On Thu, 2006-04-06 at 14:29 +0200, May, Roel wrote: > Dear R-users, > > I intend to do a spatial analysis on the genetic structuring within a > population. For this I had thought to prepare a kernel density estimate > map showing the spatial distribution of individuals, while incorporating > the genetic distances among individuals. I have a dataset of locations > of N unique individuals (XY-coordinates) and an NxN matrix with the > genetic distances given as a fraction between 0 and 1. As far as I > understand the methodology, a kernel density estimate works with the > geographic distance matrix. My idea was to somehow incorporate the > genetic distance matrix (e.g. as an among-individual-based smoothing > factor???) in the estimation. Does anyone know if this is possible? To > me it sounds a logical inclusion which may be interesting for a wide > variety of topics (i.e., "not all individuals are equal"). I hope > someone knows of any way to proceed. Thanks in advance, > >
Dear Roel -- it is not entirely clear what you wish to achieve. Sampling weights associated with a unit can be incorporated at least in the locfit package, which also allows you to do a 2-dimensional density estimate, but this does not sound like what you are interested in. >From your description, it sounds like you have a data set which consists of 1/2*N*(N-1) unique pairs of individuals with data x1 y1 x2 y2 w where (x1, y1) and (x2, y2) are the (x,y) coordinates and w is the genetic distance between the two (there are only 1/2*N*(N-1) on the assumption that the genetic distance for any i,j individuals is symmetric so w(i,j) = w(j, i) and w(i, i) = 1). Are you interested in plotting on a map of (x, y) coordinates some measure of how genetically related the population at the that coordinate are with their surroundinds? I.e., value at x1, y1 of w summarised by a kernel function over all x2, y2? Best wishes, Markus > Cheers Roel May > > > Roel May > Norwegian Institute for Nature Research (NINA) > Tungasletta 2, NO-7485 Trondheim, Norway > Tlf. +47 73 80 14 65, Mob. +47 95 78 59 95 > Email [EMAIL PROTECTED] > Internett www.nina.no, www.jerv.info > > ______________________________________________ > [email protected] mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Markus Jantti Abo Akademi University [EMAIL PROTECTED] http://www.iki.fi/~mjantti ########################################### This message has been scanned by F-Secure Anti-Virus for Mic...{{dropped}} ______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
