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aphalo (Pedro J. Aphalo) · GitHub

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aphalo/README.md

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 246 since 2016-01-29.

I have published in CRAN one package update roughly every 16 days, or about 1.92 package updates per month, since 2016-01-29.

The most recent of these updates was published in CRAN on 2026-07-05.

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

R package Title Version Date
ggpmisc Miscellaneous Extensions to ‘ggplot2’ 1.0.0 2026-07-05 21:40:02 UTC
ggpp Grammar Extensions to ‘ggplot2’ 0.6.1 2026-07-02 22:10:10 UTC
ggspectra Extensions to ‘ggplot2’ for Radiation Spectra 0.4.0 2026-03-17 22:50:03 UTC
photobiology Photobiological Calculations 0.14.2 2026-03-15 06:10:19 UTC
photobiologyInOut Read Spectral and Logged Data from Foreign Files 0.4.33 2026-03-13 23:10:02 UTC
photobiologySensors Response Data for Light Sensors 0.5.3 2026-03-13 21:50:02 UTC
gginnards Explore the Innards of ‘ggplot2’ Objects 0.2.0-2 2025-11-12 15:20:02 UTC
photobiologyPlants Plant Photobiology Related Functions and Data 0.6.1-1 2025-10-04 15:40:02 UTC
photobiologyLEDs Spectral Data for Light-Emitting-Diodes 0.5.3 2025-09-27 23:10:09 UTC
photobiologySun Data for Sunlight Spectra 0.5.1 2025-09-27 17:10:03 UTC
photobiologyFilters Spectral Transmittance and Spectral Reflectance Data 0.6.1 2025-09-24 20:30:02 UTC
photobiologyLamps Spectral Irradiance Data for Lamps 0.5.3 2025-09-24 15:30:02 UTC
SunCalcMeeus Sun Position and Daylight Calculations 0.1.3 2025-09-22 05:10:50 UTC
photobiologyWavebands Waveband Definitions for UV, VIS, and IR Radiation 0.5.4 2025-09-14 05:10:18 UTC
learnrbook Datasets and Code Examples from P. J. Aphalo’s “Learn R” Book 2.0.1 2024-04-28 11:40:02 UTC

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

The site R for Photobiology contains 101 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 36 days, or about 0.8 posts per month, since 2016-09-15.

I published the most recent post or page 121 days ago, and most recently updated a previously published one 10 days ago.

📂 Click to expand a full list of posts.

Date Updated Title
2026-04-12 2026-04-12 “R for Photobiology”
2026-01-11 2026-01-11 “Visit to CAAS Beijing”
2025-08-19 2026-08-01 “Digital light sensors”
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 2026-04-23 “Migration 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 2026-04-24 “Is This a Polynomial?”
2024-04-17 2024-04-17 “Annotating Plot Matrices”
2024-04-01 2024-04-01 “README learnr folder”
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 2026-06-05 “Fitted-model labels with ggpmisc and plotly or ggiraph”
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 2026-04-21 “ggplot2 Basics”
2023-04-27 2023-05-10 “Spectral fluorescence with ooacquire”
2023-04-27 2026-02-02 “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 2026-04-22 “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 2026-04-23 “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 2026-04-23 “Geometries geom_text_s() and geom_label_s()”
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 37 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 107 days, or about 0.3 posts per month, since 2015-10-18.

I published the most recent post or page 65 days ago.

📂 Click to expand a full list of posts.

Date Updated Title
2026-06-07 2026-06-07 “Technical Photography”
2026-06-06 2026-06-06 “Data Analysis and Visualization”
2025-06-02 2025-06-03 “Spectral Imaging”
2025-03-17 2026-06-15 “DXO PureRaw 4, 5 and 6”
2025-03-07 2025-03-30 “NIR Sources for Photography”
2025-03-06 2026-06-07 “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”
2023-08-21 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 2026-06-11 “UV short-pass filters”
2023-04-12 2025-11-29 “Notes on the OM-1 (digital) camera”
2022-10-15 2025-03-06 “Small fill/video LED lights”
2022-10-15 2025-11-22 “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 2026-06-11 “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 2026-06-07 “UV-IR-cut filters”
2019-08-21 2025-11-24 “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 2026-06-07 “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 2026-08-11 22:49:52.605389

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

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