Re: [R-sig-phylo] quantitative state dependent diversification of another quantitative trait

2018-04-05 Thread Zach Culumber 
Thank you Brian and Julien!  Those packages do indeed make it easier to get
at our question!

Cheers,
Zach

On Wed, Apr 4, 2018 at 5:57 PM, Julien Clavel 
wrote:

> Hi Zach,
>
>
>
> In addition to SLOUCH (for a OU tracking a BM process) you can use mvMORPH
> for fitting a model where a trait evolving under an OU process follow
> another trait evolving under OU with some evolutionary lag (see p. 14-15 of
> the package vignette “How to use mvMORPH”).
>
>
>
> Best wishes,
>
>
>
> Julien
>
> --
> *De :* R-sig-phylo  de la part de
> Brian O'Meara 
> *Envoyé :* mercredi 4 avril 2018 22:39
> *À :* Zach Culumber
> *Cc :* mailman, r-sig-phylo
> *Objet :* Re: [R-sig-phylo] quantitative state dependent diversification
> of another quantitative trait
>
> I think you want SLOUCH: Hansen et al. 2008:
> https://onlinelibrary.wiley.com/doi/pdf/10./j.1558-5646.2008.00412.x.
> One trait evolves under Brownian motion, another trait follows it.
>
> Best,
> Brian
>
> ___
> Brian O'Meara, http://www.brianomeara.info, especially Calendar
> <http://brianomeara.info/calendars/omeara/>, CV
> <http://brianomeara.info/cv/>, and Feedback
> <http://brianomeara.info/teaching/feedback/>
>
> Associate Professor, Dept. of Ecology & Evolutionary Biology, UT Knoxville
> Associate Head, Dept. of Ecology & Evolutionary Biology, UT Knoxville
> Associate Director for Postdoctoral Activities, National Institute for
> Mathematical & Biological Synthesis <http://www.nimbios.org> (NIMBioS)
>
>
>
> On Wed, Apr 4, 2018 at 2:43 PM, Zach Culumber  wrote:
>
> > Hi everyone,
> >
> > We are interested in examining whether shifts in one continuous trait
> have
> > preceded shifts in another continuous trait through evolutionary time
> for a
> > phylogeny of ~80 species.  To do this we were thinking of calculating the
> > change in the value of each trait for each tip to its most recent
> ancestor
> > (i.e., node) and then for each node to its most recent ancestral node.
> We
> > have all the tip values and conducted ASR to get the node values.
> However,
> > we are unaware of any functions or packages that would automate
> calculation
> > of all these distances for teach tip and node to its most recent
> ancestor.
> > Does anyone have any suggestions of functions or packages that might
> > possibly do this?  Alternatively, are there better existing options for
> > exploring this question? I.e., something similar to QuaSSE but for
> analysis
> > between two quantitative traits rather than traits and species
> > diversification?  Something like Bayes Traits or PGLS would allow tests
> of
> > correlated evolution, but not the order of evolutionary shifts.
> >
> > Thank you for any insights!
> >
> > Zach
> >
> > [[alternative HTML version deleted]]
> >
> > ___
> > R-sig-phylo mailing list - R-sig-phylo@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
> > Searchable archive at http://www.mail-archive.com/r-
> > sig-ph...@r-project.org/
> >
>
> [[alternative HTML version deleted]]
>
> ___
> R-sig-phylo mailing list - R-sig-phylo@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
> Searchable archive at http://www.mail-archive.com/r-
> sig-ph...@r-project.org/
>



-- 
Zachary W. Culumber
Postdoctoral Research Associate
Florida State University
Department of Biological Science
http://www.zwcresearch.com

[[alternative HTML version deleted]]

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Re: [R-sig-phylo] quantitative state dependent diversification of another quantitative trait

2018-04-04 Thread Julien Clavel 
Hi Zach,

In addition to SLOUCH (for a OU tracking a BM process) you can use mvMORPH for 
fitting a model where a trait evolving under an OU process follow another trait 
evolving under OU with some evolutionary lag (see p. 14-15 of the package 
vignette �How to use mvMORPH�).

