On Wed, Oct 8, 2008 at 6:17 AM, milton ruser <[EMAIL PROTECTED]> wrote: [snip] > > 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). hth, Kingsford Jones > > Regards a lot. > Savava. > > > Miltinho Astronauta > Brazil > > > On Wed, Oct 8, 2008 at 6:02 AM, Clément Calenge < > [EMAIL PROTECTED]> 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 >> >> > > [[alternative HTML version deleted]] > > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > > ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
