Computing-related Skills

Programing: R, (Python), C++, (Java), C, bash, awk, Perl, sh, (FORTRAN), Modula-2, Pascal, BASIC, Forth.

Text mark up: $\LaTeX$, $\TeX$, Quarto, Rmarkdown, markdown, HTML.

Revision control systems: git, svn, (cvs), rss.

Drafting: Inkscape, OpenSCAD, Adobe Illustrator.

Image/photography: Capture One, Helicon Focus, Lumariver Profile Designer, RawDigger, VueScan, LightRoom, Photoshop.

Video- and interactive tutorials: FlashBack Pro, R shiny.

IDE/GUI’s I like

WinEdt (for $\LaTeX$, $\TeX$, with embedded R code or not), RStudio (for R scripts, Quarto and Rmarkdown), GitKraken (for git).

Elsewhere

ORCID profile: https://orcid.org/0000-0003-3385-972X

Web site for the book Learn R: As a Language.

R Packages

The sources of the R packages I have published are in public Git repositories at GitHub. Out of the packages that I have authored and maintain, 15 are currently available through CRAN. The total number of package submissions (mostly updates) as author and maintainer is 230 since 2016-01-29.

I have published in CRAN one package update roughly every 15 days, or about 1.96 package updates per month, since 2016-01-29.

The most recent of these updates was published in CRAN on 2025-09-24.

📂 Click to expand a list of my packages at CRAN with the most recently updated one at the top.

R package	Title	Version	Date
ggspectra	Extensions to ‘ggplot2’ for Radiation Spectra	0.3.17	2025-09-24
photobiologyInOut	Read Spectral and Logged Data from Foreign Files	0.4.32	2025-09-24
photobiologyLamps	Spectral Irradiance Data for Lamps	0.5.3	2025-09-24
photobiologyPlants	Plant Photobiology Related Functions and Data	0.6.1	2025-09-24
photobiologySensors	Response Data for Light Sensors	0.5.2	2025-09-24
SunCalcMeeus	Sun Position and Daylight Calculations	0.1.3	2025-09-22
photobiologyWavebands	Waveband Definitions for UV, VIS, and IR Radiation	0.5.4	2025-09-14
photobiology	Photobiological Calculations	0.13.2	2025-07-31
ggpmisc	Miscellaneous Extensions to ‘ggplot2’	0.6.2	2025-07-08
ggpp	Grammar Extensions to ‘ggplot2’	0.5.9	2025-06-28
gginnards	Explore the Innards of ‘ggplot2’ Objects	0.2.0-1	2024-11-14
learnrbook	Datasets and Code Examples from P. J. Aphalo’s “Learn R” Book	2.0.1	2024-04-28
photobiologySun	Data for Sunlight Spectra	0.5.0	2024-04-01
photobiologyFilters	Spectral Transmittance and Spectral Reflectance Data	0.6.0	2024-02-27
photobiologyLEDs	Spectral Data for Light-Emitting-Diodes	0.5.2	2023-11-01

Updates under development are published at R-Universe as soon as merged or commited into the main branch in the repositories at GitHub. Two packages that depend on a commercial closed-source driver, but usable with a free runtime of the driver, are published only at R-Universe. Preliminary/experimental incomplete versions of a couple of new packages are already partly usable are also only at R-Universe and here in GitHub.

R-Universe profile: https://aphalo.r-universe.dev.

Posts and Pages at R for Photobiology

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The site R for Photobiology contains 97 posts and pages published since 2016-09-15! I have recently rebuilt the site using Quarto, and I have transferred only some of the posts originally published using WordPress. I am slowly adding more old posts, but only those that remain relevant. The figure below shows original publication date even when posts have been later updated. The source files are in a public repository at GitHub.

I have published one post or page roughly every days, or about 0.9 posts per month, since 2016-09-15.

I published the most recent post or page 220 days ago, and most recently updated a previously published one 7 days ago.

📂 Click to expand a full list of posts.

