August 2020 – Using R for photobiology

learnrbook 1.0.1

Pedro J. Aphalo 2020-08-20 2020-08-26Books, Learn R: As a Language, Package update, R packages 0

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

This is the first version submitted to CRAN for the book as published in the R Series.

Versions starting from 1.0.0 are for the book as published in the R Series. Earlier versions were for various partial drafts of the book, as pre-published through LeanPub. The book was published a few of weeks ago, but shipping has started in the last few days.

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/learnrbook-pkg/issues

photobiology 0.10.5

Pedro J. Aphalo 2020-08-20 2020-08-28Package update, R packages 0

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

Word cloud figure from LaTeX index entries

Pedro J. Aphalo 2020-08-04 2020-08-20Books, Learn R: As a Language, Publications, Tips on using R 0

I created the word cloud on the cover of “Learn R as a Language” using an R script that takes as input the file for the book index, as generated when creating the PDF from the LaTeX source files. This input file contained quite a lot of additional information, like font changes and page numbers that needed to be stripped into a clean list of words. Only later I realized that it would have been easier to produce a cleaner word list to start with. So, I first present the code revised to work with a simpler word list. This is actually tested with the book files to work. If you want to do something similar for your own book, follow the revised code in first section below. If you want to see the “hacked-up” code I really used for the cover as included in the book, it is in the second section below.