Dear All, I have a set of environental maps and presence-only points for some species. How can I generate distributions models on R using these presence-only data? What packages and functions can I use to do so? Kind regards, Miltinho Brazil [[alternative HTML version deleted]]
milton ruser wrote:> Dear All, > > I have a set of environental maps and presence-only points for some species. > How can I generate distributions models on R using these presence-only data? > What packages and functions can I use to do so? > > Kind regards, > > Miltinho > BrazilIf you have location data for each absence/presence (such as linear location data, easting and northing) consider using geoRglm. Christensen, O. F., and Ribeiro, P. J. 2002. geoRglm: a package for generalized linear spatial models. R-NEWS, 2: 26?28. HTH Rub?n
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. -- Alejandro Gonz?lez Fern?ndez de Castro Departamento de Biodiversidad y Conservaci?n Real Jard?n Bot?nico (Consejo Superior de Investigaciones Cient?ficas) Plaza de Murillo, 2 28014 Madrid - Spain 00 34 91 4203017
Ecological Niche Factor Analysis (ENFA) is implemented in the adehabitat package available on CRAN. Cheers, Alejandro Gonz?lez 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. > > >-- St?phane DRAY (dray at biomserv.univ-lyon1.fr ) Laboratoire BBE-CNRS-UMR-5558, Univ. C. Bernard - Lyon I 43, Bd du 11 Novembre 1918, 69622 Villeurbanne Cedex, France Tel: 33 4 72 43 27 57 Fax: 33 4 72 43 13 88 http://biomserv.univ-lyon1.fr/~dray/
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, Cl?ment Calenge. St?phane Dray wrote:> Ecological Niche Factor Analysis (ENFA) is implemented in the adehabitat > package available on CRAN. > > Cheers, > > > > Alejandro Gonz?lez 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. >> >> >> >> > >-- Cl?ment 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