[adegenet-forum] adegenet package: Monmonier function data export

[Thibaut Jombart]

James Cheshire wrote:
> Dear adegenet users,
>
> When I print the Monmonier object class it only lists the coordinates 
> of the the first three points in each run as follows:
>
> $call:monmonier(xy = Coordinates, dist = Dist, cn = nbDelaunay, nrun = 
> 20,
>     scanthres = TRUE)
>
>       # Object content #
> Class:  monmonier
> $nrun (number of successive runs):  20
> $run1 ... $run20: runs of the algorithm
> $threshold (minimum difference between neighbours):  0.4003
> $xy: spatial coordinates
> $cn: connection network
>
>       # Runs content #
> # Run 1
> # First direction
> Class:  list
> $path:
>                x        y
> Point_1 361546.4 280420.0
> Point_2 376145.2 284840.4
> Point_3 387056.9 281490.3
> ...
>
>
> Is it possible to print or extract all the coordinates used to plot 
> the Monmonier boundaries? My reason for doing this is so that I can 
> export them into a Geographical Information System software package.
>
> Many thanks for your help in advance, it is greatly appreciated.
>
> James Cheshire
>
> PhD Student
> University College London
>
Hello James,

yes, it is possible (see ?monmonier, "value" section for a description 
of monmonier objects). Here is an example:

##
library(adegenet)
load(system.file("files/mondata2.rda",package="adegenet"))
cn2 <- chooseCN(mondata2$xy,type=1,ask=FALSE)
mon2 <- monmonier(mondata2$xy,dist(mondata2$x2),cn2,threshold=2, nrun=3)
plot(mon2,mondata2$x2,method="greylevel",add.arr=FALSE,bwd=6,col=c("red","blue","green"),csize=.5)

mon2$run1 # gives the content of first boundary
mon2$run1$dir1 # gives the content of first boundary, 1st direction
mon2$run1$dir1$path  # gives the content of first boundary, 1st 
direction, coordinates
##

Another simpler way maybe using Peter Solymos's coords.monmonier (see 
?coords.monmonier):
##
 > coords.monmonier(mon2)

$run1
$run1$dir1
            x.hw     y.hw first second
Point_1 5.585655 3.353934    16     50
Point_2 6.175788 3.745792    16     37
Point_3 6.050270 4.321076    37     50
Point_4 6.456283 4.801207    36     37
Point_5 7.097451 5.369001    21     36
Point_6 6.246300 5.912191    26     36
Point_7 5.534326 6.166065    26     34

$run1$dir2
            x.hw     y.hw first second
Point_1 5.585655 3.353934    16     50
Point_2 5.304805 3.512757     3     50
Point_3 4.769548 3.836670     3     15
[...]
##

Best,

Thibaut.

-- 
######################################
Dr Thibaut JOMBART
CNRS UMR 5558 - Laboratoire de Biométrie et Biologie Evolutive
Universite Lyon 1
43 bd du 11 novembre 1918
69622 Villeurbanne Cedex
Tél. : 04.72.43.29.35
Fax : 04.72.43.13.88
jombart at biomserv.univ-lyon1.fr
http://biomserv.univ-lyon1.fr/%7Ejombart/
http://adegenet.r-forge.r-project.org/
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