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R for photobiology (Pedro J. Aphalo)

R 3.5.0 and spaces in file paths
The R 3.5.0 update introduced a bug, at least under MS-Windows. File paths containing spaces are truncated at the first space character, leading to errors like: Fatal error: cannot open file 'C:\Users\\AppData\Roaming\WinEdt': No such file or directory for a file path like 'C:\\Users\\\\AppData\\Roaming\\WinEdt Team\\WinEdt 10\\' or […]
Pedro J. Aphalo
ggspectra 0.2.4-1
The changes from version 0.2.3, the current CRAN release, are: Track changes in package ‘photobiology’ 0.9.20: Avoid spurious message due to use of deprecated function. Enhancements: ggplot() methods for collections of spectra. plot() methods for collections of spectra. Add parameter range to all ggplot() methods for consistency with plot() methods. Revise … […]
Pedro J. Aphalo
ggpmisc 0.2.17/ggpmisc
Meanwhile waiting for the release of ‘ggplot2’ 2.2.2 I am keeping two parallel branches of  ‘ggpmisc’ under development. ‘ggpmisc’ 0.2.17 is in CRAN and is mainly a bug fix but it also incorporates all enhancements made since September 2017 which do not require ‘ggplot2’ (> 2.2.1). Changes from version 0.2.16 … […]
Pedro J. Aphalo

SenPEP (Pedro J. Aphalo)

Update on: ‘Article titles in the era of the internet’
Exponential growth in read counts continues. As ResearchGate seems to assign subjects to papers based on the subjects in the author’s profile, rather than the paper itself, all sorts of astonishing achievements are being reported for this very modest one-page-long book review… and for myself… Last week’s achievements as example. (It would have been nice if … […]
Pedro J Aphalo
Article titles in the era of the internet
A currently ongoing surprising event affecting what I considered one of my least important articles (, has made me rethink how search engines and the internet affect the impact of publications. Among web site developers “SEO” is considered a very important factor in being successful in “drawing traffic or page reads” […]
Pedro J Aphalo

CanSEE (T. Matthew Robson)

Finnish Growers’ Association highlight our research into the greenhouse light environment
  Some results from our Academy of Finland Key Funding project were recently presented by Titta Kotilainen in the Finnish Growers’ Association “Puutarha & Kauppa” magazine. Climate screens that are typically used inside greenhouses to manage humidity and temperature alter … Continue reading → […]
Herlin Foundation Funding for Twinkle Solanki
Congratulations to Twinkle Solanki who has received a year’s grant from the Herlin Foundation to continue her PhD “Improving estimates of carbon assimilation and light use by forests by scaling processes from the leaf to canopy levels”. This means that all … Continue reading → […]
Blue light advances bud burst in branches of three deciduous tree species under short-day conditions
Congratulations to Craig Brelsford on the acceptance of the first publication towards his PhD, which will shortly be published in Trees: Structure and Function.  But in particular, a big thank you to the two reviewers for this article for Trees … Continue reading → […]
Skype a Scientist Q&A: Climate Change with Antonio Serna School Alicante, Spain
Here’s a transcript of some of the best questions in Spanish and translated into English: about research into climate change followed by a discussion of what it’s like working in science. Aquí abajo hay una síntesis de la charla. Cuestiones de carácter técnico (Climate … Continue reading → […]

Photo rumblings (Pedro J. Aphalo)

Pinholes in NIR and UVA
Using the E-M1 converted to full spectrum with the Pinhole Pro objectives is possible. Using a 58 mm NIR filter (Hoya R72) attached to the front of the 11 mm Pinhole Pro S11 worked fine, with no increase in vignetting. Using the StraightEdgeU 52 mm or Baader U-filter 2″  with a step-down ring blocked the … Continue reading Pinholes in NIR and UVA → […]
Pedro J. Aphalo
Pinhole objectives arrived today
Introduction Pinholes need to be very small to provide a useful image. Consequently the corresponding f-values are small, in most cases f:100 or smaller. This results in either very long exposures, or requires the use of very high ISO values. As we will see in the example images this is less of a problem than … Continue reading Pinhole objectives arrived tod […]
Pedro J. Aphalo
Camera objectives for UV photography
I have been testing some objectives for their UV transmission using LEDs as sources of radiation. I developed a protocol for such tests. Although used in this example to measure the spectral sensitivity of a camera sensor, the protocol can be easily adapted for the measurements of biological action spectra. A draft report of these … Continue reading Camera o […]
Pedro J. Aphalo
MIDOPT filters
For those interested in photography “beyond the visible”, some of the filters available from Midwest Optical Technologies Inc. under the MIDOPT brand name should be very interesting. They are distributed in European countries by Stemmer AG. Both companies are specialised in the supply of machine vision equipment. What adds additional interest is that filters […]
Pedro J. Aphalo
Timelapse in the “dark”
Infrared (940 nm) The night of a plant, 11 h 20 min condensed into a 10 s-long video. Only source illumination were two LEDs emitting infrared radiation at 940 nm (LED Engin LZ1-10R702). Camera: Olympus E-M1, converted to full spectrum, adapted Soligor 35 mm f:3.5 objective at f:8, Heliopan RG780 long pass filter on lens. … Continue reading Timelapse in the […]
Pedro J. Aphalo

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