[R] Ecological Niche Modelling on R

Kingsford Jones kingsfordjones at gmail.com
Wed Oct 8 21:51:51 CEST 2008

On Wed, Oct 8, 2008 at 6:17 AM, milton ruser <milton.ruser at gmail.com> wrote:
> 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.

If you're interested in prediction methods based on presence-only
data, you might find Gillian Ward's dissertation interesting (
http://www-stat.stanford.edu/~hastie/students.htm ).  It includes
reference to an accompanying R package (although it does not appear to
be on CRAN).


Kingsford Jones

> Regards a lot.
> Savava.
> Miltinho Astronauta
> Brazil
> On Wed, Oct 8, 2008 at 6:02 AM, Clément 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,
>> Clément Calenge.
>> --
>> Clément CALENGE
>> Office national de la chasse et de la faune sauvage
>> Saint Benoist - 78610 Auffargis
>> tel. (33)
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