[R-sig-phylo] diversification rates

[Lilian Sayuri Ouchi de Melo]

Dear all,

I am trying to compute the diversification rates as Jetz et al. 2012 (
https://www.nature.com/articles/nature11631), where the authors have said
that the formula is the inverse of the equal splits distinctiveness value
of Redding and Moors 2006 (
https://onlinelibrary.wiley.com/doi/full/10.1111/j.1523-1739.2006.00555.x).
But, in another paper, Pyron & Jetz 2018 (
https://www.nature.com/articles/s41559-018-0515-5) 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]

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 <

Post by Lilian Sayuri Ouchi de Melo
Dear all,
I am trying to compute the diversification rates as Jetz et al. 2012 (
https://www.nature.com/articles/nature11631), where the authors have said
that the formula is the inverse of the equal splits distinctiveness value
of Redding and Moors 2006 (
https://onlinelibrary.wiley.com/doi/full/10.1111/j.1523-1739.2006.00555.x
).
But, in another paper, Pyron & Jetz 2018 (
https://www.nature.com/articles/s41559-018-0515-5) 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)
[[alternative HTML version deleted]]
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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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[Upham, Nathan]

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, OML 122, New Haven, CT, 06511, USA

personal web: Home<https://n8upham.github.io/> | Research Gate<https://www.researchgate.net/profile/Nathan_Upham> | Google Scholar<https://scholar.google.com/citations?user=zIn4NoUAAAAJ&hl=en>
lab pages: Jetz Lab<http://jetzlab.yale.edu/> | NSF VertLife grant<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: ***@yale.edu<mailto:***@yale.edu> | Skype: nate_upham | Twitter: @n8_upham






On Apr 14, 2018, at 4:58 PM, William Gearty <***@stanford.edu<mailto:***@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 <
***@gmail.com<mailto:***@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)

[[alternative HTML version deleted]]

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--
William Gearty
PhD Candidate, Paleobiology
Department of Geological Sciences
Stanford School of Earth, Energy & Environmental Sciences
williamgearty.com<http://williamgearty.com>

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[Lilian Sayuri Ouchi de Melo]

Hi Willian and Nathan,

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

Best,

Post by Upham, Nathan
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
personal web: Home <https://n8upham.github.io/> | Research Gate
<https://www.researchgate.net/profile/Nathan_Upham> | Google Scholar
<https://scholar.google.com/citations?user=zIn4NoUAAAAJ&hl=en>
lab pages: Jetz Lab <http://jetzlab.yale.edu/> | NSF VertLife grant
<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
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 <
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)
[[alternative HTML version deleted]]
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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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