Software

We enjoy testing and extending methods for understanding the world, and prefer such tools to be as open and accessible as possible. To that end we have developed and contributed to various pieces of software, including the below which are actively maintained.

pavo

An R package for the organization, visualisation, and analysis of spectral and spatial colour data.
Rafael Maia, Hugo Gruson, Thomas White

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.

If you need help with the package, take a look at the documentation and extended vignettes, and keep an eye on the latest news for changes. We’re always happy to receive feedback and suggestions via personal email or the mailing list: r-pavo@googlegroups.com. If you have a bug to report, we’d appreciate it if you could also include a reproducible example when possible.

Current release: 2.9.0

Development version: 2.10.0

Installation: The current release of pavo is available on CRAN and can be installed using install.packages('pavo') within R. The bleeding-edge version is on github, and is most easily installed with the remotes package, by running remotes::install_github('rmaia/pavo').

Citation: 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.

lightr

Import spectral data and metadata in R
Hugo Gruson, Thomas White, Rafael Maia

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.

Current release: 1.6.0

Development version: 1.7.0

Installation The current release of lightr is available on CRAN, and can be installed using install.packages('lightr') within R. The development version can be installed via GitHub using remotes::install_github("ropensci/lightr").

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

metadat

Meta-analysis datasets in R
Thomas White, Daniel Noble, Alistair Senior, W. Kyle Hamilton, Wolfgang Viechtbauer

metadat contains a large collection of meta-analysis datasets, useful for teaching purposes, illustrating/testing meta-analysis methods, and validating published analyses.

Current release: 1.0.0

Development version: 1.1.0

Installation The current release of metadat is available on CRAN, and can be installed using install.packages('metadat'). The development version is available via GitHub using remotes::install_github("wviechtb/metadat").

Gadgets

We often build our own bits & pieces for experiments, which is made simpler with the help of 3D printing. Below are some odds & ends I’ve created that might be of use. For 3D printable models I’ve included the style (.sty) files, which are ready to be edited (if desired), ‘sliced’, and sent to your printer of choice. If you don’t have access to a printer but feel something may be useful to you feel free to get in touch (especially students & ECRs) and I’ll happily try and help as time & resources allow.

Choice arena

A small arena with slots in the walls to hold 30 mm2 pieces of card. Useful for walking colour/stimulus choice assays. The download includes a six-card and eight-card version.

Download (.zip file) contains:

  • col_arena_6.sty: six-card version of the arena.
  • col_arena_8.sty: eight-card version of the arena.

Artificial ‘flowers’ with base

A set of nine ‘flower’ discs and a base to hold them. Can be topped with coloured card for flying choice assays for various pollinators. Note the flowers have a small well in the centre, for holding liquids or materials (like cotton) to wick liquids. The flowers and base are included separately.

Download (.zip file) contains:

  • flower_base.sty: the nine-hole base.
  • flower_set.sty: set of nine ‘flowers’, as depicted.