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Using R for photobiology ISSN 2343-3248 (Helsinki, Finland)

  • photobiologyWavebands 0.5.0
    by Pedro J. Aphalo on 2022-08-13

    The main changes from version 0.4.5 the previous CRAN release, are: Minor edits to documentation. Rebuilt manual to comply with HTML 5. Recognize Landsat mission "L9" as equal to "L8" as wavelengths are the same. On bad arguments to parameter std the returned value is no-longer NA (a logical value) but instead a waveband object with its wavelength fields set to NA_real_, as returned by a call to waveband(). This potentially code-breaking change ensures that the class of the returned... Continue reading

  • HTML5 compliance of R packages
    by Pedro J. Aphalo on 2022-08-13

    As of R 4.0.0 there is a requirement for compliance with the HTML5 standard. Until recently, package ‘Roxygen2’, that is used to automatically generate the documentation, included in its output in some HTML4 tags that have been removed in the upgrade to HTML5. For compliance with CRAN requirements I had to rebuild packages ‘ggspectra’, ‘photobiologyWavebands’, ‘photobiologyInOut’, ‘photobiologyLamps’ and ‘photobiologyLEDs’. There were no other changes in ‘ggspectra’. Some minor changes were included in the updates to ‘photobiologyLamps’, ‘photobiologyLEDs’ and ‘photobiologyInOut’. Changes... Continue reading

  • ggpmisc 0.5.0
    by Pedro J. Aphalo on 2022-08-04

    Version 0.5.0 (previously announced as 0.4.8) brings enhancements to the annotations based on model fits. The most significant change for all users is the new convenience function use_label() that greatly simplifies the assembly of labels from components and their mapping to aesthetics. We examplify its use and some of the other new features. It also contains two changes that are not backwards compatible and that can in isolated cases break existing code (hence the version-number change into 0.5.0). In the... Continue reading

Canopy Spectral Ecology and Ecophysiology Matthew Robson's Research Group Pages

  • A walk through the awakening Arboretum
    by Matt on 2022-05-15

    We recently spent the afternoon in Viikki Arboretum, Helsinki, enjoying a spring day just as the trees were coming into leaf. Janne Halme and Bart Vandeput recorded our conversation about forests and their use of light for the Painting Energies Podcast which you can listen to below.    

  • Sunflecks in the wind
    by Matt on 2021-11-09

    Our improved capacity to measure rapid changes in the under-canopy light environment allows us to look closer at how plants use sunflecks to maximise carbon gain. Our three recent publications below take the first steps towards describing the processes involved at the canopy level. The first defines sunflecks, the second explains how they are modified … Continue reading "Sunflecks in the wind"

  • Defining the success of the Montreal Protocol as a global climate treaty
    by Matt on 2021-11-09

    With COP26 so prominently in the headlines it is prescient to consider the effects of the Montreal Protocol limiting ozone depleting chemicals as both a success in halting the increase in UV radiation & as a global effort to reduce greenhouse gas emissions. This success story is explained in our recent piece: Barnes et al., … Continue reading "Defining the success of the Montreal Protocol as a global climate treaty"

Sensory and Physiological Ecology of Plants Decoding the acquisition and use of information by wild and cultivated plant species

  • What is plant intelligence? and what it is not?
    by Pedro J Aphalo on 2021-10-20

    The opinions in this post are those of the author (Pedro J. Aphalo). The scientific discussion about “plant intelligence” was started by Anthony Trewavas nearly 20 years ago, culminating with the publication of his book Plant Behaviour and Intelligence. The use of the word “intelligence” for plants was then controversial and remains nowadays still controversial. … Continue reading "What is plant intelligence? and what it is not?"

  • How did we work out that UVR8 is a solar-UV-B plus UV-A photoreceptor?
    by Pedro J Aphalo on 2021-10-17

    What were our findings? We reported in two recent research papers and an update review, that functional UVR8 is required for the perception by plants of solar UV-radiation with wavelengths shorter than approximately 340 nm, which includes the whole UV-B band plus the shorter wavelengths in the UV-A band. In sunlight, cryptochromes are required for … Continue reading "How did we work out that UVR8 is a solar-UV-B plus UV-A photoreceptor?"

  • Brighter times for our growth chambers
    by Pedro J Aphalo on 2021-10-17

    The latest LEDs from Nichia and other suppliers are game changers. I designed a replacement light source for our Aralab Fitoclima 1200 growth chambers and Nikolai Belevich (Biotechnology Institute) assembled a prototype before the start of the pandemic. This post was written time ago, but I am publishing it now that the final design of … Continue reading "Brighter times for our growth chambers"

Photo rumblings and whispers Techniques, equipment, approaches, commentaries and more

  • Broad band VIS+NIR LEDs
    by Pedro J. Aphalo on 2021-10-25

    Broadbands LED based on a blue LED and “phosphors” have appeared in the market. One example is type SMB1N-BB450 from Roithner LaserTechnik (Vienna, Austria). The primary LED has a peak of emission at 450 nm and the spectrum as a whole covers the range 400 nm to 1000 nm. Except for the prominent blue peak the spectrum is rather flat, making it useful light source for VIS and specially NIR …

  • NIR-pass filters
    by Pedro J. Aphalo on 2021-01-31

    All the near-infrared (NIR) long-pass filters described in this post are absorptive glass filters and sold for special photography effects. All modern photography digital cameras have internal UVIR-cut filters. Use of these filters requires special film, special digital cameras or modified DSLR or DML cameras. Some filters can be used with unmodified digital cameras with very long exposure times. Few normal camera objectives are designed to work well in NIR. …

  • Hemispherical time-lapse under a tree
    by Pedro J. Aphalo on 2020-09-28

    In two earlier posts titled “Lens adapter with filter drawer” and “Lens adapters: flange-to-flange distance” I discussed how crucial it is to achieve the exact effective flange-to-flange distance when dealing with adapted objectives with a very short focal distance. I also described how I shimmed an adapter to achieve this. Recently I had an opportunity to use the Sigma 4.5mm 1:2.8 circular fisheye objective in Nikon AF mount adapted to …

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