Add §"Working with phylogenetic data"

[ms609]

List packages that handle phylogenetic data, incorporating suggestions from #33.

Closes #33.

[ms609]

A section to this effect is a useful addition and doesn't introduce much duplication. Before merging, it would be good if others could check that:

• (i) the package descriptions are intelligible;
• (ii) there are other packages that might be included against these themes (particularly the simulation of data);
• (iii) there are other themes/methods that might be included under this heading

[hlapp]

Should this include rphenoscape too?

[willgearty]

I'd say it seems to fit @hlapp

[willgearty]

Should this be a ### heading? The table of contents near the top lists the first ## heading as follows:
Working with trees in R: packages dedicated to the handling, manipulation, and visualization of phylogenetic data
It seems to me that this new category would fall under that?

[willgearty]

In fact, I wonder if the top heading should be changed to "Working with phylogenetic data in R", and then this new subcategory could be changed to e.g., "Working with other phylogenetic data in R"?

[ms609]

Hmm, good point; I usually use "phylogenetic data" to refer to the observations from which phylogenies are reconstructed, but in the ToC it is almost used as though the trees themselves are the phylogenetic data.

In my view the new content represents a step before reconstructing trees, so fits logically before tree reconstruction in the current structure. On this view, perhaps we ought to move the current "working with trees in R" section after "Building trees in R" (you can't work with trees if you haven't (re)constructed them yet!).

[willgearty]

Ah yes, that makes a lot more sense. I could see this new category then remaining a separate category (the first category?), followed by the current second category and then the current first category? (perhaps with some editing of the ToC?)