photobiologyLamps 0.5.0

This is a major and code-breaking update. Naming conventions have been slightly changed and several new spectra have been added. Previously included spectra have in most cases been recomputed and may slightly differ from earlier versions of the same data. In part this was done to reduce the size of the data objects, making it possible to include more spectra while keeping the size of the package reasonable. Continue reading

photobiology 0.10.9

The package documentation web site at https://docs.r4photobiology.info/photobiology/ includes a changelog with information for each release since version 0.1.0.

Changes from version 0.10.8 the most recent CRAN release, are:

  • Update smooth_spct() methods so that NA values in wl.range are handled as documented and consistently with other methods in the package.
  • Update to accommodate code-breaking change in ‘dplyr’ (>= 1.0.8).

NOTE: Version 0.10.9 is in CRAN.

Please raise issues concerning bugs or enhancements to this package through GitHub at https://github.com/aphalo/photobiology/issues

photobiologyWavebands 0.4.5

Package documentation web site at: https://docs.r4photobiology.info/photobiologyWavebands/

The main changes from version 0.4.4 the previous CRAN release, are:

  • Major bug fixed! The definitions of UVA1() and UVA2()  were swapped.
  • Git repository moved to GitHub

NOTE: The updated package is on its way to CRAN.

Please raise issues concerning bugs or enhancements to this package through Bitbucket at https://github.com/aphalo/photobiologyWavebands/issues/

 

photobiology 0.10.8

The package documentation web site at https://docs.r4photobiology.info/photobiology/ includes a changelog with information for each release since version 0.1.0.

This release includes bug fixes and a minor enhancement:

Changes from version 0.10.7 the most recent CRAN release, are:

  • Update functions normalize(), setNormalized() and getNormalized(), and add new function getNormalization(). These changes implement the storage in attribute normalization of the operation done.
  • Fix bug in mat2mspct() affecting matrices with more than 26 columns and without colnames set.
  • Fix a major bug in rowwise methods for collections of spectra.

NOTE: Version 0.10.8 is on its way to CRAN.

Please raise issues concerning bugs or enhancements to this package through GitHub at https://github.com/aphalo/photobiology/issues

photobiologyInOut 0.4.23

Fifteen months since the previous release, this update adds support for one new spectrometer from LI-COR and multiple spectrometers from Wasatch Photonics. Updates to the tidyverse were triggering deprecation notices which are now avoided. Updates to package ‘photobiology’ revealed some minor bugs that are also fixed. Unnecessary progress messages during file realing and text scanning have been silenced.

The main changes from version 0.4.22 the previous CRAN release, are:

  • Add parameters na and ... to read_csi_data().
  • Add function read_wasatch_csv() supporting data import from long form CSV spectrum files saved by Wasatch’s Enlighten program.
  • Add function read_li180_txt() supporting data import from files saved by the LI-180 handheld array spectrometer from LI-COR.
  • Avoid spurious progress messages when reading files.
  • Track various changes in the tidyverse that deprecated functions used in this package.
  • Fix bugs in some imports from ‘photobiology’.
  • Move git repository from Bitbucket to Github.
  • Set up Github action for CRAN-checks on Windows, OS X and Ubuntu.
  • 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://github.com/aphalo/photobiologyinout/issues

photobiology 0.10.7

The package documentation web site at https://docs.r4photobiology.info/photobiology/ includes a changelog with information for each release since version 0.1.0.

This release includes enhancements related to the computations of reference evapotranspiration:

Changes from version 0.10.6 the most recent CRAN release, are:

  • Add function ET_ref() for computation of reference
    evapotranspiration, implementing the original FAO56 formulation of the Penman-Monteith method as well as modified in 2005 for tall and short vegetation according to ASCE-EWRI. The formulation is that for ET expressed in mm/h, but modified to use as input flux rates in W/m2 and pressures expressed in Pa.
  • Add function net_radiation() that computes the long wave net radiation balance if downwelling long wave radiation is available and otherwise estimates it.
  • Add function irrad_extraterrestrial() that computes down-welling solar irradiance on a horizontal plane at the top of the atmosphere based on the Sun to Earth distance.
  • Revise function sun_angles() to also return the Sun to Earth distance.

NOTE: The updated package is on its way to CRAN.

Please raise issues concerning bugs or enhancements to this package through GitHub at https://github.com/aphalo/photobiology/issues

photobiology 0.10.6

The package documentation web site at https://docs.r4photobiology.info/photobiology/ includes a changelog with information for each release since version 0.1.0.

This release includes fixes to several minor bugs that were reported during the last seven months. In addition to these fixes new specializations of existing methods were added to improve the consistency across the different methods and classes. The Git repository was recently moved from Bitbucket to GitHub and continuous integration using Git actions set up.

Changes from version 0.10.5 the most recent CRAN release, are:

  • Fix boundary-condition bug in msmsply().
  • Fix handling of na.rm = TRUE in find_peaks().
  • Revise the computation of the default for dyn.range in cps2Tfr() and cps2Rfr() so that it takes into account the relative signal in
    the reference spectrum.
  • Add parameter missing.pixs to cps2irrad() so that corrupted too-short spectra can be converted if the location of missing pixels
    is known.
  • Add row-wise summaries for raw_mspct and cps_mspct objects.
  • Add support of multiple spectra in long form to irrad(), e_irrad(), q_irrad(), q_ratio(), e_ratio(), qe_ratio(), eq_ratio(), absorbance(), absorptance(), trasmittance(), reflectance() methods.
  • Add warning for handling of multiple spectra in long form to integrate_spct() method.

