Re: [MORPHMET] help with "classify" in RRPP

[Diogo Borges Provete]

Hi all,
let me take advantage of this discussion and quickly add one more question. 

I have a similar scenario, in which I want to test if a set of specimens 
from one species belong to a separate species ("good species" scenario) or 
one already included in the dataset ("junior synonym" scenario). 
My problem is that, differently from Nicole, I only have two species, so 
when I build the linear model done only with the putative senior synonym it 
surely crashes because I ended up with only one level of the factor. 

How can I deal with that?

Thank you in advance,
Diogo

Em terça-feira, 7 de maio de 2019 11:10:04 UTC-4, Mike Collyer escreveu:
>
> Nicole,
>
> I assume that your intention is to summarize a species probability from 
> the several probabilities of specimens, if data sets are combined?  (I 
> think you might have used “species” twice but meant “specimen" once, below).
>
> If so, there are two ways you could do this.  One would be as you 
> suggested, summarize the distribution of posterior probabilities for a 
> species (mean, median, quartiles, etc.).  The other would be to calculate 
> something akin to species means and use these as test data, based on the 
> coefficients calculated from training data.  It might require some thought 
> as to what the training data should be, as leave one out cross-validation 
> would not make much sense.  Calculating the posterior probability for a 
> species mean after using individual specimens to estimate the mean also 
> does not make sense.  However, a resampling procedure that arbitrarily 
> divides the specimens into training and testing groups, using the first to 
> estimate coefficients and the second to obtain a mean, could be used to 
> generate a confidence interval for the posterior classification 
> probabilities of a particular species to its and other species’s groups.
>
> The second approach would involve some scripting.  The first approach can 
> be done quickly with the by() and summary() functions, e.g.,
>
> by(my.posterior.probs, species, summary)
>
> Hope that helps!
> Mike
>
> On May 7, 2019, at 9:13 AM, Nicole Ibagón  > wrote:
>
> Dear all
> I'm working with five different datasets (lateral and dorsal view of the 
> skull and jaw) of a neotropical bat genus. My research question is if one 
> species (described with a single sample), is a synonym of one of the other 
> species of the genus. I used classify function of RRPP for this purpose, 
> and it solved my question generating one posterior probability for each 
> species of each dataset. However, I would like to know there is a way to 
> generate a single posterior probability for each species.
> Should I join all the datasets before doing the classification analysis? 
> Or should I average the posterior probabilities of all the datasets? Is 
> there a better way to do it?
> Thanks
>
> -- 
> Nicole Estefanía Ibagón Escobar
> PhD Candidate in Ecology  - UFV (Brazil) 
> BSc Marine Biologist  - Utadeo (Colombia)
> ResearchGate 
> Curriculo CVLAC 
> 
> Curriculo lattes 
> 
> http://evolutionlbe.wix.com/lbeufv
>
> < <<  
>
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Re: [MORPHMET] help with "classify" in RRPP

[Mike Collyer]

Nicole,

I assume that your intention is to summarize a species probability from the 
several probabilities of specimens, if data sets are combined?  (I think you 
might have used “species” twice but meant “specimen" once, below).

If so, there are two ways you could do this.  One would be as you suggested, 
summarize the distribution of posterior probabilities for a species (mean, 
median, quartiles, etc.).  The other would be to calculate something akin to 
species means and use these as test data, based on the coefficients calculated 
from training data.  It might require some thought as to what the training data 
should be, as leave one out cross-validation would not make much sense.  
Calculating the posterior probability for a species mean after using individual 
specimens to estimate the mean also does not make sense.  However, a resampling 
procedure that arbitrarily divides the specimens into training and testing 
groups, using the first to estimate coefficients and the second to obtain a 
mean, could be used to generate a confidence interval for the posterior 
classification probabilities of a particular species to its and other species’s 
groups.

The second approach would involve some scripting.  The first approach can be 
done quickly with the by() and summary() functions, e.g.,

by(my.posterior.probs, species, summary)

Hope that helps!
Mike

> On May 7, 2019, at 9:13 AM, Nicole Ibagón  wrote:
> 
> Dear all
> I'm working with five different datasets (lateral and dorsal view of the 
> skull and jaw) of a neotropical bat genus. My research question is if one 
> species (described with a single sample), is a synonym of one of the other 
> species of the genus. I used classify function of RRPP for this purpose, and 
> it solved my question generating one posterior probability for each species 
> of each dataset. However, I would like to know there is a way to generate a 
> single posterior probability for each species.
> Should I join all the datasets before doing the classification analysis? Or 
> should I average the posterior probabilities of all the datasets? Is there a 
> better way to do it?
> Thanks
> 
> -- 
> Nicole Estefanía Ibagón Escobar
> PhD Candidate in Ecology  - UFV (Brazil) 
> BSc Marine Biologist  - Utadeo (Colombia)
> ResearchGate 
> Curriculo CVLAC 
> 
> Curriculo lattes 
> 
> http://evolutionlbe.wix.com/lbeufv 
> 
> < <<  
> 
> -- 
> 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+unsubscr...@morphometrics.org 
> .

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[MORPHMET] help with "classify" in RRPP

[Nicole Ibagón]

Dear all
I'm working with five different datasets (lateral and dorsal view of the
skull and jaw) of a neotropical bat genus. My research question is if one
species (described with a single sample), is a synonym of one of the other
species of the genus. I used classify function of RRPP for this purpose,
and it solved my question generating one posterior probability for each
species of each dataset. However, I would like to know there is a way to
generate a single posterior probability for each species.
Should I join all the datasets before doing the classification analysis? Or
should I average the posterior probabilities of all the datasets? Is there
a better way to do it?
Thanks

-- 
Nicole Estefanía Ibagón Escobar
PhD Candidate in Ecology  - UFV (Brazil)
BSc Marine Biologist  - Utadeo (Colombia)
ResearchGate 
Curriculo CVLAC

Curriculo lattes

http://evolutionlbe.wix.com/lbeufv

< <<

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