A picture of a NutNet site. I’ve no idea what site, or who took it, but it was part of the front page of the NutNet website where it was also unattributed, so I’m assuming no one minds me displaying it here too!
trait.space is based around a simple assumption: given a co-existence matrix of species (0–> species coexist always, 1–> species don’t co-exist at all) we should be able to plot all those species in 2-D space (i.e., on a piece of paper) and their distance be proportional to their coexistence. It’s perhaps not the most complicated model in the world, and it makes absolutely no attempt to link to mechanism in any way.
It does have the advantage that you can make predictions for whether species you haven’t observed together (perhaps they’re in different continents) could potentially co-exist if given the chance. Since all species are put somewhere in the 2-D space, and species are only parameterised on the basis of species that overlap (via the ‘mask’ argument), if the space in some way reflects reality then position in it should have predictive power.
I worked on all this at a recent NutNet meeting. I was quite shocked at how nice everyone in the room was: they let a horrible data parasite like me just tag along for the ride, and I’m very grateful for it. So, if you’re a member of NutNet, thank you, and here’s that code I was working on during the meeting. I’m putting this up here in the spirit of how nice and friendly those guys were; a few people have expressed surprise that I put all these things that I work on here online before publishing them. Like it has for the people at NutNet, I’m hoping that being nice pays off in the long-run.
Species across a landscape, as simulate by Boucher et al. It’s this pretty stained-glass-esque diagram that inspired me to do this!
Lots of people have written code to simulate phylogenies, and yet more have written code that simulate traits across phylogenies. I’m not claiming any great novelty in what I’ve just done, but sim.bd.tree simulates a phylogeny under given speciation and extinction rates, and sim.bd.tr.tree simulates a phylogeny, and a trait that affects speciation and extinction rate.
What I like about this is that the dependence on trait values is actually a dependence on what values of that trait other species have – in other words, it’s a niche-packing kind of model. Again, I’m not claiming any great novelty in these sorts of models (read this excellent paper, for example), but this was my first stab in what I hope will be a long stream of work. This is very raw code (a quick skim of it makes me realise a refactor would more than halve its length) but it does get the job done (I hope!).
My first impression is that this stuff isn’t very hard, so if you have any interest you should definitely give it a go. Moreover, the insight I gained from it was quite important – the shape and size of a phylogeny changes a great deal over different simulations, and while on some level I knew this it was only while checking to see if I’d messed something up that I really gathered a true appreciation for it.
Next post… either a model incorporating communities/biogeography (–> some model of allopatric speciation), or a vague attempt at fitting estimting the parameters I set once the phylogeny/traits are calculated. I have a feeling those two will be much harder!…