colRverse R packages for analysing colour in nature


Organize, visualise, and analyse spectral and spatial colour data

pavo offers a flexible and integrated workflow for working with spectral and spatial colour data. It includes functions that take advantage of new data classes to work seamlessly from importing raw spectra and images, to publication-quality visualisations, and analyses via a suite of analytical methods and visual models.
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Install: install.packages('pavo'), or the development version, via remotes::install_github("rmaia/pavo")

Cite: Maia R, Gruson H, Endler JA, White TE (2019) pavo 2: new tools for the spectral and spatial analysis of colour in R. Methods in Ecology and Evolution 10, 1097-1107.


Import spectral data and metadata

lightr offers a unified, user-friendly interface for reading UV-VIS reflectance, transmittance, and/or absorbance spectral files and associated metadata from a suite of proprietary (and generally unfriendly) file formats, across all systems.
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Install: install.packages('lightr')

Cite: Gruson H, White TE, Maia R (2019) lightr: import spectral data and metadata in R. Journal of Open Source Software.


Represent the effects of visual acuity

AcuityView offers an intuitive method for representing scenes as they may appear to viewers with less acute visual systems, either as a valuable end unto itself or as part of a broader analysis.

Install: The AcuityView 2.0 algorithm is fully implemented in pavo and can be accessed via the procimg() function, while the original package remains available via CRAN (install.packages('AcuityView')). Either way, please remember to cite and read the accompanying publication for full details.

Cite: Caves E, Johnsen S (2018) AcuityView: An r package for portraying the effects of visual acuity on scenes observed by an animal. Methods in Ecology and Evolution 9:793-797.