[adegenet-forum] IBD test: Adding spatial variable to "optional content" of genepop object

[Thibaut Jombart]

Hello,

the practice you describe is a Mantel correlogram. It is not, to my
knowledge, implemented in ade4, but I think it is in the package vegan.

Best
Thibaut


--
Dr Thibaut Jombart
Lecturer, Department of Infectious Disease Epidemiology
Imperial College London
https://sites.google.com/site/thibautjombart/
https://github.com/thibautjombart
Twitter: @TeebzR <https://twitter.com/TeebzR>

On 2 September 2016 at 20:28, Alan Garcia-Elfring <alangarcia87 at hotmail.com>
wrote:

>
> Thanks!
> However, is there a way to check for IBD  for a subset of the genetic a
> geographical distances, like the in the data frame below?
> My sites are separated by 2 rivers (3 transects) so I'd like to test for
> IBD within transects.
>
> Ex: the differentiation and the distance of 10 sites relative to their
> southern-most site
>
> Sites                     (km)                   Fst
> N2                       37.56             0.0431971
> N3                      120.05             0.0521581
> N4                      148.25             0.0570743
> SW2                       19.94             0.0365175
> SW3                       23.55             0.0340058
> SW4                       55.50             0.0412582
> SW5                       56.83             0.0404807
> SE2                       40.35             0.0374914
> SE3                       66.39             0.0357506
> SE4                      89.53             0.0404285
>
> It may not be applicable to the mantel.randtest() but I'm not sure.
> Thanks, again.
> Alan
>
>
> ------------------------------
> From: thibautjombart at gmail.com
> Date: Fri, 2 Sep 2016 10:18:49 +0100
> Subject: Re: [adegenet-forum] IBD test: Adding spatial variable to
> "optional content" of genepop object
> To: alangarcia87 at hotmail.com
> CC: adegenet-forum at lists.r-forge.r-project.org
>
>
> Hi there
>
> You can read xy coordinates separately using read.csv, read.table etc. For
> the test there is no need to attach the xy coordinates to the object. But
> to do so, use other(x)$xy <- xy
> Where 'x' is your genind or genpop. Accessors are documented in the basics
> tutorial (adegenetTutorial()).
>
> Cheers
> Thibaut
>
> On 1 Sep 2016 20:15, "Alan Garcia-Elfring" <alangarcia87 at hotmail.com>
> wrote:
>
> Hi everyone,
>
> I'm trying to use the IBD test shown on chapter 7 of the tutorial. The
> example data used, spcaIllus, has spatial information that my .genepop
> files do not have.
>
> How does one incorporate the spatial data into the "optional content" ?
>
> Any help is greatly appreciated.
>
> Best,
> Alan
>
>
>
>
> _______________________________________________
> adegenet-forum mailing list
> adegenet-forum at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo
> /adegenet-forum
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.r-forge.r-project.org/pipermail/adegenet-forum/attachments/20160905/f294e692/attachment.html>