Dear All,
Thanks for all very interesting replies.

In fact I have read all the recent publications on ENM (Ecological Niche
Modeling), and many of them use GARP (Genetic Algorithm for Rule Prediction;
sensu STockwell & Peterson 2001) and Maxent (Maximum Entropy sensu Philips &
Dudik, 2008a, b) algorithms. I can run my modeling on DescktopGarp, Maxent,
and also on OpenModeller (which have implementation of a large set of
algoritms). I agree with Dr. Calenge that Elith et al (2006) is an
interesting reading. But, unfortunatelly up to now none of papers regarding
ENM use R as a modelling tools. And my intent on last email was to start a
comparative modelling using both R and non-R solution.

Whem I require "adehabitat" package I get the following message:

Type:
demo(rastermaps) for demonstration of raster map analysis
demo(homerange) for demonstration of home-range estimation
demo(managltraj) for demonstration of animals trajectory management
demo(analysisltraj) for demonstration of animals trajectory analysis
demo(nichehs) for demonstration of niche/habitat selection analysis

So, I was thinking if the last demo(nichehs) could be used on this task once
visually this suggests that the package could help someone on both niche
model/habitat selection analysis. So, Dr. BBolker, I think the adehabitat is
not only for "GIS(Geographic Information System) functions, methods to
analyze radio-trackingdata and habitat selection", but mainly for it.

By the way, Dr. BBolker, I read your book three rimes, and I each time that
I read I get more facinated (Thanks and congratulations!). In fact, after
read the book on digital format, I am waiting the hard-copy arrive on next
week. By the way, after read Ecological Detectives and the BBolker book, I
hardly suggest those interested on Ecological Modelling and Data Analysis
start reading from the BB´s book. Mainly if one have R-capability as we
almost on some levels have.

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. Dr. BB,
I read all the available documentations on GRASP, but unfortunatelly the
preparation of input data (a set of tables instead of conventional layers
and XY coordinates) is not so clear thoughout the text.

Good data modelling for all. Thanks for your time.

Regards a lot.
Savava.


Miltinho Astronauta
Brazil


On Wed, Oct 8, 2008 at 6:02 AM, Clément Calenge <
calenge@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) 01.30.46.54.14
>
>

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