[R-sig-Geo] error in dudi.pca (adehabitat)

[Mathieu Basille]

Dear Consuelo,

I guess the error just propagates from the initial import, and has 
nothing to do with dudi.pca (which is by the way from the ade4 package 
-- not directly related to adehabitat).

Your approach otherwise seems (quite) OK. Unfortunately, you didn't 
provide enough details to check. Could you provide the whole code, with 
possibly some data, so that we can reproduce the problem?

Cheers,
Mathieu.



Consuelo Hermosilla a écrit :
> Hi folks,
> 
> I'm trying to implement an ecological niche factor analysis with octopus but
> I have some problems. I think it is related to the fact I have No-data
> values. Since it's a marine species, I have land areas where I have no-data
> values. Can I have grids with no-data values?
> 
> The thing is I'm able to import the ascii grid (using import.asc) and I'm
> even able to plot it (and see the image), so I guessed I have no problems
> with the no-data values. If I checked the grid, I got this:
> 
> str(chl)
>  asc [1:1214, 1:761] NA NA NA NA NA NA NA NA NA NA ...
>  - attr(*, "xll")= num -18.6
>  - attr(*, "yll")= num 16.7
>  - attr(*, "cellsize")= num 0.05
>  - attr(*, "type")= chr "numeric"
> 
> It looks wrong, but it's OK since my first values are indeed NA. In fact,
> besides the fact I'm able to plot it, I can calculate grid means and other
> stats, so I think the problem is not here. Then, when I grouped all the
> grids (with the as.kasc function), I got this:
> 
> str(env_maps)
> Classes ?kasc? and 'data.frame':        923854 obs. of  13 variables:
>  $ : num  NA NA NA NA NA NA NA NA NA NA ...
>  $ : num  NA NA NA NA NA NA NA NA NA NA ...
>  $ : num  NA NA NA NA NA NA NA NA NA NA ...
>  $ : num  NA NA NA NA NA NA NA NA NA NA ...
>  $ : num  NA NA NA NA NA NA NA NA NA NA ...
>  $ : num  NA NA NA NA NA NA NA NA NA NA ...
>  $ : num  NA NA NA NA NA NA NA NA NA NA ...
>  $ : num  NA NA NA NA NA NA NA NA NA NA ...
>  $ : num  NA NA NA NA NA NA NA NA NA NA ...
>  $ : num  NA NA NA NA NA NA NA NA NA NA ...
>  $ : num  NA NA NA NA NA NA NA NA NA NA ...
>  $ : num  NA NA NA NA NA NA NA NA NA NA ...
>  $ : num  NA NA NA NA NA NA NA NA NA NA ...
>  - attr(*, "cellsize")= num 0.05
>  - attr(*, "xll")= num -18.6
>  - attr(*, "yll")= num 16.7
>  - attr(*, "ncol")= int 1214
>  - attr(*, "nrow")= int 761
>  - attr(*, "type")= chr  "numeric" "numeric" "numeric" "numeric" ...
> 
> Still looks wrong, but it shouldn't be. Then, I proceed with the data2enfa
> function, that seemed to work. But in the next step, when I was calculating
> the dudi.pca, it failed, with this error:
> 
> Error in `rownames<-`(`*tmp*`, value = c("1", "2", "3", "4", "5", "6",  :
>   attempt to set rownames on object with no dimensions
> 
> I checked the data2enfa result and I got this:
> 
> List of 4
>  $ tab  :'data.frame':  923854 obs. of  0 variables
>  $ pr   : int [1:923854] 0 0 0 0 0 0 0 0 0 0 ...
>  $ index: int [1:923854] 1 2 3 4 5 6 7 8 9 10 ...
>  $ attr :Class 'mapattr'  atomic [1:1] 0
>   .. ..- attr(*, "xll")= num -18.6
>   .. ..- attr(*, "yll")= num 16.7
>   .. ..- attr(*, "cellsize")= num 0.05
>   .. ..- attr(*, "nrow")= int 761
>   .. ..- attr(*, "ncol")= int 1214
>  - attr(*, "class")= chr "dataenfa"
> 
> When I check the $tab, I got this:
> 
> octopus.hab$tab
> data frame with 0 columns and 923854 rows*
> 
> *And I have no idea of what's wrong.... any ideas? do you suggest anything?
> Why do I have 0 columns and 923854 rows? Is that possible? Can the data2enfa
> funcion deal with no-data values?
> 
> I tried the magagNAkasc, but doesn't work...
> 
> managNAkasc (env_maps)
> Raster map of class "kasc":
> Cell size:  0.05
> Number of rows:  761
> Number of columns:  1214
> 
> Variables measured:
> 1. : numeric
> Error in .subset2(x, i, exact = exact) :
>   attempt to select less than one element
> 
> I have tried in Windows Vista and Linux (both R 2.10.1 and adehabitat v
> 1.83.
> 
> I'd appreciate any help!!
> 
> Thanks!!!
> 
> Consuelo
> 
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-- 

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Mathieu Basille, Post-Doc

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Laboratoire d'Écologie Comportementale et de Conservation de la Faune
+ Centre d'Étude de la Forêt
Département de Biologie
Université Laval, Québec

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http://ase-research.org/basille

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``If you can't win by reason, go for volume.''
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