date:20151208

[R-sig-phylo] Fwd: rate units in fitContinuous

2015-12-08 Thread Karla Shikev

Thanks, Josef (and those that answered privately).

Based on what you wrote, it seems to me that using sigsq as a measure of
rate of evolution would make sense for BM, but the interaction between sigsq
and alpha in OU would make the interpretation of sigsq as a rate measure
complicated, if not unfeasible. Would you agree?





On Mon, Dec 7, 2015 at 9:49 PM, Josef C Uyeda  wrote:

> Karla,
> The units of sigsq are in your trait units^2 per time unit of your
> phylogeny. So if your trait is in cm and your phylogeny in millions of
> years, then the units of sigsq are in cm^2/my.
>
> Comparing BM to OU units is more complicated. Gene Hunt discussed this in
> the following paper:
> http://paleobiol.geoscienceworld.org/content/38/3/351.short
> Long story short, they are in the same units, but it may not be
> particularly meaningful to compare them between OU and BM models. For
> example, you can have an extremely high sigsq in the OU model, but if alpha
> is very high as well, you may end up with very slow rates of evolution when
> observed over the lifetime of a phylogeny (specifically, the stationary
> variance of the OU process is sigsq^2/(2*alpha), thus if alpha is high
> enough the stationary variance will tend towards 0, and all the traits
> across taxa will be virtually identical).
>
> Hope this helps.
> Josef Uyeda
>
>
>
> On 12/07/2015 03:35 PM, Karla Shikev wrote:
>
>> Dear all,
>>
>> I am fitting a BM model using fitContinuous, a vector of trait values and
>> a
>> time-calibrated tree and then I use the sigsq parameter as my measure of
>> the rate of evolution of the trait in question. My questions are:
>>
>> (1) what is the unit of the sigsq parameter?
>> (2) to what extent is the sigsq in a BM model comparable to sigsq in an OU
>> model, for instance? are they on the same units?
>>
>> Thanks!
>>
>> Karla
>>
>> [[alternative HTML version deleted]]
>>
>> ___
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>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
>> Searchable archive at
>> http://www.mail-archive.com/r-sig-phylo@r-project.org/
>>
>
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> Searchable archive at
> http://www.mail-archive.com/r-sig-phylo@r-project.org/
>

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Re: [R-sig-phylo] Fwd: rate units in fitContinuous

2015-12-08 Thread Julien Clavel

Yes Karla,

I think this is clearly stated in the paper to which Josef is referring.

Julien


De : R-sig-phylo  de la part de Karla Shikev 

Envoyé : mardi 8 décembre 2015 11:57
À : r-sig-phylo@r-project.org
Objet : [R-sig-phylo] Fwd:  rate units in fitContinuous

Thanks, Josef (and those that answered privately).

Based on what you wrote, it seems to me that using sigsq as a measure of
rate of evolution would make sense for BM, but the interaction between sigsq
and alpha in OU would make the interpretation of sigsq as a rate measure
complicated, if not unfeasible. Would you agree?





On Mon, Dec 7, 2015 at 9:49 PM, Josef C Uyeda  wrote:

> Karla,
> The units of sigsq are in your trait units^2 per time unit of your
> phylogeny. So if your trait is in cm and your phylogeny in millions of
> years, then the units of sigsq are in cm^2/my.
>
> Comparing BM to OU units is more complicated. Gene Hunt discussed this in
> the following paper:
> http://paleobiol.geoscienceworld.org/content/38/3/351.short
> Long story short, they are in the same units, but it may not be
> particularly meaningful to compare them between OU and BM models. For
> example, you can have an extremely high sigsq in the OU model, but if alpha
> is very high as well, you may end up with very slow rates of evolution when
> observed over the lifetime of a phylogeny (specifically, the stationary
> variance of the OU process is sigsq^2/(2*alpha), thus if alpha is high
> enough the stationary variance will tend towards 0, and all the traits
> across taxa will be virtually identical).
>
> Hope this helps.
> Josef Uyeda
>
>
>
> On 12/07/2015 03:35 PM, Karla Shikev wrote:
>
>> Dear all,
>>
>> I am fitting a BM model using fitContinuous, a vector of trait values and
>> a
>> time-calibrated tree and then I use the sigsq parameter as my measure of
>> the rate of evolution of the trait in question. My questions are:
>>
>> (1) what is the unit of the sigsq parameter?
>> (2) to what extent is the sigsq in a BM model comparable to sigsq in an OU
>> model, for instance? are they on the same units?
>>
>> Thanks!
>>
>> Karla
>>
>> [[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-phylo@r-project.org/
>>
>
> ___
> 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-phylo@r-project.org/
>

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Re: [R-sig-phylo] Fwd: rate units in fitContinuous

2015-12-08 Thread Karla Shikev

Fantastic. Thanks so much!

