[adegenet-forum] UTMs vs lat/lon, and inverse distance network confusion

Jombart, Thibaut t.jombart at imperial.ac.uk
Sun Nov 24 15:45:30 CET 2013


Dear Katherine, 

sPCA uses a rather crude model of spatial proximities (most commonly a binary connection network), so that conversion from latitudes/longitudes, even at that regional scale, should not be much of an issue. 

As for the choice of network or the error you report, it is difficult to provide advice / guess the origin of the error without a spatial distribution of your locations, or a sample of data and code reproducing the error. In general, I would advocated using a binary connection network (e.g. Delaunay's triangulation, Gabriel's graph) where possible. If the sampling design is very uneven, treating clusters as populations (possibly with finer scale, within-population geographic analyses) might be an option.

Cheers
Thibaut

--
######################################
Dr Thibaut JOMBART
MRC Centre for Outbreak Analysis and Modelling
Department of Infectious Disease Epidemiology
Imperial College - School of Public Health
St Mary’s Campus
Norfolk Place
London W2 1PG
United Kingdom
Tel. : 0044 (0)20 7594 3658
t.jombart at imperial.ac.uk
http://sites.google.com/site/thibautjombart/
http://adegenet.r-forge.r-project.org/
________________________________________
From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of katherine.miller [katherine.miller at students.tamuk.edu]
Sent: 23 November 2013 21:36
To: adegenet-forum at lists.r-forge.r-project.org
Subject: Re: [adegenet-forum] UTMs vs lat/lon,  and inverse distance network confusion

Greetings,



I am new to SPCA analysis, and haven't used R that much either.  I have 2 somewhat related questions:



1) I read somewhere that lat and lon have to be converted to UTMs prior to analysis.  I have a rather large spatial area (Iowa to Texas), so it spans 14R to 15T regions.  I've looked at this page, http://www.inside-r.org/packages/cran/PBSmapping/docs/convUL , and I'm wondering about the erroneous results and how this will work.  Has anyone out there done SPCA with a large area?



2) Additionally, I've tried to duplicate a set of data on a smaller scale (XY data is already in UTMs, alleles from 14 loci are in a .gen file), and when I am prompted to choose a network, I choose 7 (inverse distance, the locations are not evenly distributed).  I am prompted to choose an exponent and a minimum distance.  I understand the exponent of 1, I think, but either my understanding of the min distance is wrong, or something else is producing this error:



error in if (any(x < 0)) stop("values in x cannot be negative") : missing value where TRUE/FALSE needed



I have read through the tutorials for spca and adegenet, but clearly I'm still confused.  Any help would appreciated!



Katherine S. Miller

Ph.D. candidate



Caesar Kleberg Wildlife Research Institute

Texas A&M University-Kingsville

MSC 218, 700 University Blvd

Kingsville, TX 78363



(361) 593-4486, office





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