Dear Mathieu,
Thanks for your quick reply!!! :)
I thought that too, but then, why I'm able to plot the imported map? It
makes no sense, I wouldn't be able to plot it if there was an error there,
would I?
This was my code:
library(adehabitat)
chl= import.asc("chl-box_qt.asc", type ="numeric")
sst = import.asc("sst-box_QT.asc", type ="numeric")
dep = import.asc("dep-box_QT.asc", type ="numeric")
euph = import.asc("euph-box_QT.asc", type ="numeric")
OX0 = import.asc("OX0-box_QT.asc", type ="numeric")
OX200 = import.asc("OX200-box_QT.asc", type ="numeric")
OX50 = import.asc("OX50-box_QT.asc", type ="numeric")
P0 = import.asc("P0-box_QT.asc", type ="numeric")
P100 = import.asc("P100-box_QT.asc", type ="numeric")
P125 = import.asc("P125-box_QT.asc", type ="numeric")
P150 = import.asc("P150-box_QT.asc", type ="numeric")
P200 = import.asc("P200-box_QT.asc", type ="numeric")
pre = import.asc("pre-box_QT.asc", type ="numeric")
env_maps = as.kasc(list(chl, sst, dep, euph, OX0, OX200, OX50, P0, P100,
P125, P150, P200, pre))
managNAkasc (env_maps) # just to check
presence <- read.csv("presence.csv")
octopus.hab <- data2enfa(env_maps, presence)
pca.octopus <- dudi.pca(octopus.hab$tab, scannf=FALSE)
Can I attach files? How do you want me to provide data?
Consuelo
-------------
Consuelo Hermosilla
PhD student
Departamento de Ecología y Biología Animal
Departamento de Bioquímica, Genética e Inmunología, Área de Genética
Facultad de Ciencias del Mar
Campus de As Lagoas-Marcosende
Universidad de Vigo
36310 Vigo
SPAIN
Mobile: +34 692 633 298
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Stop Gaza Massacre
On Tue, Apr 27, 2010 at 11:31 PM, Mathieu Basille <
basi...@biomserv.univ-lyon1.fr> wrote:
> 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
>>
>> [[alternative HTML version deleted]]
>>
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>>
>
> --
>
> ~$ whoami
> Mathieu Basille, Post-Doc
>
> ~$ locate
> Laboratoire d'Écologie Comportementale et de Conservation de la Faune
> + Centre d'Étude de la Forêt
> Département de Biologie
> Université Laval, Québec
>
> ~$ info
> http://ase-research.org/basille
>
> ~$ fortune
> ``If you can't win by reason, go for volume.''
> Calvin, by Bill Watterson.
>
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