Ecological Niche Modelling on R

Finally, in fact GRASP do what I am looking for, and I am starting to
compare the results of this packages with other very wel- know softwares
(DescktopGarp, Maxent, OpenModeller). If someone of you have suggestions of
other R-solutions for Ecological Niche Models, please, let-me know.

Regards a lot.
Savava.


Miltinho Astronauta
Brazil


On Wed, Oct 8, 2008 at 6:02 AM, Cl?ment Calenge <
calenge at biomserv.univ-lyon1.fr> wrote:

  It's very kind of Stephen to plug my book, but it's notwhat you're

looking for.  You need to read more about this general topic, and aboutthe
particular packages: try

http://www.unine.ch/CSCF/grasp/grasp-r/index.htmlhttp://www.unine.ch/CSCF/grasp/
 Based on downloading grasp , it doesn't look as thoughit will handle
presence-only data, though -- you may needto look further.
 It doesn't look like adehabitat is what you want.From Calenge, Clement.
2006. The package "adehabitat" for the R software: A toolfor the analysis of
space and habitat use by animals. Ecological Modelling 197,no. 3-4 (August
25): 516-519. doi:10.1016/j.ecolmodel.2006.03.017.
' ... the "adehabitat" package for the R software, which offers basic
GIS(Geographic Information System) functions, methods to analyze
radio-trackingdata and habitat selection by wildlife, and interfaces with
other R packages.'
 General advice about "I want to do X in R" -- (expandingon Stephen's
advice above):
1. read about X in general (perhaps you have already done this);2. search
for R packages and functions that do what you want  (you've already done
this, although you misidentified "adehabitat"3. install those packages and
see what they do.  Look at thedocumentation included with the packages,
including any citationsreferenced.  Try the examples.4. If you don't know
enough R to understand the examples or howto get your data into R, back up
and read the introductory Rdocumentation.

Actually, the confusion could be explained by the fact that many analyses
methods (and especially factor analyses) originally developed in community
ecology and biogeography to study the niche are also used in habitat
selection studies (e.g., OMI analysis, ENFA, etc.). As the statistical
issues (predict the species/animal presence on an area, given the value of
environmental variables) and type of data (presence-only data to be compared
with a sample/census of "available" units, etc.) involved in studies of the
niche and habitat selection are often similar, the methods used are often
similar too... However, most of the functions in adehabitat implement
/exploratory/ methods of the ecological niche, and methods suitable for
prediction are rare in the package (except one or two functions which have
already been used for that, such as mahasuhab or domain, but they are
probably not the best choice given your aim)... The package grasp may indeed
be a better choice if your aim is prediction...

But I concur with Ben and Stephen on the fact that you should first read
the (large) literature on niche modelling before choosing the method that
seems appropriate to your data/issue, and then search R archives/package for
a solution. a good start:

@ARTICLE{Elith2006,
 author = {Elith, J. and Graham, C.H. and Anderson, R.P. and Dudik, M. and
Ferrier,
  S. and Guisan, A. and Hijmans, R.J. and Huettmann, F. and Leathwick,
  J.R. and Lehmann, A. and Li, J. and Lohmann, L.G. and Loiselle, B.A.
  and Manion, G. and Moritz, C. and Nakamura, M. and Nakazawa, Y. and
  McC. Overton, J. and Peterson, A.T. and Phillips, S.J. and Richardson,
  K. and Scachetti-Pereira, R. and Schapire, R.E. and Soberon, J. and
  Williams, S. and Wisz, M.S. and Zimmermann, N.E.},
 title = {Novel methods improve prediction of species distributions from
occurrence data},
 journal = {Ecography},
 year = {2006},
 volume = {29},
 pages = {129-151}
}

and references therein.
Cheers,



Cl?ment Calenge.

--
Cl?ment CALENGE
Office national de la chasse et de la faune sauvage
Saint Benoist - 78610 Auffargis
tel. (33) 01.30.46.54.14

       [[alternative HTML version deleted]]