[adegenet-forum] function "orthobasis.listw" and global.rtest

[Josie Jackson]

Hello,
Thanks for your reply, I found some script written by Thibaut on this link:

https://github.com/thibautjombart/adegenet/blob/master/R/orthobasis.R

And it worked after running this so the problem is solved but as it says on
the link - this may only be a temporary fix.

Thanks,
Josie

On Mon, Aug 24, 2015 at 12:07 PM, Stéphane Dray <stephane.dray at univ-lyon1.fr
> wrote:

> Hi,
>
> I am not sure about which function you used. The function in adegenet
> seems to work (at least the example). If you used the function included in
> 'sedarJombart' on R-Forge (that included also the mspa function), this
> behavior is 'normal'. I will try to include both mspa and global/local
> tests this afternoon in adespatial.. It will solve the issues.
>
> Cheers
>
>
>
> Le 22/08/2015 14:54, Josie Jackson a écrit :
>
> Hello,
> I am trying to test if I have significant global structure in my sPCA
> using the global rtest however I keep getting an error saying could not
> find function orthobasis.listw. I see that it has been removed from and put
> into adespatial. I have updated R and installed adespatial but I am not
> sure how to get it working again.
> Any hints would be much appreciated!
>
> script:
> SnowyGtest <- global.rtest(objSnowy1sbsp2$tab,mySpcaSnowy1sbsp2$lw, k = 1,
> nperm=99)
>
> Thanks very much,
> Josie
>
> --
> Josie D'Urban Jackson
>
> Ph.D student
> Department of Biology & Biochemistry
> University of Bath
> Claverton Down
> Bath
> BA2 7AY
> United Kingdom
>
> Cardiff University School of Biosciences,
> The Sir Martin Evans Building
> Museum Avenue
> Cardiff
> CF103AX
> United Kingdom
>
>
> _______________________________________________
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>
>
>
> --
> Stéphane DRAY (stephane.dray at univ-lyon1.fr)
> Laboratoire BBE-CNRS-UMR-5558, Univ. C. Bernard - Lyon I
> 43, Bd du 11 Novembre 1918, 69622 Villeurbanne Cedex, France
> Tel: 33 4 72 43 27 57       Fax: 33 4 72 43 13 88http://pbil.univ-lyon1.fr/members/dray/
>
>
>


-- 
Josie D'Urban Jackson

Ph.D student
Department of Biology & Biochemistry
University of Bath
Claverton Down
Bath
BA2 7AY
United Kingdom

Cardiff University School of Biosciences,
The Sir Martin Evans Building
Museum Avenue
Cardiff
CF103AX
United Kingdom
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