Date	Updated	Title
2025-02-16	2025-06-29	“Animated plots of spectra”
2025-01-23	2025-01-24	“Introduction to Mixed Effects Models”
2024-07-13	2024-07-13	“R Packages: Timeline of Updates”
2024-07-10	2025-01-14	“Multichannel LED arrays”
2024-06-11	2024-07-13	“Move from Wordpress to Quarto”
2024-06-01	2024-06-08	“Fitted-model labels in Markdown”
2024-05-28	2024-05-28	“Looking back 40 years”
2024-05-16	2025-01-23	“Is this a polynomial?”
2024-04-17	2024-04-17	“Annotating Plot Matrices”
2024-02-10	2024-02-10	“Repository migrated to R-Universe”
2024-01-13	2024-01-19	“ooacquire: Spectral Irradiance Algorithms”
2023-11-27	2023-11-30	“Linear Models”
2023-11-21	2023-11-21	“Theoretical probability distributions”
2023-11-18	2023-11-18	“Flow of code execution”
2023-10-30	2024-04-17	“Introduction to Data Visualization”
2023-10-21	2024-08-24	“photobiology 0.11.x”
2023-10-21	2023-10-21	“Design of Experiments”
2023-09-19	2023-10-28	“R at its simplest”
2023-08-19	2023-10-19	“Research as a process”
2023-08-19	2023-10-19	“Research as a process”
2023-08-14	2024-04-15	“Multiple comparisons with ggpmisc”
2023-08-01	2024-04-22	“Pairwise labels with ggpp”
2023-07-31	2024-08-24	“Open Access Weather and Climate Data”
2023-07-30	2023-08-01	“Timelines with ggplot2”
2023-06-25	2023-06-26	“Fitted-model labels with ggpmisc and plotly”
2023-06-24	2023-06-24	“Fitted-model labels with ggpmisc and gganimate”
2023-06-10	2024-08-24	“ooacquire >= 0.4.0”
2023-06-02	2025-08-06	“Functional analysis of spectra with photobiology and fda.usc”
2023-05-30	2023-11-27	“Model fitting in R”
2023-05-30	2023-11-27	“Randomization and independent replicates”
2023-05-28	2023-06-11	“photobiology 0.10.1x”
2023-05-24	2023-07-27	“EDA with ggplot2”
2023-05-21	2023-05-21	“I have started using Mastodon…”
2023-05-11	2023-05-13	“Plant photoreceptors”
2023-05-03	2023-07-27	“ggplot2 Basics”
2023-04-27	2023-05-10	“Spectral fluorescence with ooacquire”
2023-04-27	2024-01-11	“ooacquire: Spectral Irradiance Measurement”
2023-04-15	2023-08-01	“Weather data for Finland from FMI”
2023-04-10	2023-05-10	“ooacquire 0.3.x”
2023-03-20	2025-08-12	“OmniDriver, Java and the whims of companies”
2023-03-04	2024-02-10	“R Packages”
2023-02-28	2023-02-28	“Packages ggpmisc, ggpp and gginnards”
2023-02-28	2023-12-12	“Nudging + repulsion with ggrepel and ggpp”
2023-02-27	2023-03-29	“Website migrated to Quarto”
2023-02-27	2024-06-06	“Fitted-model labels with ggpmisc”
2023-02-25	2023-07-16	“Volcano and quadrant plots with ggpmisc”
2023-02-25	2023-02-25	“Data labels in bar plots with ggpp”
2023-02-23	2025-01-16	“ggplot insets with package ggpp”
2023-02-20	2023-08-07	“Handbook on photobiological calculations with R”
2023-02-20	2023-02-20	“A handbook of best practice in plant UV photobiology”
2023-02-19	2025-03-30	“The R for Photobiology Suite”
2023-02-19	2024-09-15	“Pedro J. Aphalo”
2023-02-18	2023-06-29	“R, RStudio and Quarto”
2023-02-18	2023-07-20	“Support”
2023-02-15	2025-08-12	“About this Website”
2023-02-03	2023-10-21	“ggspectra >= 0.3.10”
2023-01-05	2023-01-05	“photobiologyWavebands 0.5.1”
2023-01-05	2023-01-05	“photobiology 0.10.15”
2022-12-30	2024-07-10	“Are plants and plant canopies flat?”
2022-12-23	2024-06-11	“Visit to Universidad Austral de Chile”
2022-12-17	2023-04-30	“Enhancing geom_text() and geom_label()”
2022-12-05	2024-06-27	“ggpp >= 0.5.0 updates”
2022-10-18	2022-10-18	“ooacquire 0.2.6”
2022-10-15	2022-10-15	“An R marathon updating packages”
2022-10-15	2023-07-25	“photobiologyInOut 0.4.25/0.4.26/0.4.27”
2022-10-15	2022-10-15	“photobiology 0.10.14”
2022-10-15	2022-10-15	“ggspectra 0.3.9”
2022-10-15	2024-04-07	“gginnards >= 0.1.1 updates”
2022-10-05	2022-10-05	“photobiology 0.10.13”
2022-10-01	2022-10-01	“ooacquire 0.2.4 and 0.2.5”
2022-09-30	2022-09-30	“ggpp 0.4.5”
2022-08-24	2022-08-24	“Learn R: As a Language”
2022-08-13	2022-08-13	“HTML5 compliance of R packages”
2022-08-13	2022-08-13	“photobiologyWavebands 0.5.0”
2022-08-05	2024-04-07	“ggpmisc >= 0.5.0 updates”
2022-07-23	2022-07-23	“photobiology 0.10.12”
2022-07-10	2022-07-10	“photobiology 0.10.11”
2022-06-15	2022-06-15	“ggpmisc 0.4.7”
2022-05-15	2022-05-15	“photobiologyInOut 0.4.24”
2022-05-14	2022-05-14	“photobiologyLEDs 0.5.0”
2022-04-29	2022-04-29	“R 4.2.0”
2022-04-16	2022-04-16	“ggspectra 0.3.8”
2022-01-30	2024-07-10	“Instrumentation”
2022-01-30	2024-07-10	“Controlled Environment Chambers”
2022-01-29	2025-09-17	“LED-based light sources”
2021-10-20	2024-06-11	“What is plant intelligence? and what it is not?”
2021-10-17	2024-07-11	“Sensing of solar UVA by plants”
2021-10-17	2024-07-12	“Cryptochromes and stomatal opening”
2021-07-13	2024-07-12	“Perception of solar UV radiation by plants”
2020-07-12	2020-07-12	“Performance of package photobiology”
2020-04-25	2024-07-12	“UVR8 is an UV-B and UV-A photoreceptor”
2019-04-24	2019-04-24	“Benchmarking function sun_angles()”
2019-02-22	2019-02-22	“Yoctopuce modules: Spectrometer”
2019-02-21	2019-02-21	“Yoctopuce modules: Introduction”
2018-08-10	2024-09-14	“Using the Quick TUV Calculator”
2017-11-24	2024-07-12	“Article titles in the era of the internet”
2016-09-15	2023-02-21	“For those interested in optical properties”

