chooseCN {adegenet}R Documentation

Function to choose a connection network

Description

The function chooseCN is a simple interface to build a connection network (CN) from xy coordinates. The user chooses from 6 types of graph and one additional weighting scheme. chooseCN calls functions from appropriate packages, handles non-unique coordinates and returns a connection network either with classe nb or listw.

Usage

chooseCN(xy, ask = TRUE, type = NULL, result.type = "nb", d1 = NULL, 
    d2 = NULL, k = NULL,  a=NULL, dmin=NULL, plot.nb = TRUE, edit.nb = FALSE) 

Arguments

xy an matrix or data.frame with two columns for x and y coordinates.
ask a logical stating whether graph should be chosen interactively (TRUE,default) or not (FALSE). Set to FALSE if type is provided.
type an integer giving the type of graph (see details).
result.type a character giving the class of the returned object. Either "nb" (default) or "listw", both from spdep package. See details.
d1 the minimum distance between any two neighbours. Used if type=5.
d2 the maximum distance between any two neighbours. Used if type=5. Can also be a character: "dmin" for the minimum distance so that each site has at least one connection, or "dmax" to have all sites connected (despite the later has no sense).
k the number of neighbours per point. Used if type=6.
a the exponent of the inverse distance matrix. Used if type=7.
dmin the minimum distance between any two distinct points. Used to avoid infinite spatial proximities (defined as the inversed spatial distances). Used if type=7.
plot.nb a logical stating whether the resulting graph should be plotted (TRUE, default) or not (FALSE).
edit.nb a logical stating whether the resulting graph should be edited manually for corrections (TRUE) or not (FALSE, default).

Details

There are 7 kinds of graphs proposed:
Delaunay triangulation (type 1)
Gabriel graph (type 2)
Relative neighbours (type 3)
Minimum spanning tree (type 4)
Neighbourhood by distance (type 5)
K nearests neighbours (type 6)
Inverse distances (type 7)

The last option (type=7) is not a true neighbouring graph: all sites are neighbours, but the spatial weights are directly proportional to the inversed spatial distances.
Also not that in this case, the output of the function is always a listw object, even if nb was requested.

Value

Returns a connection network having the class nb or listw. The xy coordinates are passed as attribute to the created object.

Author(s)

Thibaut Jombart jombart@biomserv.univ-lyon1.fr

See Also

spca

Examples

data(nancycats)
if(require(spdep) & require(ade4)){

par(mfrow=c(2,2))
cn1 <- chooseCN(nancycats@other$xy,ask=FALSE,type=1)
cn2 <- chooseCN(nancycats@other$xy,ask=FALSE,type=2)
cn3 <- chooseCN(nancycats@other$xy,ask=FALSE,type=3)
cn4 <- chooseCN(nancycats@other$xy,ask=FALSE,type=4)
par(mfrow=c(1,1))
}

[Package adegenet version 1.2-2 Index]