pavo

An R package for the spectral and spatial analysis of color patterns

Currently maintained by Thomas White and Hugo Gruson.

About

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:

• Organise data by importing and processing spectra and images (e.g., to remove noise, negative values, smooth curves, etc.).
• 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.
• Visualise the output, with multiple options provided for exploration, presentation, and analysis.

Need more information, or help with the package?

• Take a look at the package documentation for detailed examples and discussion.
• Check out the latest news for changes and updates.
• Need help or advice and can’t find what you’re looking for? Head over to the colRverse discussion board and feel free to post a message.
• If all else fails (or you don’t have a GitHub account), email Tom!

Citing pavo

pavo went through several major revisions since its first release in 2013, and two publications describe this work.

When citing the package pavo in publications, please include both citations:

Maia R, Eliason C, Bitton P, Doucet S, Shawkey M (2013). “pavo: an R Package for the analysis, visualization and organization of spectral data.” Methods in Ecology and Evolution, 4, 609-613. doi:10.1111/2041-210X.12069 https://doi.org/10.1111/2041-210X.12069.

Maia R, Gruson H, Endler J, White T (2019). “pavo 2: new tools for the spectral and spatial analysis of colour in R.” Methods in Ecology and Evolution, 10(7). doi:10.1111/2041-210X.13174 https://doi.org/10.1111/2041-210X.13174.

Install

This is the development page for pavo. The stable release is available from CRAN. Simply use install.packages("pavo") to install.

If you want to install the bleeding edge version of pavo, you can:

• use the remotes package:

# install.packages("remotes")
remotes::install_github("rmaia/pavo")

• download files from GitHub and install using $R CMD INSTALL or, from within R:

install.packages(path, type = "source", repos = NULL)