[R-sig-Geo] Using the ENFA from adehabitatHS in R with sp classes

[Mathieu Basille]

Dear Alannie,

Obviously all these "data"s are confusing :)
The 'enfa' example uses a dataset call 'lynxjura' (not 'data'), which is a 
list with several elements. One of these elements is the maps, with the 
name 'map' (singular!). This is what you want to achieve. This is simply a 
SpatialPixelsDataFrame, but as far as I can tell, a SpatialGridDataFrame 
will do too (if you want to know more about the differences between these 
two, check the sp vignette).

So, following your example, just replace "map" by "join", and it should 
work. The 'slot(map, "data")' line extracts the data frame storing the data 
of the map, since the dudi.pca and enfa functions do not directly need the 
spatial attributes.

Hope this helps,
Mathieu.


Le 08/14/2013 02:23 PM, alannie a écrit :
> Hi folks!
>
> I have been having significant difficulty using the sp classes to perform
> the ENFA in R.
> The objective of this posting is to inquire about how to "prepare data for
> the ENFA," which in previous versions of the software package adehabitat was
> carried out via 'data2enfa' and the 'dudi.pca' functions.
>
> I have been using the code:
>
> #Add table of coordinate locations
>
>> locs<-read.table("xybartsiifolia.csv", header=TRUE, sep=",")
>
> #Convert to class sp
>
>> xy.sp = SpatialPoints(locs)
>
> #Import .asc variable maps into R.
>
>> bio1<-read.asciigrid("bio1.asc", as.image = FALSE, plot.image = FALSE,
> colname = basename("bio1.asc"), proj4string = CRS(as.character(NA)))
>> bio2<-read.asciigrid("bio2.asc", as.image = FALSE, plot.image = FALSE,
> colname = basename("bio2.asc"), proj4string = CRS(as.character(NA)))
>
> #etc
>
> #Combine data maps
>
>> join<- cbind(bio1 at data, bio2 at data, bio3 at data, etc)
>
> After the last bit, I cannot go forward.
>
> I need to somehow combine the 'join' data which contains variable maps with
> the 'locs' data which has species location data so that I can get the
> principle component analysis from function dudi.pca.
>
> In the documentation for package adehabitatHS it says:
>
> ## We prepare the data for the ENFA
> tab <- slot(map, "data")
> pr <- slot(count.points(locs, map), "data")[,1]
>
> and then goes on to do the PCA and ENFA
>
> I have already tried working through the example 'lynxjura' multiple times
> and have no greater understanding of what comprises the data (noted as
> "data" in the example) or how to utilize the slot function in my own data
> set.
>
> I would like assistance to put my data in the format for the PCA and the
> ENFA.
>
> Thanks in advance for all assistance.
>
> Alannie
>
>
>
>
>
>
> --
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>
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-- 

~$ whoami
Mathieu Basille, PhD

~$ locate --details
University of Florida \\
Fort Lauderdale Research and Education Center
(+1) 954-577-6314
http://ase-research.org/basille

~$ fortune
« Le tout est de tout dire, et je manque de mots
Et je manque de temps, et je manque d'audace. »
  -- Paul Éluard