Hi Willian and Nathan,

Thanks a lot for your clarification! It is exactly what I was thinking
about!

Best,

2018-04-15 13:28 GMT-03:00 Upham, Nathan <nathan.up...@yale.edu>:

> Yeah Lilian, Will is right— “ED” or “fair proportion" in the 2018 paper is
> ~= “ES” as given in Redding and Mooers 2006.
>
> 1/ES = DR is where the confusion comes from.
>
> DR has been called the “inverse equal splits metric”, so I think that was
> just an editing error for them to write: "This measure of ED is closely
> inversely related to the equal splits metric used to characterize tip-level
> diversification rates” — instead it should read “...closely related to the
> inverse equal splits metric used to characterize tip-level diversification
> rates”.
>
> But yes, your way of calculating DR and ES using the picante function
> evol.distinct() appears legit.  DR will be your tip-level diversification
> rates.
>
> All the best
> —nate
>
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
> *Nathan S. Upham, Ph.D. *Postdoctoral Associate, Yale University, Ecology
> and Evolutionary Biology
> 165 Prospect Street
> <https://maps.google.com/?q=165+Prospect+Street&entry=gmail&source=g>,
> OML 122, New Haven, CT, 06511, USA
>
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> <http://vertlife.org/>
>
> Research Associate, Integrative Research Center, Field Museum of Natural
> History
> Chair, Biodiversity Committee, American Society of Mammalogists
>      ~> Check out the new Mammal Diversity Database
> <https://mammaldiversity.org/>
> Taxonomy Advisor, IUCN/SSC Small Mammal Specialist Group
>
> e: nathan.up...@yale.edu | Skype: nate_upham | Twitter: @n8_upham
>
>
>
>
>
>
> On Apr 14, 2018, at 4:58 PM, William Gearty <wgea...@stanford.edu> wrote:
>
> Hi Lilian,
>
> My understanding is that Jetz and Pyron 2018 use the fair proportion metric
> ('evolutionary distinctness'), which they they assert is closely inversely
> related to the equal splits metric (but not calculated in that way).
> Jetz et al 2012 use the species-level lineage diversification rate, which
> is actually calculated by taking the inverse of the equal splits metric.
>
> Hope that clears things up,
> Will
>
> On Sat, Apr 14, 2018 at 8:24 AM, Lilian Sayuri Ouchi de Melo <
> sayuriou...@gmail.com> wrote:
>
> Dear all,
>
> I am trying to compute the diversification rates as Jetz et al. 2012 (
> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.
> nature.com_articles_nature11631&d=DwIFaQ&c=cjytLXgP8ixuoHflwc-poQ&r=
> Q5p7Th8M0OGrWt3H3QohAlhP-5Yx0wuJ0zlxqhR3rfM&m=JWp0jba2pLzXNNLy_qmb_
> hmDK9c0227ePZ0WLRrFl5c&s=VDeXlzWxxytBWlCNVCqi2XMN8vst4xNYv7bBu1Am0bI&e=),
> where the authors have said
> that the formula is the inverse of the equal splits distinctiveness value
> of Redding and Moors 2006 (
> https://urldefense.proofpoint.com/v2/url?u=https-3A__
> onlinelibrary.wiley.com_doi_full_10.1111_j.1523-2D1739.
> 2006.00555.x&d=DwIFaQ&c=cjytLXgP8ixuoHflwc-poQ&r=Q5p7Th8M0OGrWt3H3QohAlhP-
> 5Yx0wuJ0zlxqhR3rfM&m=JWp0jba2pLzXNNLy_qmb_hmDK9c0227ePZ0WLRrFl5c&s=
> QH0lFnLT7AhvJP6bv3ETofxicLJMS-MZnODUFkvqLfU&e=
> ).
> But, in another paper, Pyron & Jetz 2018 (
> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.
> nature.com_articles_s41559-2D018-2D0515-2D5&d=DwIFaQ&c=
> cjytLXgP8ixuoHflwc-poQ&r=Q5p7Th8M0OGrWt3H3QohAlhP-5Yx0wuJ0zlxqhR3rfM&m=
> JWp0jba2pLzXNNLy_qmb_hmDK9c0227ePZ0WLRrFl5c&s=g2ImKVs_
> yrhXZZb9pFR0m1ReAtbqxdwvEsINRarOkEc&e=) said “is closely
> inversely related to the equal splits metric”. Looking in both formulas
> they seem to be the “same” but only the inverse of equal splits, as Jetz et
> al. said in 2012.
>
> I would like to know if some of you have already calculated this
> diversification rate and if it is in fact just the inverse, or it is a kind
> of "closely" related formula. I wrote a small example of what I’ve done,
> and would like to ask if you think that this is the right way to do that.
>
>
> library(phytools)
>
> tr <- rtree(20)
>
> plot(tr)
>
> tr <- compute.brlen(tr)
>
> plot(tr)
>
> tr$edge.length
>
> tr$edge
>
> plot(tr, show.tip.label = TRUE, show.node.label = TRUE)
>
>
>
> ES = evol.distinct(tr, type = "equal.splits")$w
>
> DR = evol.distinct(tr, type = "equal.splits")$w^-1
>
>
> Thank you in advance,
>
>
> --
> Lilian Sayuri Ouchi de Melo
> (PhD Student in Animal Biology at UNESP/IBILCE)
>
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> --
> William Gearty
> PhD Candidate, Paleobiology
> Department of Geological Sciences
> Stanford School of Earth, Energy & Environmental Sciences
> williamgearty.com
>
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-- 
Lilian Sayuri Ouchi de Melo
(PhD Student in Animal Biology at UNESP/IBILCE)

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