chooseCN {adegenet} | R Documentation |
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
.
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)
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). |
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.
Returns a connection network having the class nb
or
listw
. The xy coordinates are passed as attribute to the
created object.
Thibaut Jombart jombart@biomserv.univ-lyon1.fr
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)) }