[adegenet-forum] IBD test: Adding spatial variable to "optional content" of genepop object
thibautjombart at gmail.com
Mon Sep 5 11:48:56 CEST 2016
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.
Dr Thibaut Jombart
Lecturer, Department of Infectious Disease Epidemiology
Imperial College London
Twitter: @TeebzR <https://twitter.com/TeebzR>
On 2 September 2016 at 20:28, Alan Garcia-Elfring <alangarcia87 at hotmail.com>
> 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.
> 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()).
> On 1 Sep 2016 20:15, "Alan Garcia-Elfring" <alangarcia87 at hotmail.com>
> 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.
> adegenet-forum mailing list
> adegenet-forum at lists.r-forge.r-project.org
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