[R-sig-Geo] ENFA in Linux

[Mathieu Basille]

Dear Alannie,

I'm surprised that you have any difference from Windows to Linux, apart of 
the memory problem... This said, you should consider switching to the new 
version of adehabitat: adehabitatHS [1], which uses sp classes instead of 
the old kasc. I wouldn't be too surprised if your problem would be solved 
with this. See the vignette that comes with the package for more details on 
the procedure with the new spatial classes:

vignette("adehabitatHS")

Hope this helps,
Mathieu.


[1] http://cran.r-project.org/web/packages/adehabitatHS/index.html


Le 06/28/2013 01:35 PM, alannie a écrit :
> Hi R-Sig-Geo community!
>
> I was recently trying to run ADEHabitat ecological niche factor analysis
> (ENFA) using R in Linux. I did not get very far and would like some
> assistance on how to make it work in the future.
>
> I did the following commands:
>
> I installed both ade4 and ADEHabitat on to R in Linux
>
> Imported 26 .asc maps into R using this general syntax:
> bio2<-import.asc("ASCII Envi Variables//caorwa//bio2.asc")
>
> I added location data:
>
> locs<-read.table("XYconcolorsp.csv",head=TRUE,sep=",")
>
> added the libraries for ade4/adehaitat
>
> I compiled the .asc maps into "maps" using:
>
> maps<-as.kasc(list(bio1=bio1,bio2=bio2,bio3=bio3,........etc))
>
> Then I tried to prepare the data for the ENFA:
>
> (dataenfa1<-data2enfa(maps,locs))
>
> After this step I received an error message:
>
> Error in cut.default(x, xc) : 'x' must be numeric
> Error: unexpected 'in' in "Error in"
> data2enfa(maps,locs)
>
>
> I have done the exact same thing in just windows many times and have not
> received an error like this. In fact, it worked perfectly until the end of
> the enfa. I had to switch to Linux because Windows ran out of memory for the
> large area based analyses.
>
> What would be causing the error?
>
> Is there something that needs to be configured differently in Linux?
>
> Please let me know your suggestions!
>
> Linux Specifications:
>
> adehabitat version 1.8.12 on R version 2.15.3 (2013-03-01) running on 64-bit
> Ubuntu
> Linux 12.04.2
>
>
> Thank you, Community!
>
> Alannie
>
>
>
> --
> View this message in context: http://r-sig-geo.2731867.n2.nabble.com/ENFA-in-Linx-tp7583942.html
> Sent from the R-sig-geo mailing list archive at Nabble.com.
>
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-- 

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Mathieu Basille, PhD

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

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« Le tout est de tout dire, et je manque de mots
Et je manque de temps, et je manque d'audace. »
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