Dear Markus, I indeed have a data set consisting of 1/2*N*(N-1) unique pairs of individuals with data
x1 y1 x2 y2 w I am however not interested in, like you said, the value at x1, y1 of w summarised by a kernel function over all x2, y2 (if I understand you rightly that is...). This sounds like doing a weighted kernel density estimate as seen from the 'viewpoint' of a certain location/individual. I know could be done with sm.density in the sm library. I am interested to create a map depicted the total structuring in the entire population (both based on geographic and genetic distances). This means that the evaluation/interpolation at each location have to take into account both the geographic AND the genetic distance matrix (both with 1/2*N*(N-1) unique combinations). To clarify myself a bit more, such a map could show for example differentiation in the population (of wolverines by the way) because of large geographic distances OR because of large genetic distances. I have quickly checked locfit but I am not sure if this would work for me. Roel -----Original Message----- From: Markus Jantti [mailto:[EMAIL PROTECTED] Sent: 6. april 2006 14:56 To: [email protected] Cc: May, Roel Subject: Re: [R] weighted kernel density estimate 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
