RE: [MORPHMET] Re: allometry and phylogeny

2016-09-06 Thread Adams, Dean [EEOBS] 
Christy,

Yes, the ‘slopes’ component of the output contains the regression parameters 
for each species. These can then be used as input for ancestral state 
estimation and other down-stream analyses that you have planned.

Dean

Dr. Dean C. Adams
Professor
Department of Ecology, Evolution, and Organismal Biology
   Department of Statistics
Iowa State University
www.public.iastate.edu/~dcadams/<http://www.public.iastate.edu/~dcadams/>
phone: 515-294-3834

From: Christy Hipsley [mailto:chips...@museum.vic.gov.au]
Sent: Tuesday, September 6, 2016 2:00 AM
To: MORPHMET <morphmet@morphometrics.org>
Cc: damien.esque...@anu.edu.au
Subject: [MORPHMET] Re: allometry and phylogeny

To follow up on Damien's question and Dean's response, which values from the 
advanced.procD.lm results would one use for reconstructing species ontogenetic 
slopes? There are several outputs relating to slope from that test, like 
"slopes",  "slope.lengths", "slopes.dist", "slopes.angles".

I understand these each describe different parameters of the slope vector like 
length and orientation - basically magnitude and direction of shape change per 
unit size. So should one reconstruct ancestral states of each of these each 
separately to compare with tip taxa?

Thanks for any advice,
Christy

On Friday, July 1, 2016 at 12:31:37 AM UTC+10, dcadams wrote:
Damien,

Yes, one can take the regression parameters for each species and use these as 
‘tips’ data to obtain ancestral estimates of the regression slope. In this 
case, the species’ data is the multivariate set of slope coefficients for each 
multivariate regression. Thus, the ancestral state of the allometry is also a 
multivariate set of parameters.

Since you are using geomorph the slopes for each species’ allometry trajectory 
may be found in the output list from advanced.procD.lm.

Best,

Dean


Dr. Dean C. Adams
Professor
Department of Ecology, Evolution, and Organismal Biology
   Department of Statistics
Iowa State University
www.public.iastate.edu/~dcadams/<http://www.public.iastate.edu/~dcadams/>
phone: 515-294-3834

From: Damien Esquerre Gheur [mailto:damien@anu.edu.au]
Sent: Thursday, June 30, 2016 6:50 AM
To: morp...@morphometrics.org
Subject: [MORPHMET] allometry and phylogeny


Dear morphometricians,



I have a pretty big dataset of specimens for most species of pythons 
encompassing most of the size range for every species. I have been projecting 
the allometric trajectories and doing pairwise slope comparisons and things 
like that in Geomorph. However, it seems very obvious that the is a very strong 
phylogenetic signal in the data, as species within the same clade tend to have 
parallel trajectories.

I have been trying to find a way to analyse this data in a phylogenetic 
framework, and so far I know there is no straightforward solution. I know in 
Adams and Nistri 2010 the trajectories where coded ad isometric and allometric 
and then reconstructed the ancestral states but the case it not so binary with 
my data.

Would there be a way, for example, to extract a value for the slope and do an 
ancestral state reconstruction on that? Also, is there a way to incorporate 
phylogeny in slope comparison models?

Any help would be greatly appreciated


Damien Esquerré
PhD Student, Keogh Lab
Division of Evolution, Ecology and Genetics, Research School of Biology
The Australian National University
44 Daley Road, ACTON ACT 2601, Australia

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[MORPHMET] Re: allometry and phylogeny

2016-09-06 Thread Christy Hipsley 
To follow up on Damien's question and Dean's response, which values from 
the advanced.procD.lm results would one use for reconstructing species 
ontogenetic slopes? There are several outputs relating to slope from that 
test, like "slopes",  "slope.lengths", "slopes.dist", "slopes.angles". 

I understand these each describe different parameters of the slope vector 
like length and orientation - basically magnitude and direction of shape 
change per unit size. So should one reconstruct ancestral states of each of 
these each separately to compare with tip taxa?

