coords.monmonier: Returns original points in results paths of an object of...

In adegenet: Exploratory Analysis of Genetic and Genomic Data

Returns original points in results paths of an object of class 'monmonier'

Description

The original implementation of monmonier in package adegenet returns path coordinates, coords.monmonier additionally displays identities of the original points of the network, based on original coordinates.

Usage

coords.monmonier(x)

Arguments

x	an object of class monmonier.

Value

Returns a list with elements according to the x$nrun result of the monmonier object. Corresponding path points are in the same order as in the original object.

run1 (run2, ...): for each run, a list containing a matrix giving the original points in the network (first and second, indicating pairs of neighbours). Path coordinates are stored in columns x.hw and y.hw. first and second are integers referring to the row numbers in the x$xy matrix of the original monmonier object.

Author(s)

Peter Solymos, [e-mail]

See Also

monmonier

Examples

## Not run: 
if(require(spdep)){

load(system.file("files/mondata1.rda",package="adegenet"))
cn1 <- chooseCN(mondata1$xy,type=2,ask=FALSE)
mon1 <- monmonier(mondata1$xy,dist(mondata1$x1),cn1,threshold=2,nrun=3)

mon1$run1
mon1$run2
mon1$run3
path.coords <- coords.monmonier(mon1)
path.coords
}

## End(Not run)

adegenet documentation built on Feb. 16, 2023, 6 p.m.