photobiology 0.10.1x – Using R for Photobiology

Introduction

The ‘photobiology’ package has been around for almost 10 years, and I initially created it in part reusing code in even older R scripts. I normally use it several times per week. When updating it I have tried to avoid code-breaking changes, and I have in most cases succeeded.

Package ‘photobiology’ has a long development history, consequently, few major features are missing. Instead, some computations have a more roundabout user interface than others. Thus, many of the recent changes are based on the addition of small functions that are in many cases wrappers on previously existing ones.

A classification of changes into bug fixes and enhancements is not always straightforward as only one of the bugs fixed in recent updates affected the validity of returned values, and this bug occurred as the result of changes to another package.

However, I have recently started measuring time series of spectra for my research. This has given me a different perspective than earlier and made obvious some enhancements needed to make it easier to work with and acquire 100’s if not 1000’s of spectra.

I have also aimed at smoothing some rough edges in ‘photobiology’ that originated from the long development history and others from limited time available over the years for polishing and seamlessly merging new features into old code.

The design of package ‘photobiology’ was from the beginning focused on reproducibility and storage of metadata together with data was implemented very early. On the other hand, ensuring that metadata remain valid requires updating them almost every time the data are altered by computations. The logic is not straightforward and coding and testing is time consuming. Some of the recent updates improved this aspect replacing inavlidation by updating of metadata.

Metadata

More detailed metadata for spectral data and its update during operations allow keeping a more complete trace or record of the operations applied to the data and its origin. The tricky aspect is how to treat objects created with earlier versions of the package. Once implemented in ‘photobiology’, other packages in the R for Photobiology Suite have to be updated to take full advantage of the changes, in particular the metadata of spectral objects included in the different packages need to be updated filling in the new “slots”.

Enhancements to normalization

Normalization is dependent on the physical quantity and basis of expression. So, for example a conversion of energy irradiance into photon irradiance, disrupts any pre-existing normalization. The more detailed metadata makes it now possible, and is now the default, to “refresh” or "update" the normalization after the conversion re-applying the previous normalization settings and adjusting the metadata.

Enhancements to collections of spectra

Now collections of spectra can contain member spectra each with multiple spectra stored in long format. Conversion between collections and spectra in long form and back are now are now easier, and in several cases automatic. Package ‘ggspectra’ has already been updated to take advantage of this in autoplot() methods.

New classes

Classes solute_spct and solute_mspct have been added. They can be used to store spectral coefficients of attenuation for substances. Most, but not yet all operators and methods have been implemented in ‘photobiology’ however not yet in any other package, so are still of limited use.

New methods and functions

summary() implemented for collections of spectra.
illuminance() to compute illuminance.
is_daytime() is a wrapper on day_night() returning a logical vector.
wl2wavenumber(), wavenumber2wl(), wl2frequency(), frequency2wl(), wl2energy() and energy2wl() implement conversions among quantities related to wavelength.
e_fraction() and q_fraction, Rfr_ratio(), Rfr_fraction() and Rfr_normdiff(), Tfr_ratio(), Tfr_fraction() and Tfr_normdiff() provide additional ways for summarizing or describing properties of spectra.

Bug fixes

Several bugs were fixed. Some existing but mostly inconsequential bugs became errors because of improved checks in recent R versions. Other bugs and “regressions” were triggered by changes in packages on which ‘photobiology’ depends, including some affecting time zones.

Unit tests

Unit tests were added for the new features, including new methods and functions. Tests’ code coverage is not yet reported. Even though the package includes more than 5000 unit tests, coverage is far from complete at 52%, and occasionally bugs in new code are caught late, i.e., during reverse dependencies’ checks. I aim to gradually improve test coverage in the next few releases.

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--- title: "photobiology 0.10.1x" subtitle: "Most significant recent changes" author: "Pedro J. Aphalo" date: 2023-05-28 date-modified: 2023-06-11 categories: [R Package Update] keywords: [photobiology pkg] format: html: code-link: true code-tools: true --- ## Introduction The 'photobiology' package has been around for almost 10 years, and I initially created it in part reusing code in even older R scripts. I normally use it several times per week. When updating it I have tried to avoid code-breaking changes, and I have in most cases succeeded. Package 'photobiology' has a long development history, consequently, few major features are missing. Instead, some computations have a more roundabout user interface than others. Thus, many of the recent changes are based on the addition of small functions that are in many cases wrappers on previously existing ones. A classification of changes into bug fixes and enhancements is not always straightforward as only one of the bugs fixed in recent updates affected the validity of returned values, and this bug occurred as the result of changes to another package. However, I have recently started measuring time series of spectra for my research. This has given me a different perspective than earlier and made obvious some enhancements needed to make it easier to work with and acquire 100's if not 1000's of spectra. I have also aimed at smoothing some rough edges in 'photobiology' that originated from the long development history and others from limited time available over the years for _polishing_ and seamlessly merging new features into old code. The design of package 'photobiology' was from the beginning focused on reproducibility and storage of metadata together with data was implemented very early. On the other hand, ensuring that metadata remain valid requires updating them almost every time the data are altered by computations. The logic is not straightforward and coding and testing is time consuming. Some of the recent updates improved this aspect replacing inavlidation by updating of metadata. ## Metadata More detailed metadata for spectral data and its update during operations allow keeping a more complete trace or record of the operations applied to the data and its origin. The tricky aspect is how to treat objects created with earlier versions of the package. Once implemented in 'photobiology', other packages in the _R for Photobiology Suite_ have to be updated to take full advantage of the changes, in particular the metadata of spectral objects included in the different packages need to be updated filling in the new "slots". ## Enhancements to normalization Normalization is dependent on the physical quantity and basis of expression. So, for example a conversion of energy irradiance into photon irradiance, disrupts any pre-existing normalization. The more detailed metadata makes it now possible, and is now the default, to "refresh" or `"update"` the normalization after the conversion re-applying the previous normalization settings and adjusting the metadata. ## Enhancements to collections of spectra Now collections of spectra can contain member spectra each with multiple spectra stored in long format. Conversion between collections and spectra in long form and back are now are now easier, and in several cases automatic. Package 'ggspectra' has already been updated to take advantage of this in `autoplot()` methods. ## New classes Classes `solute_spct` and `solute_mspct` have been added. They can be used to store spectral coefficients of attenuation for substances. Most, but not yet all operators and methods have been implemented in 'photobiology' however not yet in any other package, so are still of limited use. ## New methods and functions - `summary()` implemented for collections of spectra. - `illuminance()` to compute illuminance. - `is_daytime()` is a wrapper on `day_night()` returning a logical vector. - `wl2wavenumber()`, `wavenumber2wl()`, `wl2frequency()`, `frequency2wl()`, `wl2energy()` and `energy2wl()` implement conversions among quantities related to wavelength. - `e_fraction()` and `q_fraction`, `Rfr_ratio()`, `Rfr_fraction()` and `Rfr_normdiff()`, `Tfr_ratio()`, `Tfr_fraction()` and `Tfr_normdiff()` provide additional ways for summarizing or describing properties of spectra. ## Bug fixes - Several bugs were fixed. Some existing but mostly inconsequential bugs became errors because of improved checks in recent R versions. Other bugs and "regressions" were triggered by changes in packages on which 'photobiology' depends, including some affecting time zones. ## Unit tests Unit tests were added for the new features, including new methods and functions. Tests' code coverage is not yet reported. Even though the package includes more than 5000 unit tests, coverage is far from complete at 52%, and occasionally bugs in new code are caught late, i.e., during reverse dependencies' checks. I aim to gradually improve test coverage in the next few releases.