[adegenet-forum] Handling Missing Spatial Data in genind2genpop

[Zhian Kamvar]

Hello Dr. Neel,

You can use an anonymous function. I.E: other.action = function(x){ mean(x, na.rm = TRUE) }

Hope that helps!
Zhian

-----
Zhian N. Kamvar, Ph. D.
Postdoctoral Researcher (Everhart Lab)
Department of Plant Pathology
University of Nebraska-Lincoln
ORCID: 0000-0003-1458-7108



> 
> Date: Sat, 4 Nov 2017 17:35:31 -0400
> From: Maile C Neel <mneel at umd.edu>
> To: adegenet-forum at lists.r-forge.r-project.org
> Subject: [adegenet-forum] Handling Missing Spatial Data in
> 	genind2genpop
> Message-ID:
> 	<CAEdnyY=WncVKKWh7cJ3ehg4LeJpRTcxvANt0DD67M3BsR15igA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
> 
> Apologies if this seemingly simple question has been answered before.  I
> have found nothing from extensive searches of manuals and adegenet archives.
> 
> In my data set of 1,110+ individuals from 25 sites, a few individuals at 2
> sites lack GPS coordinates. For pairwise comparisons of individuals that
> require coordinates, I eliminate samples with missing location data.
> 
> However, when I am collapsing the data set to populations using
> genind2genpop I would like to keep the genetic data from all samples and
> ignore the NA values in the genind at other$utms slot.  If  even one sample in
> a population is missing utm coordinates, the population values are NA
> 
> I want the population centroid returned to the genpop at other$utms slot to be
> the mean of the samples that DO have utm coordinates.  The distances among
> populations are so large that any error introduced by a small number of
> missing locations will not affect my results.
> 
> I know how to specify a basic function for other.action (e.g.,
> other.action=mean), but I can't see how to specify something like
> na.remove, na.omit, or complete.cases that would calculate the mean
> ignoring missing data..  Another option would be to replace missing
> @other$utms values with mean values for the population based on complete
> cases from within the genind2genpop call, but that also does not appear to
> be possible.
> 
> Is there an easy way to keep all my genetic observations and get a
> population centroids ignoring missing coordinates?
> 
> ____________
> Maile Neel
> Professor; Director of the Norton-Brown Herbarium
> University of Maryland
> Department of Plant Science and Landscape Architecture &
> Department of Entomology
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