[adegenet-forum] snapclust

[Thibaut Jombart]

Hi there,

I would analyse the empirical data separately. If you have clearly
identified parental populations (i.e. prior knowledge, not identified by
the method), sure you can benchmark the method using simulated hybrids.
Otherwise, simulations will have less interest.

How would you go about bootstrapping the final probabilities?

Best
Thibaut


--
Dr Thibaut Jombart
Lecturer, Department of Infectious Disease Epidemiology, Imperial College
London
Head of RECON: repidemicsconsortium.org
WHO Consultant - outbreak analysis
https://thibautjombart.netlify.com
Twitter: @TeebzR
+44(0)20 7594 3658

On 31 January 2018 at 00:18, Danielle Louise <danielledanielle89 at gmail.com>
wrote:

> Hello. I am looking at implementing your snapclust function, and I am
> reading through your recent paper.
>
>  I have a few questions regarding incorporating empirical data. I have
> simulated data sets with parental and F1 F2 and BC and I am wondering how
> to incorporate the empirical data - do I add it in to the simulated data
> and measure the accuracy of the assignment to classes to then determine the
> reliability of detection of hybrids in the empirical data? The tutorial
> gives a good outline of using the simulated data, but I think I am missing
> something when it comes to checking the empirical data, so I am asking for
> some really practical advice about how to incorporate the empirical data ?
> Also should we bootstrap the final probabilities to clarify the results?
>
> Thanks
> Dan
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