[R-sig-Geo] kernelbb: getverticeshr and kernel.area do not return same results

[Calenge Clement]

Dear Anna-Marie,


> I have a problem with calculating UD areas: I calculated UDs by
> kernelbb(). When I use the getverticeshr command and after that the
> kernel.area command, the results differ. Does anyone see my mistake?

The mistake is here:

kernelcontoursha111_50  <- getverticeshr(ha111BbKern,lev=50, unout="km2")

The level should not be defined with lev, but with percent (see the help 
page of getverticeshr). The correct code should therefore be:

kernelcontoursha111_50  <- getverticeshr(ha111BbKern, percent=50, 
unout="km2")

However, note that the two approaches do not rely on the same algorithm 
to calculate the area of the kernel home range, so that a small 
difference is expected. On one hand, getverticeshr vectorizes the 
contour of the home range (i.e. finds the coordinates of the vertices of 
the contour polygon corresponding to a given isopleth) and then 
calculates the area of the resulting polygon. On the other hand, 
kernel.area uses the raster grid used for the kernel estimation to find 
the pixels located in the home range, and then sums the areas of these 
pixels. Therefore, a small variation is expected due to the difference 
of modes (vector vs. raster) used in calculations.

For example, consider the following example (just copy and paste in R):

## use the dataset puechcirc
library(adehabitatHR)
data(puechcirc)
x <- puechcirc[1]
ud <- kernelbb(x, sig1 = 6.23, sig2 = 58, grid = 100)
kernel.area(ud, unout="km2", percent=50)
#       50
#0.3231074
getverticeshr(ud, unout="km2", percent=50)
#Object of class "SpatialPolygonsDataFrame" (package sp):
#
#Number of SpatialPolygons:  1
#
#Variables measured:
#                 id      area
#homerange homerange 0.3164564

as you can see, the two results are pretty similar, though not exactly 
identical.

Best regards,


Clément Calenge




>
> Thanks a lot and best regards,
> Anna
>
>
>> head(dcol[,c(1:11,17,25:27)])
>           date day month year hour minute second time_sec time_diff latitude longitude
> 1 13.05.2011  13     5 2011   21     11     33    76293       186 54.70463  8.349938
> 2 13.05.2011  13     5 2011   21     14     37    76477       184 54.70479  8.349722
> 3 13.05.2011  13     5 2011   21     17     40    76660       183 54.70548  8.344133
> 4 13.05.2011  13     5 2011   21     20     44    76844       184 54.71007  8.338260
> 5 13.05.2011  13     5 2011   21     23     48    77028       184 54.72099  8.320427
> 6 13.05.2011  13     5 2011   21     26     52    77212       184 54.73233  8.312453
>      bird_id                 cet   xKoord  yKoord
> 1 HA1_2011 2011-05-13 21:11:33 458111.9 6062117
> 2 HA1_2011 2011-05-13 21:14:37 458098.1 6062135
> 3 HA1_2011 2011-05-13 21:17:40 457738.7 6062216
> 4 HA1_2011 2011-05-13 21:20:44 457365.1 6062730
> 5 HA1_2011 2011-05-13 21:23:48 456227.9 6063956
> 6 HA1_2011 2011-05-13 21:26:52 455726.7 6065223
>
>
>
> #### create ltraj elements:
> ##HA1_2011
> ha111<-subset(dcol,bird_id=="HA1_2011")
> ha111time <- ha111[, c("cet")]
> ha111XY <- ha111[,c("xKoord", "yKoord")]
> ha111ltraj <- as.ltraj(ha111XY, ha111time, id="HA1_2011")
> ha111Liker <- liker (ha111ltraj, sig2=20, rangesig1=c(1,100) )
> ha111Liker
> head(ha111Liker)
> ha111BbKern <- kernelbb(ha111ltraj, sig1=18.5405, sig2=20)
>
> kernelcontoursha111_50  <- getverticeshr(ha111BbKern,lev=50, unout="km2")
> # Object of class "SpatialPolygonsDataFrame" (package sp):
>
> Number of SpatialPolygons:  1
>
> Variables measured:
>                    id     area
> homerange homerange 6.055773
>
> ## kernel areas:
> ha111area<-kernel.area(ha111BbKern, unout=c("km2"),percent=50) ## 0.9744107
>
>
>
>
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>
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>


-- 
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