Hi Susana (and Diogo):
Yes, the reciprocal of ES (1 / ES) == DR as described in Jetz et al. 2012.
This tip DR metric is a useful approximator of tip-level (species specific)
speciation rates, as shown thoroughly in Title & Rabosky (2019 DOI:
10.1111/2041-210X.13153).
But keep in mind that these tip rates need to be calculated on ‘completed’
trees where all extant species are included, either with data directly, or
indirectly via taxonomic constraints in a program like PASTIS
(10.1111/2041-210X.12117), TACT (10.1093/sysbio/syz081), or CorSiM
(10.1093/sysbio/sys031). The lack of complete modern sampling will ‘pull’ these
instantaneous present-day rates downward in the manner described in Louca &
Pennell (2020 10.1038/s41586-020-2176-1).
All the best,
—nate
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Assistant Research Professor & Associate Curator of Mammals
Arizona State University, School of Life Sciences
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On May 30, 2020, at 10:05 AM, Diogo B. Provete
<dbprov...@gmail.com<mailto:dbprov...@gmail.com>> wrote:
Hi Susana,
yes, the function picante::evol.distinct calculates the ES metric used in
Jetz's et al DR metric
https://www.rdocumentation.org/packages/picante/versions/1.8.1/topics/evol.distinct
Best,
Diogo
Em sáb., 30 de mai. de 2020 às 06:02, <r-sig-phylo-requ...@r-project.org>
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Today's Topics:
1. DR metric of Jetz et al. 2012 (Susana Lopez)
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Message: 1
Date: Fri, 29 May 2020 20:10:20 +0000
From: Susana Lopez <susana.lopez...@outlook.com>
To: "r-sig-phylo@r-project.org" <r-sig-phylo@r-project.org>
Subject: [R-sig-phylo] DR metric of Jetz et al. 2012
Message-ID:
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ro1p152mb1211a012cd0ce864d0a58868ab...@ro1p152mb1211.lamp152.prod.outlook.com
Content-Type: text/plain; charset="utf-8"
Hello:
I'm looking for a package/function that will implement the DR metric
(species-level lineage diversification rate) of Jetz et al. (2012).
Any suggestions?
Susy
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