Guane

Phylogenetic comparative methods in a local, point-and-click R app.

Guane is a R/Shiny platform for phylogenetic comparative analyses through a user-friendly and multilingual graphical interface

What Guane does

It joins a phylogenetic tree to species-level traits, makes data preparation visible, fits selected models through R scientific packages, and presents figures, numerical results, diagnostics, and editable R code, through established R packages. The interface is available in English, Spanish and Portuguese.

Guane window with the four module pills and the Phylo traits Data card showing the 20-tip example tree — Guane opens on the Phylo traits module with the bundled example tree loaded.

Four modules

Each module has its own Data card and its own analysis cards.

Phylo traits

Phylogenetic signal, PGLS, Pagel’s correlation and PGLM.

Ancestral state reconstruction

Continuous, discrete (Mk) and polymorphic traits.

Diversification

Lineage through time, constant-rate, time-varying, clade and diversity-dependent models.

SSE models

BiSSE, MuSSE, QuaSSE and hidden-state models.

Each module also has an advanced tutorial: Advanced phylo traits, Advanced ancestral states, Advanced diversification and Advanced SSE models.

Start here

You study evolution and want to run an analysis. Install and launch Guane, then take the interface tour.
You teach a comparative methods course. Start with the example data and the Data card. Each tutorial then uses the same bundled example.
You want reproducible R scripts. Read exports and reproducibility.
You already run your own data. Use the advanced tutorials to change controls beyond the defaults and judge the diagnostics.

Honest science

Scientific caution

The bundled example is synthetic. It teaches the interface; its results are not biological evidence. Before you report any result, read the scientific limitations for the method you used.