On Tue, Dec 8, 2015 at 10:19 AM, Julien Clavel 
wrote:

> Yes Karla,
>
> I think this is clearly stated in the paper to which Josef is referring.
>
> Julien
>
> 
> De : R-sig-phylo  de la part de Karla
> Shikev 
> Envoyé : mardi 8 décembre 2015 11:57
> À : r-sig-phylo@r-project.org
> Objet : [R-sig-phylo] Fwd:  rate units in fitContinuous
>
> Thanks, Josef (and those that answered privately).
>
> Based on what you wrote, it seems to me that using sigsq as a measure of
> rate of evolution would make sense for BM, but the interaction between
> sigsq
> and alpha in OU would make the interpretation of sigsq as a rate measure
> complicated, if not unfeasible. Would you agree?
>
>
>
>
>
> On Mon, Dec 7, 2015 at 9:49 PM, Josef C Uyeda 
> wrote:
>
> > Karla,
> > The units of sigsq are in your trait units^2 per time unit of your
> > phylogeny. So if your trait is in cm and your phylogeny in millions of
> > years, then the units of sigsq are in cm^2/my.
> >
> > Comparing BM to OU units is more complicated. Gene Hunt discussed this in
> > the following paper:
> > http://paleobiol.geoscienceworld.org/content/38/3/351.short
> > Long story short, they are in the same units, but it may not be
> > particularly meaningful to compare them between OU and BM models. For
> > example, you can have an extremely high sigsq in the OU model, but if
> alpha
> > is very high as well, you may end up with very slow rates of evolution
> when
> > observed over the lifetime of a phylogeny (specifically, the stationary
> > variance of the OU process is sigsq^2/(2*alpha), thus if alpha is high
> > enough the stationary variance will tend towards 0, and all the traits
> > across taxa will be virtually identical).
> >
> > Hope this helps.
> > Josef Uyeda
> >
> >
> >
> > On 12/07/2015 03:35 PM, Karla Shikev wrote:
> >
> >> Dear all,
> >>
> >> I am fitting a BM model using fitContinuous, a vector of trait values
> and
> >> a
> >> time-calibrated tree and then I use the sigsq parameter as my measure of
> >> the rate of evolution of the trait in question. My questions are:
> >>
> >> (1) what is the unit of the sigsq parameter?
> >> (2) to what extent is the sigsq in a BM model comparable to sigsq in an
> OU
> >> model, for instance? are they on the same units?
> >>
> >> Thanks!
> >>
> >> Karla
> >>
> >> [[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-phylo@r-project.org/
> >>
> >
> > ___
> > 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-phylo@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-phylo@r-project.org/
>

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Re: [R-sig-phylo] Plotting sampled-ancestor trees in R

2015-12-08 Thread Emmanuel Paradis


Hi Jo & Roger,

edgelabels() has the option 'date' which helps to annotate the branches 
of a tree:


set.seed(1)
tx <- rcoal(3)
plot(tx)
axisPhylo()
edgelabels(edge = 1, date = 1, pch = 19, col = "red")

Best,

Emmanuel

Le 08/12/2015 16:32, Joseph Brown a écrit :

Roger,

Are you looking for something like this?









It is just a matter of finding the coordinates on the last plot:

lastPP<- get("last_plot.phylo", envir=.PlotPhyloEnv);

and laying down points where you want them.

If this is along the lines of what you want, I can make the code a bit
more general and send it along.

JWB.

