[adegenet-forum] Specifying Maximum Distance in a Connection network

[Jombart, Thibaut]

Hi David, 

yes you can do that, though it is not directly implemented in chooseCN. The idea is to get the adjacency matrix, put '0's where needed, and convert it back to a nb object.

Here's an example:
## load data
 > library(adegenet)
> data(nancycats)

## Delaunay triangulation
> cn1 <- chooseCN(nancycats at other$xy,ask=FALSE,type=1)

## that's the adj. matrix
> neig2mat(nb2neig(cn1))
   1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17
1  0 0 0 0 1 0 0 0 1  0  0  1  0  0  0  1  1
2  0 0 0 0 1 0 0 1 1  1  0  0  0  0  0  0  0
3  0 0 0 0 0 1 0 0 0  0  1  0  0  1  0  1  1
4  0 0 0 0 0 0 0 0 0  1  0  1  1  0  1  1  0
5  1 1 0 0 0 1 1 0 1  0  0  0  0  0  0  0  1
6  0 0 1 0 1 0 1 0 0  0  0  0  0  1  0  0  1
7  0 0 0 0 1 1 0 0 0  0  1  0  0  1  0  0  0
8  0 1 0 0 0 0 0 0 1  1  0  1  0  0  0  0  0
9  1 1 0 0 1 0 0 1 0  0  0  1  0  0  0  0  0
10 0 1 0 1 0 0 0 1 0  0  0  1  0  0  0  0  0
11 0 0 1 0 0 0 1 0 0  0  0  0  1  1  1  1  0
12 1 0 0 1 0 0 0 1 1  1  0  0  0  0  0  1  0
13 0 0 0 1 0 0 0 0 0  0  1  0  0  0  1  1  0
14 0 0 1 0 0 1 1 0 0  0  1  0  0  0  0  0  0
15 0 0 0 1 0 0 0 0 0  0  1  0  1  0  0  0  0
16 1 0 1 1 0 0 0 0 0  0  1  1  1  0  0  0  1
17 1 0 1 0 1 1 0 0 0  0  0  0  0  0  0  1  0

## store it
> matConnect <- neig2mat(nb2neig(cn1))

## get geographic distances
> D <- as.matrix(dist(nancycats$other$xy))
> range(D)
[1]   0.0000 369.1358

## new adj. matrix to be pruned
> matConnect2 <- matConnect

## these are links for distances > 150m
> matConnect2[D>150]
  [1] 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0
 [38] 0 0 1 0 1 0 0 0 0 1 1 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0
 [75] 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
[112] 0 0 0 0 0 0 1 0 0 0 0 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0
[149] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 1 0 0 1 0
[186] 0 0 0 0 1

## set these to be all 0
> matConnect2[D>150] <- 0
> library(spdep)

## convert back to nb object
> cn2 <- mat2listw(matConnect2)$neighbours
> cn2
Neighbour list object:
Number of regions: 17 
Number of nonzero links: 60 
Percentage nonzero weights: 20.76125 
Average number of links: 3.529412 

## plot to check the differences
> plot(cn1, coords=nancycats$other$xy)

> plot(cn2, coords=nancycats$other$xy)

If others think it is useful, post a feature request on github:
https://github.com/thibautjombart/adegenet/issues

Cheers
Thibaut

==============================
Dr Thibaut Jombart
MRC Centre for Outbreak Analysis and Modelling
Department of Infectious Disease Epidemiology
Imperial College - School of Public Health
Norfolk Place, London W2 1PG, UK
Tel. : 0044 (0)20 7594 3658
http://sites.google.com/site/thibautjombart/
http://sites.google.com/site/therepiproject/
http://adegenet.r-forge.r-project.org/
Twitter: @thibautjombart



________________________________________
From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Phair, D, Mnr <16187393 at sun.ac.za> [16187393 at sun.ac.za]
Sent: 18 June 2015 09:33
To: adegenet-forum at lists.r-forge.r-project.org
Subject: [adegenet-forum] Specifying Maximum Distance in a Connection network

Hi there


I am a masters Student working on spatial sorting in an invasive Bird.

I am looking at comparing patterns of spatial sorting in a species over two continents.

I am not having any issues with the running of the analysis but i wondered if it was possible to specify a maximum distance for any of the connection network methods other than the minimum spanning tree. as the connectivity in that is to high.

I.E. I would like to use something like Delunay Triangulation but limit the maximum distance so that it is the same in South Africa and Australian Dataset.


Regards


David Phair