Thanks for any advice,
Christy

On Friday, July 1, 2016 at 12:31:37 AM UTC+10, dcadams wrote:
>
> Damien,
>
>  
>
> Yes, one can take the regression parameters for each species and use these 
> as ‘tips’ data to obtain ancestral estimates of the regression slope. In 
> this case, the species’ data is the multivariate set of slope coefficients 
> for each multivariate regression. Thus, the ancestral state of the 
> allometry is also a multivariate set of parameters. 
>
>  
>
> Since you are using geomorph the slopes for each species’ allometry 
> trajectory may be found in the output list from advanced.procD.lm.
>
>
> Best, 
>
>  
>
> Dean
>
>  
>
>  
>
> Dr. Dean C. Adams
>
> Professor
>
> Department of Ecology, Evolution, and Organismal Biology
>
>Department of Statistics
>
> Iowa State University
>
> www.public.iastate.edu/~dcadams/
>
> phone: 515-294-3834
>
>  
>
> *From:* Damien Esquerre Gheur [mailto:damien@anu.edu.au ] 
>
> *Sent:* Thursday, June 30, 2016 6:50 AM
> *To:* morp...@morphometrics.org 
> *Subject:* [MORPHMET] allometry and phylogeny
>
>  
>
> Dear morphometricians,
>
>  
>
> I have a pretty big dataset of specimens for most species of pythons 
> encompassing most of the size range for every species. I have been 
> projecting the allometric trajectories and doing pairwise slope comparisons 
> and things like that in Geomorph. However, it seems very obvious that the 
> is a very strong phylogenetic signal in the data, as species within the 
> same clade tend to have parallel trajectories. 
>
> I have been trying to find a way to analyse this data in a phylogenetic 
> framework, and so far I know there is no straightforward solution. I know 
> in Adams and Nistri 2010 the trajectories where coded ad isometric and 
> allometric and then reconstructed the ancestral states but the case it not 
> so binary with my data. 
>
> Would there be a way, for example, to extract a value for the slope and do 
> an ancestral state reconstruction on that? Also, is there a way to 
> incorporate phylogeny in slope comparison models? 
>
> Any help would be greatly appreciated
>
>  
>
> Damien Esquerré 
>
> PhD Student, Keogh Lab
>
> Division of Evolution, Ecology and Genetics, Research School of Biology
>
> The Australian National University
>
> 44 Daley Road, ACTON ACT 2601, Australia
>
>  
>
> -- 
> MORPHMET may be accessed via its webpage at http://www.morphometrics.org
> --- 
> You received this message because you are subscribed to the Google Groups 
> "MORPHMET" group.
> To unsubscribe from this group and stop receiving emails from it, send an 
> email to morphmet+u...@morphometrics.org .
>

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[MORPHMET] RE: allometry and phylogeny

2016-06-30 Thread Adams, Dean [EEOBS] 
Damien,

Yes, one can take the regression parameters for each species and use these as 
‘tips’ data to obtain ancestral estimates of the regression slope. In this 
case, the species’ data is the multivariate set of slope coefficients for each 
multivariate regression. Thus, the ancestral state of the allometry is also a 
multivariate set of parameters.

Since you are using geomorph the slopes for each species’ allometry trajectory 
may be found in the output list from advanced.procD.lm.

Best,

Dean


Dr. Dean C. Adams
Professor
Department of Ecology, Evolution, and Organismal Biology
   Department of Statistics
Iowa State University
www.public.iastate.edu/~dcadams/
phone: 515-294-3834

From: Damien Esquerre Gheur [mailto:damien.esque...@anu.edu.au]
Sent: Thursday, June 30, 2016 6:50 AM
To: morphmet@morphometrics.org
Subject: [MORPHMET] allometry and phylogeny


Dear morphometricians,



I have a pretty big dataset of specimens for most species of pythons 
encompassing most of the size range for every species. I have been projecting 
the allometric trajectories and doing pairwise slope comparisons and things 
like that in Geomorph. However, it seems very obvious that the is a very strong 
phylogenetic signal in the data, as species within the same clade tend to have 
parallel trajectories.

I have been trying to find a way to analyse this data in a phylogenetic 
framework, and so far I know there is no straightforward solution. I know in 
Adams and Nistri 2010 the trajectories where coded ad isometric and allometric 
and then reconstructed the ancestral states but the case it not so binary with 
my data.

Would there be a way, for example, to extract a value for the slope and do an 
ancestral state reconstruction on that? Also, is there a way to incorporate 
phylogeny in slope comparison models?

Any help would be greatly appreciated


Damien Esquerré
PhD Student, Keogh Lab
Division of Evolution, Ecology and Genetics, Research School of Biology
The Australian National University
44 Daley Road, ACTON ACT 2601, Australia

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