Joseph W. Brown
Post-doctoral Researcher, Smith Laboratory
University of Michigan
Department of Ecology & Evolutionary Biology
Room 2071, Kraus Natural Sciences Building
Ann Arbor MI 48109-1079
josep...@umich.edu 




On 8 Dec, 2015, at 07:46, Roger Close > wrote:

Hi all,

Does anyone know of a way to plot sampled-ancestor trees in R such that
ancestors lie on branches, rather than being zero-length terminals that
follow a bifurcation?

Many thanks,
Roger

---
Roger Close, Postdoctoral Research Associate
Department of Earth Sciences, Oxford University
South Parks Road
Oxford OX1 3AN
United Kingdom

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Re: [R-sig-phylo] Plotting sampled-ancestor trees in R

2015-12-08 Thread David Bapst

Hi Roger,

I'm not aware of any existing solution. Could you send around a small
example of the data format of an output sampled ancestor tree from
BEAST or MrBayes? Are they just typical Newick/NEXUS format with
ancestors indicated tipis with zero-length branches or something more
complicated?

Remarkably I've not looked at the formatting of one, but obviously
plotting SA trees is something the community will need in the near
future.

Cheers,
-Dave

On Tue, Dec 8, 2015 at 5:46 AM, Roger Close  wrote:
> Hi all,
>
> Does anyone know of a way to plot sampled-ancestor trees in R such that
> ancestors lie on branches, rather than being zero-length terminals that
> follow a bifurcation?
>
> Many thanks,
> Roger
>
> ---
> Roger Close, Postdoctoral Research Associate
> Department of Earth Sciences, Oxford University
> South Parks Road
> Oxford OX1 3AN
> United Kingdom
>
> [[alternative HTML version deleted]]
>
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-- 
David W. Bapst, PhD
Adjunct Asst. Professor, Geology and Geol. Eng.
South Dakota School of Mines and Technology
501 E. St. Joseph
Rapid City, SD 57701

http://webpages.sdsmt.edu/~dbapst/
http://cran.r-project.org/web/packages/paleotree/index.html

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[R-sig-phylo] Fwd: Community analysis of average plant trait values with phylogenetic context

2015-12-08 Thread Benjamin O'Leary

-- Forwarded message --
From: *Benjamin O'Leary* 
Date: Tuesday, 8 December 2015
Subject: Community analysis of average plant trait values with phylogenetic
context
To: Xianyun Mao , tm...@psu.edu,
rossellda...@gmail.com, steve.kem...@gmail.com, dacke...@berkeley.edu,
s.blombe...@uq.edu.au, cornw...@zoology.ubc.ca, p...@berkeley.edu,
mrhel...@wisc.edu, morlon.hel...@gmail.com, cw...@oeb.harvard.edu

Hi All,

My name is Ben O'Leary, i am a student at Monash university in Melbourne
Australia. I have recently completed an honours project which i now hope to
publish as a paper. I have studied a range of leaf trait values of
Australia's Eucalyptus species. I have also built a phylogenetic tree for
the species. We have produced regional averages for a number of traits
which we then compared against regional averages in environmental
variables. There appears to be some correlation between trait values and
environmental data, however we now want to perform a similar analysis which
takes community averaged/regional phylogenetic relationships into account.
We have run a PGLS analysis but that focuses on individuals species rather
than regional assemblages. Is there a PGLS equivalent for analyzing mean
trait values for mutiple communities as a function of environmental
variables, taking into account the phylo relationships of the community
members, and if so can you suggest a package/paper/example? We have used
within and between region mean phylogenetic distance and mean nearest
neighbour phylogenetic distance as our metrics and we will now also
investigate the Sorenson index.

For any statistical analysis we will run, i'm wondering how the covariance
matrix is built. As an alternative if no predesigned system exists, could
we incorporate something like a between community MPD as our covariance?
What then would make up the line of variance? Also does the matrix need to
ultra metric?

Thanks very much for your help

Kind regards
Ben

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[R-sig-phylo] Fwd: rate units in fitContinuous

Re: [R-sig-phylo] Fwd: rate units in fitContinuous

Re: [R-sig-phylo] Fwd: rate units in fitContinuous

Re: [R-sig-phylo] Plotting sampled-ancestor trees in R

Re: [R-sig-phylo] Plotting sampled-ancestor trees in R

[R-sig-phylo] Fwd: Community analysis of average plant trait values with phylogenetic context

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