[adegenet-forum] dist.genpop giving NaNs

[Thibaut Jombart]

Hi there,

+1 to a reproducible example.

Usual reasons for this would be missing data in  your allele counts.
Check tab(x) where 'x' is your genpop object to have an idea.

Cheers
Thibaut

--
Dr Thibaut Jombart
Lecturer, Department of Infectious Disease Epidemiology, Imperial College London
Head of RECON: repidemicsconsortium.org
sites.google.com/site/thibautjombart/
github.com/thibautjombart
Twitter: @TeebzR
+44(0)20 7594 3658


On 28 March 2017 at 13:28, Roman Luštrik <roman.lustrik at biolitika.si> wrote:
> Can you make a reproducible example and post an issue at GitHub?
> https://github.com/thibautjombart/adegenet/issues
>
> Cheers,
> Roman
>
> ----
> In god we trust, all others bring data.
>
> ________________________________
> From: "Bourne S." <S.Bourne at soton.ac.uk>
> To: adegenet-forum at lists.r-forge.r-project.org
> Sent: Tuesday, March 28, 2017 2:02:01 PM
> Subject: [adegenet-forum] dist.genpop giving NaNs
>
> Hi there,
>
>
> I've got three species I'm looking to do a mantel test on, but for some
> reason only one of them gives results when calculating the genetic distance
> between populations with dist.genpop. All three are based off genepops which
> are generated the same way and in the exact same format. I import them as a
> genind, then reconvert to genpop to run the dist.genpop on. One of them
> works fine, the others give NaN, and then do not work when performing the
> mantel test as NaNs are present.
>
>
> I'm a bit confused because they're all in the same format, and if one works
> then all should work.
>
>
> Has anyone come across this and been able to overcome it?
>
>
> Cheers,
>
> Steve
>
> ---------------------------------------------
> Steven Bourne
> PhD Student - Adaptation and Genomics of Biological Invasions
> School of Ocean and Earth Science
> National Oceanography Centre
> University of Southampton
>
>
>
>
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