<div dir="ltr">Hello, <div><br></div><div>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.</div><div><br></div><div>Best</div><div>Thibaut</div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div><div><br>--<br>Dr Thibaut Jombart<br>Lecturer, Department of Infectious Disease Epidemiology<br></div></div>Imperial College London<br><a href="https://sites.google.com/site/thibautjombart/" target="_blank">https://sites.google.com/site/thibautjombart/</a><br></div><div><a href="https://github.com/thibautjombart" target="_blank">https://github.com/thibautjombart<br></a></div>Twitter: <a href="https://twitter.com/TeebzR" target="_blank">@TeebzR</a><br></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On 2 September 2016 at 20:28, Alan Garcia-Elfring <span dir="ltr"><<a href="mailto:alangarcia87@hotmail.com" target="_blank">alangarcia87@hotmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div><div dir="ltr"><br>Thanks!<div>However, i<span style="color:rgb(68,68,68);font-size:15px;line-height:21.3px;background-color:rgb(255,255,255)">s there a way to check for IBD for a subset of the genetic a geographical distances, like the in the data frame below? </span></div><div><span style="color:rgb(68,68,68);font-size:15px;line-height:21.3px;background-color:rgb(255,255,255)">My sites are separated by 2 rivers (3 transects) so I'd like to test for IBD within transects.</span></div><div><span style="color:rgb(68,68,68);font-size:15px;line-height:21.3px;background-color:rgb(255,255,255)"><br></span></div><div><span style="color:rgb(68,68,68);font-size:15px;line-height:21.3px;background-color:rgb(255,255,255)">Ex: the differentiation and the distance of 10 sites relative to their southern-most site</span><div style="line-height:21.3px;color:rgb(68,68,68);font-size:15px;background-color:rgb(255,255,255)"><br style="line-height:21.3px"></div><div style="line-height:21.3px;color:rgb(68,68,68);font-size:15px;background-color:rgb(255,255,255)"><div style="line-height:21.3px">Sites (km) Fst</div><div style="line-height:21.3px">N2 37.56 0.0431971</div><div style="line-height:21.3px">N3 120.05 0.0521581</div><div style="line-height:21.3px">N4 148.25 0.0570743</div><div style="line-height:21.3px">SW2 19.94 0.0365175</div><div style="line-height:21.3px">SW3 23.55 0.0340058</div><div style="line-height:21.3px">SW4 55.50 0.0412582</div><div style="line-height:21.3px">SW5 56.83 0.0404807</div><div style="line-height:21.3px">SE2 40.35 0.0374914</div><div style="line-height:21.3px">SE3 66.39 0.0357506</div><div style="line-height:21.3px">SE4 89.53 0.0404285</div><div style="line-height:21.3px"><br style="line-height:21.3px"></div><div style="line-height:21.3px">It may not be applicable to the mantel.randtest() but I'm not sure. </div><div style="line-height:21.3px">Thanks, again. </div><span class="HOEnZb"><font color="#888888"><div style="line-height:21.3px">Alan</div></font></span></div><br><div class="hm HOEnZb"><br></div><div><div class="hm HOEnZb"><hr>From: <a href="mailto:thibautjombart@gmail.com" target="_blank">thibautjombart@gmail.com</a><br>Date: Fri, 2 Sep 2016 10:18:49 +0100<br>Subject: Re: [adegenet-forum] IBD test: Adding spatial variable to "optional content" of genepop object<br>To: <a href="mailto:alangarcia87@hotmail.com" target="_blank">alangarcia87@hotmail.com</a><br>CC: <a href="mailto:adegenet-forum@lists.r-forge.r-project.org" target="_blank">adegenet-forum@lists.r-forge.<wbr>r-project.org</a></div><div><div class="h5"><br><br><p dir="ltr">Hi there</p>
<p dir="ltr">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<br>
Where 'x' is your genind or genpop. Accessors are documented in the basics tutorial (adegenetTutorial()). </p>
<p dir="ltr">Cheers<br>
Thibaut</p>
<div><br><div>On 1 Sep 2016 20:15, "Alan Garcia-Elfring" <<a href="mailto:alangarcia87@hotmail.com" target="_blank">alangarcia87@hotmail.com</a>> wrote:<br><blockquote style="border-left:1px #ccc solid;padding-left:1ex">
<div><div dir="ltr">Hi everyone, <div><br></div><div>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. </div><div><br></div><div>How does one incorporate the spatial data into the "optional content" ?</div><div><br></div><div>Any help is greatly appreciated. </div><div><br></div><div>Best, </div><div>Alan</div><div><br></div><div><br></div><div> </div> </div></div>
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