Photobiological Calculations

Definitions of classes, methods, operators and functions for use in photobiology and radiation meteorology and climatology. Calculation of effective (weighted) and not-weighted irradiances/doses, fluence rates, transmittance, reflectance, absorptance, absorbance and diverse ratios and other derived quantities from spectral data. Local maxima and minima: peaks, valleys and spikes. Conversion between energy-and photon-based units. Wavelength interpolation. Astronomical calculations related solar angles and day length. Colours and vision. This package is part of the 'r4photobiology' suite, Aphalo, P. J. (2015) .

Waveband Definitions for UV, VIS, and IR Radiation

Constructors of waveband objects for commonly used biological spectral weighting functions (BSWFs) and for different wavebands describing named ranges of wavelengths in the ultraviolet (UV), visible (VIS) and infrared (IR) regions of the electromagnetic spectrum. Part of the 'r4photobiology' suite, Aphalo P. J. (2015) .

Datasets and Code Examples from P. J. Aphalo's "Learn R" Book

Data, scripts and code from chunks used as examples in the book "Learn R: As a Language" by Pedro J. Aphalo. ISBN 9780367182533 (pbk); ISBN 9780367182557 (hbk); ISBN 9780429060342 (ebk).

Extensions to 'ggplot2' for Radiation Spectra

Additional annotations, stats, geoms and scales for plotting "light" spectra with 'ggplot2', together with specializations of ggplot() and autoplot() methods for spectral data and waveband definitions stored in objects of classes defined in package 'photobiology'. Part of the 'r4photobiology' suite, Aphalo P. J. (2015) .

Miscellaneous Extensions to 'ggplot2'

Extensions to 'ggplot2' respecting the grammar of graphics paradigm. Statistics: locate and tag peaks and valleys; label plot with the equation of a fitted polynomial or other types of models; labels with P-value, R^2 or adjusted R^2 or information criteria for fitted models; label with ANOVA table for fitted models; label with summary for fitted models. Model fit classes for which suitable methods are provided by package 'broom' and 'broom.mixed' are supported. Scales and stats to build volcano and quadrant plots based on outcomes, fold changes, p-values and false discovery rates.

Grammar Extensions to 'ggplot2'

Extensions to 'ggplot2' respecting the grammar of graphics paradigm. Geometries: geom_table(), geom_plot() and geom_grob() add insets to plots using native data coordinates, while geom_table_npc(), geom_plot_npc() and geom_grob_npc() do the same using "npc" coordinates through new aesthetics "npcx" and "npcy". Statistics: select observations based on 2D density. Positions: radial nudging away from a center point and nudging away from a line or curve; combined stacking and nudging; combined dodging and nudging.

Automatically Position Non-Overlapping Text Labels with 'ggplot2'

Provides text and label geoms for 'ggplot2' that help to avoid overlapping text labels. Labels repel away from each other and away from the data points.

Explore the Innards of 'ggplot2' Objects

Extensions to 'ggplot2' providing low-level debug tools: statistics and geometries echoing their data argument. Layer manipulation: deletion, insertion, extraction and reordering of layers. Deletion of unused variables from the data object embedded in "ggplot" objects.

Spectral Data for Light-Emitting-Diodes

Spectral emission data for some frequently used light emitting diodes available as electronic components. Part of the 'r4photobiology' suite, Aphalo P. J. (2015) .

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. Part of the 'r4photobiology' suite, Aphalo P. J. (2015) .