The model in this post is based on the one in Cameron et al. (2009), improving how seed dispersal is modelled and the dynamics are visualised. I have become a bit obsessed with hemiparasitic plants recently. When I found Cameron et al.’s paper on how Yellow Rattle can create interesting spatial dynamics in grasslands¹, I got quite excited. I have been learning python this year so I thought I may as well try to replicate their model.

I rather skirted around the notion of "taxonomic concepts" in the previous post, partly because it's easy to end up with trying to have a concept for each utterance every made by a taxonomist, and that doesn't seem, er, scalable. So, I have a more limited view of a taxonomic concept, namely a name attached to some data.

Modelling taxa is a bit trickier. I've sketched my ideas for distinguishing name strings and taxonomic names earlier. That's the easy stuff. What about "taxonomic concepts" and "OTUs"? As a first pass, I'm looking at linking taxon names to classifications via GUIDs.

Time to make some notes. I've been playing with using Sematic Mediawiki to create a database of taxonomic names, literature, specimens, sequences, and phylogenies. One challenge is to come up with simple ways to model these entities, in a way that makes both data entry simple and querying as simple as possible. Some things are straightforward. For example, a publication can be modelled like this:OK, I've ignored the attributes.