Handbook on photobiological calculations with R

Book coverA handbook on how to do calculations used in photobiological research with R has been under preparation for a long time. An  80% complete version has been available through LeanPub for several years. The book describes the use of our suite of R packages and also of functions from base R and a few other packages available through CRAN. I (Pedro J. Aphalo) am the lead author, while Andreas Albert, T. Matthew Robson and Titta Kotilainen have contributed text and examples and feedback.

Although we haven’t had time to finish writing the book, I have been checking that the code examples work with current versions of R and packages. Rather recently I made small edits to a few code chunks that had stopped working and uploaded the new version of the PDF file to LeanPub.

Some minutes ago I tried to build all examples with R 4.2.o, a major update to R released some days ago. R 4.2.o contains a bug, that unluckily prevents a couple some examples in the book from running under MS-Windows. The already available patched version of R 4.2.0 solves this problem. Anyway, this bug affects only a very specific use related to data acquisition.

The book is sold for the amount the buyer wishes to pay, including getting it for free.

R 4.0.3

A minor update to R was released recently as version 4.0.3. As always it is recommended to keep R up-to-date. R for photobiology packages and their dependencies are not affected by this are previous updates and pass checks on R >= 3.6.0.

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

R 4.0.1 and R 4.0.2

Two minor updates to R were released recently. R 4.0.1 contained a major bug under MS-Windows (affecting R-commander), so it was very soon followed by R 4.0.2 that fixes the problem. As always it is recommended to keep R up-to-date. R for photobiology packages and their dependencies are not affected and pass checks on R >= 3.6.0.

photobiologyFilters 0.5.0

The main changes from version 0.4.4, the current CRAN version, released 18 months ago are:

  • Code breaking! Names of some member spectra in the collection have been modified. In most cases, the change is the addition of the name of the supplier (e.g. filters.mspct$RG9 has become filters.mspct$Schott_RG9 ).
  • Rebuild data objects with current version of  ‘photobiology’ package (0.9.28).
  • Add data for MIDOPT filters released in the mean time.
  • Add data for an assortment photography filters of various brands.
  • Add data for the old “WG” UV pass filters from Schott, which have been replaced some years ago by “N-WG” filters.
  • Improve the metadata and documentation.

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

NOTE: The updated package is in CRAN.

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

ggplot2 3.0.0

As the updated ‘ggplot2’ 3.0.0 became today available through CRAN, I will soon submit the new package ‘gginnards’ and a new enhanced version of package ‘ggpmisc’. That the first digit of the version of ‘ggplot2’ was increased reflects the fact that this is a major update to ‘ggplot2’ with some code breaking changes. The versions of packages ‘ggpmisc’ and ‘ggspectra’ now in CRAN are compatible with both ‘ggplot2’ 2.2.1 and 3.0.0. See https://ggplot2.tidyverse.org/ for details on ‘ggplot2’ updates.

 

ggpmisc roadmap

I am planning to split the ‘ggpmisc’ package into two separate packages for the next CRAN release. The low level functions and methods useful mainly to programmers will be transferred to a new package with possible name ‘ggpguts’ or ‘gginspector’. The remaining stats, geoms and scales, will remain in ‘ggpmisc’.

photobiologySun 0.4.0

The main changes from version 0.3.7, the most recent version are:

  • Group reference spectra into a collection.
  • Rebuild all data objects adding metadata.
  • New vignette.
  • Because of some object name changes this update can break code developed with earlier non-CRAN releases.

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

NOTE: The updated package is available through CRAN.

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

photobiologySensors 0.4.0

This is the first version in CRAN.

The main changes from version 0.3.3 the most recent version are:

  • Reorganise data storage into a single collection of spectra.
  • Add character vectors of names for use in sub-setting the collection.
  • This is a code-breaking update, that will require revision to match the new data structure and naming scheme.

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

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/photobiologySensors/issues

photobiologyLamps 0.4.2

The main changes from version 0.4.1, the most recent version, released 16 months ago are:

  • Add data for several fixed-spectrum lamps.
  • Add data for a variable spectrum four-channel WRGB LED bulb.
  • Add indexing vectors and rename some of the existing ones.
  • Update documentation and vignette.

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

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/photobiologylamps/issues

photobiologyFilters 0.4.4

Version 0.4.4 is the first version to be available through CRAN.

The main changes from version 0.4.3, the most recent version, released 16 months ago are,

  • Put all spectra into a single collection object and provide vectors of names to access them based on different criteria.
  • Rebuild data objects with current version of  ‘photobiology’ package (0.9.18).
  • Add data for MIDOPT filters.
  • Add data for an assortment of window glass types as used by CIE.
  • Fix bugs.
  • Translate User Guide to R markdown and remove the Data Catalogue vignette.

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

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/photobiologyfilters/issues