photobiologyInOut 0.4.19

The main changes from version 0.4.18 the previous CRAN release, are:

  • Track reverted previous code breaking change in ‘readr’ (>= 1.3.0).

Because of a code breaking change in package ‘readr’ this version of ‘photobiologyInOut’ requires ‘readr’ >= 1.3.0 to be installed. Function read_oopi_data() from ‘photobiologyInOut’ < 0.4.19 will not work as expected under ‘readr’ >= 1.3.0. (I thank Jim Hester for making a pull request that solved the problem introduced by the change in ‘readr’.)

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

NOTE: This version of the package is on its way to CRAN.

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

photobiology 0.9.25

Changes from version 0.9.24, the most recent CRAN release, are:

  • Fix bug in merging of attributes which was causing errors in operations between spectra which had specific differences in their attributes.
  • Fix incompatibility with tibble (>= 2.0.0).

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 on its way to CRAN.

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

ooacquire 0.1.6

Improvements aiming at continuing the expansion of the support of different Ocean Optics spectrometers and of  additional measurement methods.

  • Update acq_irrad_interactive() adding alternative user-interface modes, allowing users to set comment and what.measured attributes, and to construct collections of spectra.
  • Add pre-built calibrations and methods for additional FLAME-S instruments.
  • Improve algorithm for automatic tuning of integration time to achieve faster convergence.
  • Fix various minor bugs.
  • Update vignettes.
  • Test against OmniDriver 1.2.56
  • Update read_ooov_files() for compatibility with ‘readr’ >= 1.2.0 which is now required

Add support for measurement of pulsed light sources (under development)

The new features described below are under development, subject to change without previous notice and not yet well tested!! (double-check any results and please report any bugs by raising an issue!)

Implement support for measuring output from xenon flashes, including use of such flashes as light sources for measurement of spectral transmittance and reflectance. Use of multiple exposures per integration is also supported and the number of exposures stored as metadata is used during later processing. In the case of pulsed light sources the first conversion of RAW spectra is into counts per exposure, and instead of spectral irradiance spectral fluence per exposure is computed. All changes are backwards compatible with raw data acquired with earlier versions of ‘ooacquire’ and the user interface remains unaltered for the measurement of continuous light sources.

  • Add function acq_fluence_interactive() for measuring spectral fluence of pulsed light sources.
  • Add acq_fraction_pulsed_interactive() for measuring transmittance and reflectance using a pulsed light source.

Documentation website is at http://docs.r4photobiology.info/ooacquire/.

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

NOTE: This package is NOT available through CRAN.

This version of the package is available through the r4photobiology repository  and through Bitbucket.

INSTALLATION:

  1. from the binary or source packages from the CRAN-compatible repository at http://r.r4photobiology.info/
  2. from sources retrieved from the Git repository at Bitbucket.
devtools::install_github("tidyverse/ggplot2")

devtools::install_bitbucket("aphalo/ooacquire", ref = "0.1.6")

devtools::install_bitbucket("aphalo/photobiology")  # only if not automatically installed/updated

devtools::install_bitbucket("aphalo/photobiologyWavebands")  # only if not automatically installed/updated

devtools::install_bitbucket("aphalo/ggspectra")  # only if not automatically installed/updated

photobiologyInOut 0.4.18

The main changes from version 0.4.17-1 the previous CRAN release, are:

  • Track code breaking change in ‘readr’ (>= 1.2.0)
  • Fix bug in read_oo_pidata() that was preventing reading of Ocean Optics “Raspberry Pi” Flame files with a sequence header line at the top.
  • Add decoding of file header to extract integration time and number of scans to read_oo_pidata().
  • Improve decoding of file header to extract instrument settings in read_oo_jazdata().

Because of code breaking change in package ‘readr’ this version of ‘photobiologyInOut’ requires ‘readr’ >= 1.2.0 to be installed. Function read_oopi_data() from ‘photobiologyInOut’ < 0.4.18 will not work as expected under ‘readr’ >= 1.2.0. (I thank Jim Hester for making a pull request that solved the problem introduced by the change in ‘readr’.

