Ah, right, yes. Then, the only solution would be to calculate with populations instead of individuals, but it also has a lot of drawbacks... Thank You for all the information, Vojtěch
Dne Po 14. července 2014 10:23:08, Jombart, Thibaut napsal(a):
> Should not in principle, but technically will. Monmonier relies on a
> tesselation, and this tesselation will differ each time you jitter your
> coordinates. Cheers
> Thibaut
> ________________________________________
> From: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org]
> on behalf of Vojtěch Zeisek [vo...@trapa.cz] Sent: 14 July 2014 11:19
> To: mailinglist R
> Subject: Re: [R-sig-phylo] [adegenet-forum] Not working Monmonier
>
> Hi,
> thank You for clarification. I tried sPCA, it looks very good. But it was
> also complaining about identical coordinates. One of my questions is about
> amount of migrants among areas, so that sPCA is not the best tool here, I
> think... For Monmonier, I think when I have localities from scale of almost
> 400 km, jitter them to make uncertainty few meters shouldn't matter at all,
> right? Sincerely,
> Vojtěch
>
> Dne Po 14. července 2014 09:54:47 jste napsal(a):
> > Hi Vojtěch
> >
> > Monmonier is not designed for spatial distribution with duplicate
> > locations. Problem is, if you jitter the data, you'll get a different
> > boundary every time you run the analysis.
> >
> > If you're looking for spatial structures, sPCA may be more useful there.
> >
> > Cheers
> > Thibaut
> >
> >
> > ________________________________________
> > From: adegenet-forum-boun...@lists.r-forge.r-project.org
> > [adegenet-forum-boun...@lists.r-forge.r-project.org] on behalf of Vojtěch
> > Zeisek [vo...@trapa.cz] Sent: 13 July 2014 21:18
> > To: Adegenet R-Forum
> > Subject: [adegenet-forum] Not working Monmonier
> >
> > Hello,
> > I tried Monmonier analysis as described in Adegent tutorial. I'm not
> > familiar with that method (for similar question I used IMa2 last time), so
> > I was curious what it does. :-) I tried with relatively relatively large
> > dataset.
> >
> > Individuals from one locality usually have same coordinates. The code:
> > > monmonier <- monmonier(xy=genind$other$xy, dist=dist(genind$tab),
> >
> > cn=chooseCN(genind$other$xy, ask=FALSE, type=5, d1=0, d2=2.5,
> > plot.nb=FALSE, edit.nb=FALSE), nrun=1)
> > Indicate the threshold ('d' for default): d
> >
> > > coords.monmonier(monmonier)
> >
> > Error in output[[runname]]$dir1[i, ] <- halfway[which(eval.x == TRUE & :
> > number of items to replace is not a multiple of replacement length
> >
> > Calls: coords.monmonier
> >
> > > plot(monmonier)
> >
> > Warning messages:
> > 1: In arrows(obj$dir1$path[1:(nrow(obj$dir1$path) - 1), 1],
> > obj$dir1$path[1:>
> > (nrow(obj$dir1$path) - :
> > zero-length arrow is of indeterminate angle and so skipped
> >
> > 2: In arrows(obj$dir1$path[1:(nrow(obj$dir1$path) - 1), 1],
> > obj$dir1$path[1:>
> > (nrow(obj$dir1$path) - :
> > zero-length arrow is of indeterminate angle and so skipped
> >
> > 3: In arrows(obj$dir2$path[1:(nrow(obj$dir2$path) - 1), 1],
> > obj$dir2$path[1:>
> > (nrow(obj$dir2$path) - :
> > zero-length arrow is of indeterminate angle and so skipped
> >
> > 4: In arrows(obj$dir2$path[1:(nrow(obj$dir2$path) - 1), 1],
> > obj$dir2$path[1:>
> > (nrow(obj$dir2$path) - :
> > zero-length arrow is of indeterminate angle and so skipped
> >
> > genind$other$xy contains geographical coordinates in WGS 84 (from GPS).
> > The
> > only problem coming to my mind are those repetitive coordinates (for
> > individuals from one locality) - because of that, chooseCN practically
> > allows only methods 5 and 6. Might be, I could try it with populations,
> > but
> > then I'm afraid to get little bit different information... Or might be I
> > could add some little uncertainty to the coordinates...? I was also
> > thinking if it could be because of missing data, but when I tried with
> > genind object corrected for missing data, I ended up with same errors. Any
> > ideas?
> > Sincerely,
> > Vojtěch
--
Vojtěch Zeisek
http://trapa.cz/en/
Department of Botany, Faculty of Science
Charles University in Prague
Benátská 2, Prague, 12801, CZ
http://botany.natur.cuni.cz/en/
Institute of Botany, Academy of Science
Zámek 1, Průhonice, 25243, CZ
http://www.ibot.cas.cz/en/
Czech Republic
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