Add reference to DDD package

[richelbilderbeek]

• 1. As an initial remark, I imagine the models pirouette support have all been implemented in tested in other packages like geiger, ape, etc.? It might be interesting to list where the tree models are coming from, maybe merging Table 1 with section 6. If such models were implemented from scratch, there must evidence that they're working as intended.

Your assumption is correct: the tree models used in the Bayesian inference are all standard BEAST2 tree models. The phylogenies used in this manuscript are from the DDD [...] and ?TESS [...] R packages.

• [x] Add reference to DDD package here

[richelbilderbeek]

I also needed to look up the reference, so I could simply copy-and-paste. Sorry I stole the Issue :rainbow:

[Giappo]

@richelbilderbeek where did you mention the reference?

[richelbilderbeek]

In the response letter. I did so on the GitHub and manually sync the Overleaf and repo. Now it's on the Overleaf for sure :+1: .

[Giappo]

Sorry, I was not clear enough. Where did you mention it in the manuscript? I am asking because I am trying to understand what the reviewer exactly wants. See #82

[richelbilderbeek]

I added the reference to diversity dependence (Etienne et al., 2011) when describing we (will) use a DD tree. It's in line 981.

richel@sonic:~/GitHubs/pirouette_article$ cat -n content.tex  | egrep etienne
   [...]
   981  We'll use the diversity-dependent tree model \cite{etienne2011diversity},