[R-sig-Geo] FANTER? (adehabitat)
Clément Calenge
clement.calenge at gmail.com
Mon May 31 09:43:43 CEST 2010
On 05/31/2010 02:28 AM, Consuelo Hermosilla wrote:
> I have a doubt. I'd like to implement the FANTER analysis, described in
> Calenge& Basille (2008), which should be a type of Gnesfa analysis, right?
> But I don't know how to implement it (in adehabitat)... the gnesfa default
> option is equivalent to FANTER?
No. Actually, depending on the distribution chosen, the GNESFA will
correspond to the MADIFA or the FANTER. Consider the examples of the
help page of this function:
## Loads the data
data(bauges)
kasc <- bauges$kasc
locs <- bauges$locs
## Prepares the data for the GNESFA:
litab <- kasc2df(kasc)
pc <- dudi.pca(litab$tab, scannf = FALSE)
Dp <- count.points(locs, kasc)[litab$index]
In this case, pc stores the environmental information. Conceptually, it
can be considered as a table storing the value of the environmental
variables (columns) in each pixel of the map (rows). Dp is a vector
containing the utilization weights, i.e. the number of animals in each
pixel of the map. The MADIFA corresponds to a GNESFA with the reference
distribution corresponding to the utilization weights, that is, to
perform the MADIFA, type:
gn <- gnesfa(pc, Reference = Dp)
If you want to perform a FANTER, you have to set the utilization weights
as the Focus distribution, that is:
gn <- gnesfa(pc, Focus = Dp)
> I understand the modifications leading to
> ENFA and MADIFA (using gnesfa fuction), but I'm kind of lost in how to
> implemet FANTER...
> I know (following the paper) that I should keep the first and last
> eigenvalue, but what about the other options of the function?
>
You can choose the number of first and last axes that you keep in your
analysis, not necessarily only the first and last one.
The options nfFirst and nfLast are easier to understand if you do not
set scannf=FALSE, so that the eigenvalue barplot is displayer. For
example, if you can identify visually a clear "break" in the decrease of
the eigenvalues after the second eigenvalue, then, it would be a good
idea to keep the first two axes. Similarly, if you can identify a strong
"break" in the increase of 1/eigenvalues just before the eigenvalue P-3
(where P is the total number of eigenvalues), then it would be a good
idea to keep the last three axes. Then factorial maps and other tools
described on the help page and in the paper would help to interpret the
results.
Hope this helps,
Clément Calenge
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