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

NOTE: This version of the package is on its way to CRAN.

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

ggspectra 0.3.1

The changes from version 0.3.0, the current CRAN release, are:

  • Fix major bug in plot() and autoplot() methods for classes source_spct and response_spct which prevented plotting of spectra with the time.unit attribute set to any value different from "second".

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

ggspectra 0.3.0


BUG WARNING

Occasional R crashes when stat_label_peaks() and 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.peaks" and "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_peaks() and stat_label_valleys() now have a new parameter, label.fill which can be used to set the content of ..x.label.. and ..y.label.. for labels not labelled as peaks or valleys. The earlier default of "" is maintained.
  • Add the new stat_find_wls() and stat_find_qtys(), two new statistics useful for highlighting features in spectra.
  • Add parameter ylim to all plot() methods. By default previous behaviour is preserved.
  • Revise plot() methods to support objects with multiple spectra in long form.
  • Revise plot() methods to NOT display by default calculated numerical summaries in annotations when a plot contains multiple spectra.
  • Revise 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.
  • Add 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

photobiologyInOut 0.4.17-1

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 POSIXct objects 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

photobiology 0.9.24

Changes from version 0.9.23, the most recent CRAN release, are:

  • 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 raw_spct, chroma_spct and object_spct and 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 the light output from 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

photobiologyInOut 0.4.16

The main changes from version 0.4.15 the previous CRAN release, are:

  • Revise read_fmi_dat() to extract date from file header and save the file header to the spectral object as a comment.
  • Add new function read_fmi2mspct() for reading spectral irradiance data.
  • Bug fix: decoding of dates in fmi import functions for daily data not always returned POSIXct objects triggering errors in downstream code.

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

NOTE: The updated package is in CRAN.

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

photobiology 0.9.23

Changes from version 0.9.22, the most recent CRAN release, is:

  • Bug fix: Ensure that getWhenMeasured() always returns an object of class POSIXct. Avoids occasional crashes in ‘PhotobiolgyInOut’.
  • Add scale.factor as formal parameter to methods irrad(), q_irrad(), e_irrad(), response(), q_response() and e_response(). Previous behaviour remains the default.
  • Change default value for parameter idx in the various summary methods for collections of spectra. Also add parameter idx to “add attributes to tibble” methods. The new default argument does not affect the default behaviour of the methods. The change in handling of idx = NULL, the old default might break old code in exceptional cases when idx = NULL was passed explicitly in user code instead of relying on it being the default.
  • Rewrite the “get” methods for attributes using a simpler, and possibly faster approach.
  • Add parameter sep to function convolve_each(). Previous behaviour remains the default.

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

photobiologyInOut 0.4.15

The main changes from version 0.4.14 the previous CRAN release, are:

  • Add read_yoctopuce_csv() to read CSV files from YoctoPuce modules.
  • Add read_qtuv_txt() to read spectral data output files from the on-line Quick TUV calculator.
  • Add read_tuv_usrout2mspct() wrapper of read_tuv_usrout() and subset2mspct() useful to import multiple TUV simulations into a collection of spectra.
  • Revise read_tuv_usrout() with new formal parameter ozone.du and fix a bug in the setting of "where.measured" attribute.
  • Revise all read functions so that they store the header of the imported file as a vector of character strings to attribute "file.header".

The main changes from version 0.4.13 an earlier CRAN release, are:

  • Implement class coercion methods (“as.” methods) to complement earlier functions, tracking changes in ‘photobiology’ 0.9.20.
  • Move coercion methods from and to matrix objects to ‘photobiology’ 0.9.20.
  • Update to track API changes in ‘colorSpec’ 0.7-3.
  • Translate vignette to Rmarkdown.

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

NOTE: The updated package is in CRAN.

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