I had a nail. @rOpenSci had the hammer. Photo by Zorro.
The helpful folks over at rOpenSci have come up with exactly the tool I needed, exactly when I needed it.
I had a list of plant species, and I needed to determine which had ever been categorized as “invasive” and which had not. The taxize package easily lets you check 5 global databases, curated by the Encyclopedia of Life, to assess invasive status. Done!
Then I needed to know how invasiveness was distributed across a phylogenetic tree. Given this list of species, how were they related? Well taxize has a tool for building trees from a species list (though currently limited to plants – but all the cool kids are working on plants anyways, right?). Then all I had to do was fiddle with the tree plot a bit to get it to display which species were known to be invasive, based on the database searches. Boom! Done!
The rOpenSci folks liked my tree, so I passed along my code, and now it is all tidied up as a use case for all the world to see! Check it! My original tree is below – sorry for the colors, this was just for my notes.
That’s my tree!
