[R-sig-eco] AdehabitatHR package on R

[Clement Calenge]

On 05/23/2013 07:22 PM, Dylann Kersusan wrote:
> Dear list,
>
> I have been "handling" the adehabitatHR package quit a lot these last days.
> I have few questions regarding this:
>
> -first: regarding the getverticehr() "function". I am actually estimating
> activity UDs with the Biased Random Bridges method (from Benhamou 2011). Is
> there any way to get the UD's size?

 From the help page of the function BRB():

‘BRB’ returns an object of class ‘estUDm’ when the UD is estimated
for several animals, and ‘estUD’ when only one animal is studied.

 From the help page of the function getverticeshr(), the main argument x is:

x: For ‘getverticeshr.estUD’, an object of class ‘estUD’. For
‘getverticeshr.estUDm’, an object of class ‘estUDm’. For
‘getverticeshr.MCHu’, an object of class ‘MCHu’.

So yes, you can use getverticeshr() to estimate the home range size.

>   Is the function getverticehr() is
> working fine for such purpose?

Yes.


> And is this function by default giving UD's
> size in ha (I think so)?

 From the help page of getverticeshr(), there are two arguments:

unin: the units of the relocations coordinates. Either "m" for
meters (default) or "km" for kilometers

unout: the units of the output areas. Either "m2" for square
meters, "km2" for square kilometers or "ha" for hectares
(default)

So yes, if your input units are meters, the default output units are 
hectares.

> -second: regarding the kernelUD() method for UDs estimation. I applied this
> method to estimate UDs, using the h="href", and later on extracting the h
> value from it. So I can re estimate a new UD with the h value (the
> extracted one). But I have also been calculating the h value thanks to this
> formula: sigma*n^-1/6; which gives me a slightly different h value. So, I
> was wondering how exactly the function calculates the h value? Why do I get
> a different value (I do the calculation under R and there is no "possible"
> error)?
> sigma=0.5(sd(x)+sd(y))

Actually, there is an error on the help page. The value of Sigma is 
actually calculated with:

Sigma = sqrt(0.5*(var(x) + var(y)))

as recommended by Silverman (1986. Density estimation, p. 87). The help 
page will be corrected in the next version of the package.
Thanks for reporting.
Best regards,

Clément Calenge

-- 
Clément CALENGE
Cellule d'appui à l'analyse de données
Direction des Etudes et de la Recherche
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