Best wishes,

Julien


De : R-sig-phylo  de la part de Brian 
O'Meara 
Envoy� : mercredi 4 avril 2018 22:39
� : Zach Culumber
Cc : mailman, r-sig-phylo
Objet : Re: [R-sig-phylo] quantitative state dependent diversification of 
another quantitative trait

I think you want SLOUCH: Hansen et al. 2008:
https://onlinelibrary.wiley.com/doi/pdf/10./j.1558-5646.2008.00412.x.
One trait evolves under Brownian motion, another trait follows it.

Best,
Brian

___
Brian O'Meara, http://www.brianomeara.info, especially Calendar
<http://brianomeara.info/calendars/omeara/>, CV
<http://brianomeara.info/cv/>, and Feedback
<http://brianomeara.info/teaching/feedback/>

Associate Professor, Dept. of Ecology & Evolutionary Biology, UT Knoxville
Associate Head, Dept. of Ecology & Evolutionary Biology, UT Knoxville
Associate Director for Postdoctoral Activities, National Institute for
Mathematical & Biological Synthesis <http://www.nimbios.org> (NIMBioS)


On Wed, Apr 4, 2018 at 2:43 PM, Zach Culumber  wrote:

> Hi everyone,
>
> We are interested in examining whether shifts in one continuous trait have
> preceded shifts in another continuous trait through evolutionary time for a
> phylogeny of ~80 species.  To do this we were thinking of calculating the
> change in the value of each trait for each tip to its most recent ancestor
> (i.e., node) and then for each node to its most recent ancestral node.  We
> have all the tip values and conducted ASR to get the node values.  However,
> we are unaware of any functions or packages that would automate calculation
> of all these distances for teach tip and node to its most recent ancestor.
> Does anyone have any suggestions of functions or packages that might
> possibly do this?  Alternatively, are there better existing options for
> exploring this question? I.e., something similar to QuaSSE but for analysis
> between two quantitative traits rather than traits and species
> diversification?  Something like Bayes Traits or PGLS would allow tests of
> correlated evolution, but not the order of evolutionary shifts.
>
[[elided Hotmail spam]]
>
> Zach
>
> [[alternative HTML version deleted]]
>
> ___
> R-sig-phylo mailing list - R-sig-phylo@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
> Searchable archive at http://www.mail-archive.com/r-
> sig-ph...@r-project.org/
>

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Re: [R-sig-phylo] quantitative state dependent diversification of another quantitative trait

2018-04-04 Thread Brian O'Meara 
I think you want SLOUCH: Hansen et al. 2008:
https://onlinelibrary.wiley.com/doi/pdf/10./j.1558-5646.2008.00412.x.
One trait evolves under Brownian motion, another trait follows it.

Best,
Brian

___
Brian O'Meara, http://www.brianomeara.info, especially Calendar
, CV
, and Feedback


Associate Professor, Dept. of Ecology & Evolutionary Biology, UT Knoxville
Associate Head, Dept. of Ecology & Evolutionary Biology, UT Knoxville
Associate Director for Postdoctoral Activities, National Institute for
Mathematical & Biological Synthesis  (NIMBioS)


On Wed, Apr 4, 2018 at 2:43 PM, Zach Culumber  wrote:

> Hi everyone,
>
> We are interested in examining whether shifts in one continuous trait have
> preceded shifts in another continuous trait through evolutionary time for a
> phylogeny of ~80 species.  To do this we were thinking of calculating the
> change in the value of each trait for each tip to its most recent ancestor
> (i.e., node) and then for each node to its most recent ancestral node.  We
> have all the tip values and conducted ASR to get the node values.  However,
> we are unaware of any functions or packages that would automate calculation
> of all these distances for teach tip and node to its most recent ancestor.
> Does anyone have any suggestions of functions or packages that might
> possibly do this?  Alternatively, are there better existing options for
> exploring this question? I.e., something similar to QuaSSE but for analysis
> between two quantitative traits rather than traits and species
> diversification?  Something like Bayes Traits or PGLS would allow tests of
> correlated evolution, but not the order of evolutionary shifts.
>
> Thank you for any insights!
>
> Zach
>
> [[alternative HTML version deleted]]
>
> ___
> R-sig-phylo mailing list - R-sig-phylo@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
> Searchable archive at http://www.mail-archive.com/r-
> sig-ph...@r-project.org/
>

[[alternative HTML version deleted]]

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