggplot2’ at least commit #2034 (2017-02-09).

If you install ‘ggplot2’ from Github after May 17, 2018 (selecting any commit from this day onwards) you will need this new version of  ‘ggpmisc’  or the CRAN version. If you are using ‘ggplot2’ from CRAN, or an earlier commit from Github, to use this new version you will need first to install the latest development version of ‘ggplot2’ from Github.

After ‘ggplot2’ (>= 2.3.0) makes it to CRAN, a version from this enhanced branch will be submitted to CRAN.

Changes from version 0.2.17.9902 (4 May 2018)

  • Track a code breaking change (renaming of a function) in the development version of ‘ggplot2’ at commit #2620 (May 17, 2018).

NOTE: This version of the package is available from https://r.r4photobiology.info/. 


Documentation website is at https://docs.r4photobiology.info/ggpmisc/.

Please raise issues concerning bugs or enhancements to this package through Bitbucket at https://bitbucket.org/aphalo/ggpmisc/issues

photobiology 0.9.20.9001

The main changes from version 0.9.20, the most recent CRAN release, are:

  • Handle gracefully attempts to apply smooth_spct() method to spectra containing NAs. (Warn and return as is.)
  • Add parameter na.rm to peaks(), valleys() and related methods and functions.
  • Add parameter na.rm to normalize() methods.
  • Option "photobiology.verbose" is initialized to the value of option "verbose" at the time the package is attached, making ‘photobiology’ obey the --verbose command line switch of R.
  • If photobiology.verbose == TRUE, starting from this version the presence of NAs in spectral data triggers warnings.

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 can be installed from the CRAN-like repository at https://r.r4ohotobiology.info.

Please raise issues concerning bugs or enhancements to this package through Bitbucket https://bitbucket.org/aphalo/photobiology/issues

ggspectra 0.2.4-1

The changes from version 0.2.3, the current CRAN release, are:

Track changes in package ‘photobiology’ 0.9.20:

  • Avoid spurious message due to use of deprecated function.

Enhancements:

  • ggplot() methods for collections of spectra.
  • plot() methods for collections of spectra.
  • Add parameter range to all ggplot() methods for consistency with plot() methods.
  • Revise examples in the User Guides to use the new methods. Revise other documentation.

Documentation web site at http://docs.r4photobiology.info/ggspectra/.

The updated package has been accepted to CRAN and will be available soon.

Please raise issues concerning bugs or enhancements to this package through Bitbucket at https://bitbucket.org/aphalo/ggspectra/issues

ggpmisc 0.2.17/ggpmisc 0.2.17.9902

Meanwhile waiting for the release of ‘ggplot2’ 2.2.2 I am keeping two parallel branches of  ‘ggpmisc’ under development.


‘ggpmisc’ 0.2.17 is in CRAN and is mainly a bug fix but it also incorporates all enhancements made since September 2017 which do not require ‘ggplot2’ (> 2.2.1).

Changes from version 0.2.16

  • Add stat_quadrat_count() a stat that computes the number of observations in each quadrat of a plot panel ignoring grouping.
  • Fix bugs, one of which is code breaking: the names of returned parameter estimates have changed in stat_fit_tidy() now pasting "_estimate" to avoid name clashes with mapped variables.

NOTE: This version of the package is available from CRAN


‘ggpmisc’ 0.2.17.9902 is in the CRAN-like repository at this site. It is as thoroughly tested as the CRAN version but contains geom_table and the stats that use this geometry, which make use of the development version of ‘ggplot2’, at least ‘ggplot2’ >= 2.2.1.9000 (>= commit of 2017-02-09).

After ‘ggplot2’ (>= 2.2.2) makes it to CRAN, a version from this enhanced branch will be submitted to CRAN.

Changes from version 0.2.16.9003 (November 2017)

  • Fix bugs, one of which is code breaking: the names of returned parameter estimates have changed in stat_fit_tidy() now pasting "_estimate" to avoid name clashes with mapped variables.

NOTE: This version of the package is available from https://r.r4photobiology.info/. 


Documentation website is at https://docs.r4photobiology.info/ggpmisc/.

Please raise issues concerning bugs or enhancements to this package through Bitbucket at https://bitbucket.org/aphalo/ggpmisc/issues

photobiology 0.9.20

The main changes from version 0.9.19, the most recent CRAN release, are:

  • To improve clarity of user code, define wrappers for methods max(), min(), range(), midpoint(), and spread() with names with wl_ prepended (e.g. wl_max()).
  • Rename method spread() to expanse() and deprecate use of spread(). In the case of wl_expanse() and expanse() the new names prevent a name clash with tidyr::spread().
  • Redefine all ‘as.’ class-coercion functions into generic methods and add specialisations. Default behaviour remains unchanged.
  • Add class-coercion methods to and from matrix (and transfer corresponding functions from package ‘photobiologyInOut’).
  • Add function relative_AM() to compute relative air mass from sun elevation.
  • Add functions for calculation of saturated water vapour pressure from air temperature water_vp_sat() and dew point from water vapour pressure water_dp().