NOTE: The updated package is on its way to CRAN.

Please raise issues concerning bugs or enhancements to this package through GitHub at https://github.com/aphalo/photobiology/issues

photobiologySensors 0.5.0

Package documentation web site at: https://docs.r4photobiology.info/photobiologySensors/

The main changes from version 0.4.0, the current CRAN version:

New

  • Rename member spectra by prepending suppliers’ names and rebuild sensors.mspct with ‘photobiology’ (0.10.5) which is now required.
  • Add data for angular responses saved in a list of data frames named diffusers.lst.
  • Update the User Guide.

Backward incompatibilities

Code breaking because of renaming of members of the collection of sensor response spectra.

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/photobiologySensors/issues

photobiologyFilters 0.5.2

Package documentation web site at: https://docs.r4photobiology.info/photobiologyFilters/

The main changes from version 0.5.1, the current CRAN version, released 10 months ago are:

New

  • Add data for some Chinese absorptive filters from Yixing Purshee Optical Elements Co., Ltd.
  • Add thickness metadata for several photography filters.
  • Add reflectance data for various materials (previously contained in package ‘photobiologyReflectors’.
  • Add refraction index data.
  • Update the User Guide.

Fixed

  • Correct wrong thickness metadata in PC and PET_G sheet spectra.

Backward incompatibilities

Use of package ‘photobiologyReflectors’, which was never released through CRAN, is deprecated as the same data are now contained in ‘photobiologyFilters’ (>= 5.2).

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/photobiologyfilters/issues

ggspectra 0.3.7

Package documentation web site at: https://docs.r4photobiology.info/ggspectra/

The changes from version 0.3.6, the current CRAN release, are:

New

  • Track and profit from updated ‘photobiology’ (>= 0.10.4), with (>= 0.10.5) now required.
  • Use performance-optimized computation for colors from wavelengths.
  • Improve stat_wl_strip() performance by simplifying data before plotting.
  • Add support for plotting action spectra (preliminary).
  • Update y-axis scales to support scaled and normalized data.
  • Update y-scales to generate more compact axis labels and use IUPAC-recommended symbols.
  • Update x-axis- and y-axis scales to allow users to override the default label text.
  • Implement scale_y_Afr_continuous() for absorptance spectra.
  • Implement scale_y_mult_continuous() for calibration spectra.
  • Implement scale_y_Tfr_continuous() for transmittance spectra, to complement the internal and total versions earlier available.
  • Implement scale_y_A_continuous() for absorbance spectra, to complement the internal and total versions earlier available.
  • Implement scale_y_Rfr_continuous() for reflectance spectra, to complement the specular and total versions earlier available.
  • Update autoplot() methods to generate more compact axis labels (preliminary).
  • Update autoplot() methods to to natively support facets (partial).
  • Update stat_wb_box() adding parameter box.height (default behavior unchanged).

Bugs fixed

  • Fix a documentation example that stopped working because of changes to ‘ggplot2’.

Backward incompatibilities

  • Although this update should not break any code, the plots created will in some cases differ slighttly from those created with earlier versions. These changes affect the formatting of axis labels, and are readily visible.
  • Colors may differ very slightly while stat_wl_strip() draws fewer rectangles (in most cases these changes are barely visible).

NOTE: The updated package is on its way to CRAN.

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

photobiology 0.10.5

Package documentation web site at: https://docs.r4photobiology.info/photobiology/

This update adds a new attribute to objects of class response_spct to enable storage of metadata to distinguish action spectra from response spectra. All other changes are tweaks to make use easier or are minor bug fixes, which do not add important new functionality.

Changes from version 0.10.4 the most recent CRAN release, are:

New

  • Implement attribute "response.type" to distinguish between response spectra and action spectra stored in response_spct objects.
  • Add methods setResponseType() and getResponseType().
  • Add method drop_user_cols() to remove user-defined columns from spectra.
  • Add method collect2mspct() and rename method uncollect() into uncollect2spct().
  • Add convenience function spct_metadata() to query the value of metadata attributes.
  • Revise add_attr2tb() expanding support to all metadata attributes.
  • Revise smooth_spct() methods adding new parameter wl.range.
  • Revise compare_spct() function to accept scaled and normalized spectra with a warning (instead of triggering an error).

Fixed

  • Make the pre-computed color data private.
  • Revise rbindspct() to gracefully handle duplicate member names in its input.
  • Revise smooth_spct() methods to fix bug in handling of strength in "custom" method.

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

photobiology 0.10.4

Package documentation web site at: https://docs.r4photobiology.info/photobiology/

This release was triggered by a bug that made the package fail CRAN checks with an ERROR.

Changes from version 0.10.3 the most recent CRAN release, are:

New

  • Improve performance of color-related computations.

Fixed

  • Bugs affecting boundary cases in the new color related functions.
  • Bad code in one example in documentation. This was causing ERRORs to be reported in CRAN checks.

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