Dear Dr. Tobler,
I am doing some simulations and would like to
create UDs directly as rasters (as opposed to
simulating point locations and then using a
kernel to create the UD). The most simple example
would be a bivariat-normal UD. I would then like
to calculate contour lines on those UDs using the
standard functions in adehabitat. However, I
realized that I don't know how the raster values
of the UD are scaled. I thought that this was a
probability surface and that they would sum to 1,
but that does not seem to be the case. So right
now my volume calculations and therefore my
contour lines are off. Any suggestions on how to
scale my UD rasters in order to get correct results?
The UD is a probability density function, i.e. a function such that the
*volume* under the surface of the UD is equal to 1. Therefore, for each
pixel, you have to multiply the values of the UD by the cellsize of the
map to obtain the volume. Taking the dataset puechabon as an example
(just copy and paste):
library(adehabitat)
data(puechabon)
loc <- puechabon$locs[, c("X", "Y")]
id <- puechabon$locs[, "Name"]
## Estimation of UD for the four animals
ud <- kernelUD(loc, id)
## Sum of the UD for the first animal:
sum(ud[[1]]$UD)
## [1] 0.0005146571
## Does not sum to one. But see the cellsize of the map:
ud[[1]]$UD
## Raster map of class "asc":
## Cell size: 44.025
## Number of rows: 58
## Number of columns: 80
## Type: numeric
## Each pixel covers 44.025x44.025 m
## Therefore:
sum(ud[[1]]$UD)*44.025*44.025
## [1] 0.9975087
## This is the same calculation:
sum(ud[[1]]$UD)*((attr(ud[[1]]$UD, "cellsize"))^2)
## [1] 0.9975087
When multiplied by the cellsize, the sum of the UD over the whole plane
is equal to 1. In this case, the result is not exactly one, because the
map does not cover the whole plane (it is a limited area, i.e. not the
infinite plane). But the result is close to 1.
To have more information on the derivation of home-ranges from UD, see
the function getvolumeUD.
HTH,
Clément Calenge.
--
Clément CALENGE
Cellule d'appui à l'analyse de données
Direction des Etudes et de la Recherche
Office national de la chasse et de la faune sauvage
Saint Benoist - 78610 Auffargis
tel. (33) 01.30.46.54.14
_______________________________________________
AniMov mailing list
[email protected]
http://lists.faunalia.it/cgi-bin/mailman/listinfo/animov
