Plant Photobiology Related Functions and Data

Provides functions for quantifying visible (VIS) and ultraviolet (UV) radiation in relation to the photoreceptors Phytochromes, Cryptochromes, and UVR8 which are present in plants. It also includes data sets on the optical properties of plants.


Package 'photobiologyPlants' provides pre-defined functions for quantifying visible ('VIS') and ultraviolet ('UV') radiation in relation to the photoreceptors 'Phytochromes', 'Cryptochromes', and 'UVR8' which are present in plants. It also includes data sets on the optical properties of plants.

This package is part of a suite of R packages for photobiological calculations described at the r4photobiology web site.

News

TODO: add CRY1, PHOT1, PHOT2, BLUF and carotenoids absorbance spectra. Add chlorophyll a and b absorbance spectra.

photobiologyPlants 0.4.0

Rebuild data objects with photobiology 0.9.9, after updating scripts to create collections of spectra instead of separate objects for related data sets. Add functions for frequently used photon ratios. Remove some redundant phytochrome-related functions.

photobiologyPlants 0.3.3

Compatibility update for photobiology 0.9.1 and ggplot2 2.0.0. Use ggspectra instead of photobiologygg.

photobiologyPlants 0.3.2

Set spectral absorbance data for photoreceptors as of type "internal". Fix minor error in UVR8 data. Rebuild all data and the package under photobiology 0.8.5.

photobiologyPlants 0.3.1

Rebuild all data and the package under photobiology 0.8.0. Removed dependency on data.table.

photobiologyPlants 0.3.0

Changed naming of phytochrome related functions, which were all misnamed! Rebuilt all data and the package under photobiology 0.6.0.

photobiologyPlants 0.1.2

Updated versions of dependencies.

New generic function Pr_Ptot() for phytochrome photoequiibrium with methods for numeric values of wavelengths and source.spct objects.

Updated phytochrome chapter of User Guide.

photobiologyPlants 0.1.1

Added JaLTER additional data for spectral properties of leaves.

Rebuilt JaLTER data as it was missing the Rfr.type attribute.

photobiologyPlants 0.1.0

Removed all waveband objects as it was confusing to have waveband objects and functions for spectral absorbance data.

Rebuilt all data as .spct objects.

Edited the vignettes.

photobiologyPlants 0.0.3

Added JaLTER data for spectral properties of leaves.

photobiologyPlants 0.0.2

Added McCree's action spectra for photosynthesis in oat and amaranth as response.spct objects. Now the absorbance spectra of UVR8 and CRY2 are included as filter.spct objets.

photobiologyPlants 0.0.1

New package created by merging the CRY and PHY related apckages, and adding UVR8 functions and data. Vignettes were editted, but only the User Guide was merged.

photobiologyCry 0.1.3

Minute update to vignette.

photobiologyCry 0.1.2

Added missing import directive.

photobiologyCry 0.1.1

Added vignettes.

photobiologyCry 0.1.0

First release. Only CRY2.

photobiologyPhy 0.2.5

Now cache is created in emptyenv().

photobiologyPhy 0.2.4

Updated to adjust code to changes introduced in photobiology 0.2.16.

photobiologyPhy 0.2.3

New function Phy_reaction_rates added.

photobiologyPhy 0.2.2

Bumped required version of photobiology package.

Reference manual

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install.packages("photobiologyPlants")

0.4.1 by Pedro J. Aphalo, 6 months ago


http://www.r4photobiology.info/ https://bitbucket.org/aphalo/photobiologyplants


Report a bug at https://bitbucket.org/aphalo/photobiologyplants/issues


Browse source code at https://github.com/cran/photobiologyPlants


Authors: Pedro J. Aphalo [aut, cre]


Documentation:   PDF Manual  


GPL (>= 2) license


Depends on photobiology, photobiologyWavebands

Suggests ggplot2, knitr, ggspectra


See at CRAN