Pull Phylogeny from PhyloPic

[keesey]

Pull Phylogeny from PhyloPic

[sckott]

Hey @keesey, Thanks for the help on this.

What's an example of a call to get a phylogeny? The example call for that method doesn't seem to give a phylogeny. Or is the phylogeny the inclusions part of the result? Do you have an option to return a newick or other format instead?

[sckott]

@keesey Let me know if you want me to rename the repo - i.e., is fylopic too close to phylopic?

[keesey]

The example has the supertaxa flag set to immediate -- simply change it to all and it will pull the whole lineage back to (presumably) Panbiota. (And, yes, inclusions stores all the arcs for the phylogenetic graph.)

It is bit awkward -- you have to pull the lineage for each terminal unit and then work out the phylogeny by combining the lineages into one graph.

I could devise a different method that, given a list of name UIDs, returns a phylogeny from their most proximate common ancestor. Would that be helpful?

[keesey]

As for the name, I don't mind it being similar. It does seem like there might be a better choice, though -- something that more clearly tells what it is. I don't know if there are conventions for R libraries, but maybe something like PhyloPicR? I dunno, it's up to you.

[sckott]

Ah, okay, thanks for pointing out all instead of immediate. It's just that I have never seen this format that you use, so I'm not familiar with any way to get the data into a format that can be used in R. I could probably write a little parser that would do it though.

[sckott]

wrt the name - I don't think there are any conventions for package naming - other than you can't use a name that's already been used.