[adegenet-forum] Calculating Distances from a connection Network

[Jombart, Thibaut]

Hi there,

yes, the simplest way might be to get the adjacency matrix from the graph and then multiply it by the matrix of geographic distances. Example using nancycats:

## get network
library(adegenet)
data(nancycats)
cn1 <- chooseCN(nancycats at other$xy,ask=FALSE,type=1)

## get adj matrix
M <- neig2mat(nb2neig(cn1))

## get geo dist matrix
G <- as.matrix(dist(other(nancycats)$xy))

## get distances on Delaunay graph
d.delau <- G[M>0]

## range
range(d.delau)

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: 03 June 2015 13:57
To: adegenet-forum at lists.r-forge.r-project.org
Subject: [adegenet-forum] Calculating Distances from a connection Network


Hi there


I am a Masters student running an MSPA to look for Spatial structuring in an invasive species in a South African and Australian context. I am able to run the analyses with no apparent issues but was wondering if anyone knew of a method to calculate the minimum and maximum distances from a Delaunay triangulation connection network.

The reason being that i would like to compare my results between South Africa and Australia but want to be sure the connection extents are comparable. i.e. that the minimum/maximum distance between connected individuals are similar within South Africa and Australia.

I am fairly new to both R and Adegenet and so have only a basic working knowledge.


Regards


David Phair
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