[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]]
>>
>> ___
>> 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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> 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 Julien Clavel 
Yes Karla,

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

Julien


De : R-sig-phylo <r-sig-phylo-boun...@r-project.org> de la part de Karla Shikev 
<karlashi...@gmail.com>
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 <pseudac...@gmail.com> 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 <julien.cla...@hotmail.fr>
wrote:

> Yes Karla,
>
> I think this is clearly stated in the paper to which Josef is referring.
>
> Julien
>
> 
> De : R-sig-phylo <r-sig-phylo-boun...@r-project.org> de la part de Karla
> Shikev <karlashi...@gmail.com>
> 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 <pseudac...@gmail.com>
> 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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