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 <nicole...@gmail.com
> <javascript:>> 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 <https://www.researchgate.net/profile/Nicole_Ibagon>
> Curriculo CVLAC
> <http://190.216.132.131:8081/cvlac/visualizador/generarCurriculoCv.do?cod_rh=0001219782>
> Curriculo lattes
> <http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4371000E6>
> http://evolutionlbe.wix.com/lbeufv
>
> <o)))>< <o)))>< <o)))><
>
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