[adegenet-forum] Dealing with "Duplicate" Locations

[Thibaut Jombart]

Dear Maile,

can you file an issue on github about this? The fix should be quick to make.
https://github.com/thibautjombart/adegenet/issues

Best
Thibaut


--
Dr Thibaut Jombart
Lecturer, Department of Infectious Disease Epidemiology, Imperial College
London
Head of RECON: repidemicsconsortium.org
sites.google.com/site/thibautjombart/
github.com/thibautjombart
Twitter: @TeebzR <http://twitter.com/TeebzR>

On 22 October 2016 at 19:29, Maile C Neel <mneel at umd.edu> wrote:

> I am having the same problem described in the link below in which
> duplicate locations are erroneously identified when I try to create a CN
> object using chooseCN in adegenet 2.0.1 to implement Monomonier's
> algorithm.
>
> http://lists.r-forge.r-project.org/pipermail/adegenet-forum/
> 2011-October/000427.html
>
> I could not find how the previous thread was resolved despite extensive
> searching. Apologies if it was in the archives and I missed it.
>
> I call chooseCN using the following command for which my genind object
> holds genetic and spatial data for 374 unique genotypes at unique
> locations.  The minimum distance between nearest neighbors is 5 m. The
> (admittedly non-reproducible) code I use is
>
> hudnet <- chooseCN(hudson_noreps.ind$other$latlong, ask=FALSE, type=1)
>
> Although all my locations are in fact unique, checking my data with
> tableXY and sunflowerplot as suggested in the old thread show me that many
> unique locations are being pooled due to rounding.  Even with jittering
> with default settings (which I don't really want to do) duplicates
> remain. I do not want to delete the close individuals because they
> contribute to the local estimates of genetic diversity.
>
> The thread indicates it is possible to alter the function chooseCN to
> force it to pass the proper argument to tableXY.  The minimum distances
> appear to be adjusted in lines 91 & 92 in the code for the chooseCN
> function at GitHub
> <https://github.com/cran/adegenet/blob/master/R/chooseCN.R>:
>
> 91 d2min <- max(apply(tempmat, 1, function(r) min(r[r>1e-12])))
> 92 d2min <- d2min * 1.0001 # to avoid exact number problem
>
> Rounding to 1.0001 is collapsing samples that are 7-10 m apart given my
> latitude, which makes many of my samples ~5 m apart appear to be
> identical. Is there some way for me to modify this code in chooseCN to
> prevent the rounding of my spatial coordinates? I think it is not something
> I can modify on my own.  Are there other workarounds or solutions?
>
> I understand the problem with duplicate locations, but is there a minimum
> distance that is acceptable for the algorithms that based on connection
> networks?
>
> Thanks in advance,
>
> Maile Neel
> Associate Professor; Director of the Norton-Brown Herbarium
> University of Maryland
> Department of Plant Science and Landscape Architecture &
> Department of Entomology
>
>
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