Re: [Treebase-devel] number of leaves

[Hilmar L. <hl...@ne...>]

Thanks Carl, this is great! The context of my question is actually the 2012 iEvoBio challenge. You'll know when you see the website with the Challenge call go up. In short, we were going to suggest (all or a subset of) TreeBASE as one possible dataset, and I was wondering whether it would meet the criteria.

	-hilmar
 
On Feb 10, 2012, at 1:21 PM, Carl Boettiger wrote:

> whoops, different conventions on trees, Nnode is internal nodes only so that should have been x$Nnode+1.
> 
> tips <- unlist(sapply(all_treebase, function(x) (x$Nnode+1))))
> sum(tips)
> 116319
> > mean(tips)
> [1] 43.43503
> > max(tips)
> [1] 794
> 
> histogram
> <image.png>
> 
> 
> On Fri, Feb 10, 2012 at 9:55 AM, Carl Boettiger <cbo...@gm...> wrote:
> From a slightly dated cache in R treebase, I get:
> 
> > sum(unlist(sapply(all_treebase, function(x) (x$Nnode-1)/2)))
> 55481
> 
> that's probably way under, since it's a few months behind and some trees get dropped by treebase if the server times out, probably need a better way to handle those things.  Others can probably give a much better number.  
> 
> Carl
> 
> 
> On Thu, Feb 9, 2012 at 10:05 PM, Hilmar Lapp <hl...@ne...> wrote:
> Can anyone give me a quick estimate of how many tip nodes all published trees in TreeBASE amount to?
> 
>        -hilmar
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> Carl Boettiger
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> Carl Boettiger
> UC Davis
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