Re: [R-sig-phylo] Using Phylogenetic Signal

[Theodore Garland]

Hi Will,

What you are observing is people falling into the "classic comic books"
version of statistical analyses, i.e., something is either "significant" or
"non-significant" based on some arbitrary cutoff of, say, alpha = 0.05.
Both of the statistics you mention are, of course, continuously valued,
though bounded at zero.  In general, you want to couple your consideration
of significance levels with looking at the value of the estimated
parameter, and also, I would suggest, compare your values with those
reported previously, e.g., as in in our large compilation in this original
paper:

Blomberg, S. P., T. Garland, Jr., and A. R. Ives. 2003. Testing for
phylogenetic signal in comparative data: behavioral traits are more labile.
Evolution 57:717–745.

As you wrote, attempting to construct confidence intervals with something
like simulations or parametric bootstrapping is also useful.

Cheers,
Ted


Theodore Garland, Jr., Distinguished Professor

Department of Evolution, Ecology, and Organismal Biology (EEOB)

University of California, Riverside

Riverside, CA 92521

Office Phone:  (951) 827-3524

Facsimile:  (951) 827-4286 (not confidential)

Email:  tgarl...@ucr.edu

http://www.biology.ucr.edu/people/faculty/Garland.html

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Director, UCR Institute for the Development of
Educational
Applications 


Editor in Chief, *Physiological and Biochemical Zoology
*


Fail Lab: Episode One

*https://www.youtube.com/watch?v=c0msBWyTzU0
*

On Mon, Oct 9, 2017 at 12:17 PM, William Gelnaw  wrote:

> Hi Everyone,
>   I'm measuring phylogenetic signal in a morphometric dataset using Pagel's
> Lambda and Blomberg's K.  I tend to think of both of these as continuous
> values, but in reviewing the literature I've noticed that most authors
> treat phylogenetic signal as either there or not.  The way that the
> P-values are calculated, comparing the observed character distribution to
> that expected given no phylogenetic signal, also suggests a very binary way
> of looking at phylogenetic signal.  There are definitely some authors that
> treat K and Lambda as continuous, but they seem to be the exception.  Also,
> although parametric bootstrapping seems to be a good way to get a
> confidence interval for signal values, I've hardly seen it used.  I'm just
> wondering if there is a reason for strictly treating phylogenetic signal as
> just present or absent, or if I'm seeing a pattern that isn't really
> there.
>Best regards,
>   Will
>
> [[alternative HTML version deleted]]
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[R-sig-phylo] Using Phylogenetic Signal

[William Gelnaw]

Hi Everyone,
  I'm measuring phylogenetic signal in a morphometric dataset using Pagel's
Lambda and Blomberg's K.  I tend to think of both of these as continuous
values, but in reviewing the literature I've noticed that most authors
treat phylogenetic signal as either there or not.  The way that the
P-values are calculated, comparing the observed character distribution to
that expected given no phylogenetic signal, also suggests a very binary way
of looking at phylogenetic signal.  There are definitely some authors that
treat K and Lambda as continuous, but they seem to be the exception.  Also,
although parametric bootstrapping seems to be a good way to get a
confidence interval for signal values, I've hardly seen it used.  I'm just
wondering if there is a reason for strictly treating phylogenetic signal as
just present or absent, or if I'm seeing a pattern that isn't really
there.
   Best regards,
  Will

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Re: [R-sig-phylo] predict using the PGLS model output

[Cecile Ane]

Rphylopars can make phylogenetic predictions: it’s on CRAN and on github 
https://github.com/ericgoolsby/Rphylopars
Cécile

On Oct 9, 2017, at 9:59 AM, Clara Grilo 
> wrote:

Hi everyone,

I run a phylogenetic generalised least squares model (PGLS) to analyze the
effect of demographic parameters on the risk of extinction for 70 species.

Now I would like to predict the extinction risk based on this model for the
remaining unstudied species (~4000 species).
I have to use the  phylogenetic tree for the 4000 species and applied the
previous model.

Are you aware of a code that make predictions based on the model and
another tree of species?

Thanks you in advance.
Best regards,
Clara

--
-
Clara Grilo

Centro Brasileiro de Estudos de Ecologia de Estradas (CBEE)
Departamento de Biologia
Universidade Federal de Lavras
37200 000 Minas Gerais
Brasil

Website: http://lattes.cnpq.br/2789017774255561
 http://cbee.ufla.br

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[R-sig-phylo] predict using the PGLS model output

[Clara Grilo]

Hi everyone,

I run a phylogenetic generalised least squares model (PGLS) to analyze the
effect of demographic parameters on the risk of extinction for 70 species.

Now I would like to predict the extinction risk based on this model for the
remaining unstudied species (~4000 species).
I have to use the  phylogenetic tree for the 4000 species and applied the
previous model.

Are you aware of a code that make predictions based on the model and
another tree of species?

Thanks you in advance.
Best regards,
Clara

-- 
-
Clara Grilo

Centro Brasileiro de Estudos de Ecologia de Estradas (CBEE)
Departamento de Biologia
Universidade Federal de Lavras
37200 000 Minas Gerais
Brasil

Website: http://lattes.cnpq.br/2789017774255561
  http://cbee.ufla.br

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