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
signature.asc
Description: This is a digitally signed message part.
_______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
