Introduction to pavo

Rafael Maia, Thomas White, Hugo Gruson, John Endler, Pierre-Paul Bitton, Chad Eliason

pavo is an R package developed with the goal of establishing 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 visualisation and analysis. It provides flexible ways to input spectral data from a variety of equipment manufacturers, process these data, extract variables, and produce publication-quality figures.

pavo was written with the following workflow in mind:

1. Organise data by importing and processing spectral and image data (e.g., to remove noise, negative values, smooth curves, etc.).
2. Analyse the resulting files, using spectral analyses of shape (hue, saturation, brightness), visual models based on perceptual data, and/or spatial adjacency and boundary strength analyses.
3. Visualise the output, with multiple options provided for exploration and analysis.

A non-exhaustive overview of the colour-pattern analysis workflow in pavo, as of version 2.0, displaying some key functions at each stage.

A comprehensive tutorial to get you started with pavo is available in the pavo handbook. In this book, we begin by detailing the importing, processing and visualisation of spectral and image data, before moving on to discussion of the flexible analyses of such data that pavo allows. Our hope is to demonstrate the flexibility of pavo, and to provide a cohesive, reproducible workflow for colour pattern analysis within R. As always, the development version of pavo can be found on github, while the stable release is available via CRAN.