[R] weighted kernel density estimate

[Markus Jantti]

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 roel.may at nina.no
> Internett www.nina.no, www.jerv.info
>
> ______________________________________________
> R-help at stat.math.ethz.ch 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
markus.jantti at iki.fi
http://www.iki.fi/~mjantti

###########################################

This message has been scanned by F-Secure Anti-Virus for Mic...{{dropped}}