Re: [R] Modeling presence only data in R

From: Clément Calenge <calenge_at_biomserv.univ-lyon1.fr>
Date: Wed, 23 Apr 2008 16:50:50 +0200

Actually, the ENFA (function enfa, in the package adehabitat) is not really suitable for modelling environment suitability maps (though it is still useful to discover the patterns of the ecological niche with presence-only data). However, the package adehabitat also contains other functions allowing this kind of modelling: the Mahalanobis distances (function mahasuhab) and their factorial decomposition (function madifa) could be a useful approach. See:

Calenge C, Darmon G, Basille M, Loison A, Jullien JM. (2008) The factorial decomposition of the Mahalanobis distances in habitat selection studies. Ecology, 89, 555-566.

and references therein. You may also consider the GNESFA, a generalization of the MADIFA/ENFA approach (see the function gnesfa and references therein). Other commonly used approaches are also available in adehabitat.
Best wishes,

Clément Calenge.

Stéphane Dray wrote:
> Ecological Niche Factor Analysis (ENFA) is implemented in the adehabitat
> package available on CRAN.
>
> Cheers,
>
>
>
> Alejandro González wrote:
>
>> Dear Milton, you have 2 packages for modelling species distribution in
>> R: grasper and Biomod (by Wilfried Thuiller), but they are all
>> presence-absence models, so you must generate pseudoabsences for each
>> species, following recommendations in papers (see Lobo 2007). On the
>> other side, there are free gis tools to perform presence-only models
>> (Biomapper, GARP, Openmodeller). Write me if you need if you want some
>> advice.
>>
>>
>>
>>
>
>

-- 
Clément CALENGE
Observatoire des galliformes de montagne
Office national de la chasse et de la faune sauvage
Saint Benoist - 78610 Auffargis
tel. (33) 01.30.46.54.14

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