[R] Ecological Niche Modelling on R

[Ben Bolker]

stephen sefick <ssefick <at> gmail.com> writes:

> 
> that is a pretty big question.  And I am not qualified to answer it,
> but my suggestion- from figuring out how to use other things- is to
> find out how other people have modeled ecological niches- not
> necessarily with R,  and then try and find out functions that preform
> the pieces or the whole analysis.  I believe there is a book out there
> about modeling ecological niches with R.  I did  a google search for
> that and this is what I found:
> http://www.zoology.ufl.edu/bolker/emdbook/. 

 [snip]
> 
> On Tue, Oct 7, 2008 at 12:46 PM, 
milton ruser <milton.ruser <at> gmail.com> wrote:
> > Dear all,
> > I have strong interest on Ecological Niche Model, which in general 
> > use a set
> > of environmental variables (continuous, categorical etc) and Presence (or
> > Presense/Absence) records for species. I think that "grasp" 
> > and "adehabitat"
> > packages could help me on these tasks.
[snip]  Note that in general we 
> > don´t have real absence
> > data.
> >

  It's very kind of Stephen to plug my book, but it's not
what you're looking for. 

  You need to read more about this general topic, and about
the particular packages: try

http://www.unine.ch/CSCF/grasp/grasp-r/index.html
http://www.unine.ch/CSCF/grasp/

  Based on downloading grasp , it doesn't look as though
it will handle presence-only data, though -- you may need
to look further.

 It doesn't look like adehabitat is what you want.
>From Calenge, Clement. 2006. The package "adehabitat" for the 
R software: A tool
for 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-tracking
data and habitat selection by wildlife, and interfaces with other R packages.'

  General advice about "I want to do X in R" -- (expanding
on 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 the
documentation included with the packages, including any citations
referenced.  Try the examples.
4. If you don't know enough R to understand the examples or how
to get your data into R, back up and read the introductory R
documentation.

  If you get stuck again, you might want to try this query
on the r-sig-eco mailing list.

  cheers
    Ben Bolker