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 can be installed from CRAN.

Please raise issues concerning bugs or enhancements to this package through Bitbucket https://bitbucket.org/aphalo/photobiology/issues

photobiology 0.9.19

The main changes from version 0.9.18, the most recent CRAN release, are:

  •  Fix bug in sun_angles() that resulted in wrong azimuth values returned in some circumstances. (Bug introduced in version 0.9.12 when the astronomy code was overhauled in December 2016.)
  • Fix bug in day_night() that resulted in a small time shift when a datetime was passed instead of a date as an argument to parameter date.
  • Fix bug in irrad(), e_irrad() and q_irrad() methods for collections of spectra which was resulting in arguments passed to parameter quantity being silently ignored.
  • Add explicit support for optional parallel execution of apply functions, and methods for collections of spectra. Apparently of no use under Windows 10, even for large collections of spectra.
  • Revise documentation.

Documentation web site at http://docs.r4photobiology.info/photobiology/.

NOTE: The updated package will be available soon from CRAN.

Please raise issues concerning bugs or enhancements to this package through Bitbucket at https://bitbucket.org/aphalo/photobiology/issues

photobiologyLEDs 0.4.3

The main changes from version 0.4.2, the current CRAN release, are:

  • Add data for additional LEDs, and rebuild all data objects with current version of  ‘photobiology’ package (0.9.18).
  • Add a “what.measured” attribute to old data when possible.
  • Fix bug in one example.
  • Revise User Guide and object documentation and remove the Data Catalogue vignette.

Documentation web site at http://docs.r4photobiology.info/photobiologyLEDs/.

NOTE: The updated package is available from CRAN.

Please raise issues concerning bugs or enhancements to this package through Bitbucket at https://bitbucket.org/aphalo/photobiologyLEDs/issues

photobiology 0.9.18-1

The main changes from version 0.9.17, the current CRAN release, are:

  • Add functions add_attr2tb(), when_measured2tb(), lon2tb(), lat2tb(), geocode2tb() and what_measured2tb().
  • Add a formal parameter "attr2tb" to all summary methods for collections of spectra, used to automatically call add_attr2tb() to add attributes to their output.
  • Add calibration_spct class and its methods. Update all operators and maths functions to support this new class.
  • Add calibration_mspct class and its methods.
  • Fix bug in calculation of solar time of day which could result in values > 24 h.
  • Fix a bug in the extraction operator for spectral objects (could lead to infinite recursion in rare occasions).
  • Fix wrong value returned in some cases by is_tagged() due to a bug in the definition of  tag().
  • Revise vignettes and documentation.
  • Rebuild some of the example data objects adding metadata attributes.

Documentation web site at http://docs.r4photobiology.info/photobiology/.

NOTE: The updated package is available from CRAN.

Please raise issues concerning bugs or enhancements to this package through Bitbucket at https://bitbucket.org/aphalo/photobiology/issues

ggspectra 0.2.3

The changes from version 0.2.2, the current CRAN release, are:

Track changes in package ‘photobiology’ 0.9.18:

  • Add plot.calibration_spct()
  • Add ggplot.calibration_spct()

Enhance handling of plot titles:

  • Add utility function ggtitle_spct()
  • Update all plot() methods to allow flexible contents in automatic titles including setting of the time zone used for displaying times.
  • Revise vignettes and help pages.

Documentation web site at http://docs.r4photobiology.info/ggspectra/.

The updated package has been accepted by CRAN and will be available in a few days time.

Please raise issues concerning bugs or enhancements to this package through Bitbucket at https://bitbucket.org/aphalo/ggspectra/issues

photobiology 0.9.17.9003

The main changes from version 0.9.17, the current CRAN release, are:

  • Add functions add_attr2tb(), when_measured2tb(), lon2tb(), lat2tb(), geocode2tb() and what_measured2tb().
  • Add a formal parameter "attr2tb" to all summary methods for collections of spectra, used to automatically call add_attr2tb() to add attributes to their output.
  • Add calibration_spct class and its methods. Update all operators and maths functions to support this new class.
  • Add calibration_mspct class and its methods.

Documentation web site at http://docs.r4photobiology.info/photobiology/.

NOTE: The updated package is available from the repository at this site

Please raise issues concerning bugs or enhancements to this package through Bitbucket at https://bitbucket.org/aphalo/photobiology/issues

ggspectra 0.2.2.9002

The changes from version 0.2.2, the current CRAN release, are:

Track changes in package ‘photobiology’ 0.9.17.9003:

  • Add plot.calibration_spct()
  • Add ggplot.calibration_spct()

Enhance handling of plot titles:

  • Add utility function ggtitle_spct()
  • Update all plot() methods to allow flexible contents in automatic titles including setting of the time zone used for displaying times.
  • Revise vignettes.

Documentation web site at http://docs.r4photobiology.info/ggspectra/.

The updated package is available from the repository at this web site.

Please raise issues concerning bugs or enhancements to this package through Bitbucket at https://bitbucket.org/aphalo/ggspectra/issues