Posts and pages at Photo Rumblings and Whispers

The Photo Rumblings and Whispers has 35 posts since 2015-10-18! I have recently rebuilt the site using Quarto, and I have transferred most of the posts originally published using WordPress. I may add one or two old posts. The figure below shows original publication date even when posts and pages have been later updated. I have updated several of the posts and pages and I aim to continue updating them as needed. The source files are in a public repository at GitHub.

I have published one post or page roughly every days, or about 0.3 posts per month, since 2015-10-18.

I published the most recent post or page 114 days ago.

📂 Click to expand a full list of posts.

Date	Updated	Title
2025-06-02	2025-06-03	“Spectral Imaging”
2025-03-07	2025-03-30	“NIR Sources for Photography”
2025-03-06	2025-03-28	“Mechanic LS720 Ring Lamp”
2024-12-20	2024-12-20	“Camera spectral response”
2024-02-11	2024-11-15	“The nitty-gritty details of macrophotography”
2023-12-05	2025-03-07	“PWM dimming and digital photography”
2023-08-28	2025-05-30	“Photographing Insects: Lenses”
2023-08-22	2023-08-22	“WordPress -> Quarto”
2023-08-21	2023-08-21	“Pedro J. Aphalo”
2023-05-13	2023-05-13	“Flexible and oversized lens hoods”
2023-04-18	2025-05-30	“About this Website”
2023-04-15	2023-05-10	“UV short-pass filter stacks”
2023-04-14	2024-02-20	“UV short-pass filters”
2023-04-12	2025-03-07	“Notes on the OM-1 (digital) camera”
2022-10-15	2025-03-06	“Small fill/video LED lights”
2022-10-15	2025-01-12	“UV-A-Induced VIS Fluorescence—Methods”
2021-10-25	2023-04-20	“Broad band VIS+NIR LEDs”
2021-08-21	2021-08-21	“Photo Rumblings and Whispers”
2021-02-01	2023-04-14	“NIR long-pass filters”
2020-09-29	2023-04-21	“Hemispherical time-lapse under a tree”
2020-06-30	2023-04-18	“Lens Adapter with Filter Drawer”
2020-06-30	2023-04-18	“Lens Adapters: Flange-to-Flange Distance”
2020-06-12	2023-04-22	“UV-cut filters”
2020-06-11	2023-04-22	“UV-IR-cut filters”
2019-08-21	2023-05-13	“A time lapse video assembled in ImageJ”
2019-07-14	2023-05-16	“Godox AD200 flash for UV, VIS and IR photography”
2019-07-14	2023-05-13	“Digital UVA-photography with M43 equipment”
2019-06-19	2023-08-24	“Lautaret”
2019-05-11	2023-05-17	“Neutral Density (ND) Filters”
2018-05-13	2023-04-14	“Camera objectives for digital UV photography”
2017-12-12	2023-05-15	“Black anodised aluminium in IR”
2017-10-28	2023-05-17	“Photographs through windows”
2017-09-13	2024-11-07	Macro extension tubes—Lens mount
2017-09-11	2024-11-08	“Macro Extension Tubes—Internal Reflections”
2015-10-18	2024-11-20	“Bracketing and merging”

Updated 2025-09-24 23:22:40.634714

This README file is based on the blog post by Athanasia Mo Mowinckel and the R code by Martin Henze.