Wow, this one gave me a real hard time, especially considering how easy
the solution was.
In brief, you have to specify names in the list, in the as.kasc
function. Otherwise, none of the layers have actually names, which
induces a lot of problems afterwards.
The fix is quite easy then. I took also some the liberty to clean the
code at different places:
library(adehabitat)
chl <- import.asc("chl-box_qt.asc")
sst <- import.asc("sst-box_QT.asc")
dep <- import.asc("dep-box_QT.asc")
euph <- import.asc("euph-box_QT.asc")
OX0 <- import.asc("OX0-box_QT.asc")
OX200 <- import.asc("OX200-box_QT.asc")
OX50 <- import.asc("OX50-box_QT.asc")
P0 <- import.asc("P0-box_QT.asc")
P100 <- import.asc("P100-box_QT.asc")
P125 <- import.asc("P125-box_QT.asc")
P150 <- import.asc("P150-box_QT.asc")
P200 <- import.asc("P200-box_QT.asc")
pre <- import.asc("pre-box_QT.asc")
# The problem was here:
env_maps <- as.kasc(list(chl = chl, sst = sst, dep = dep, euph = euph,
OX0 = OX0, OX200 = OX200, OX50 = OX50, P0 = P0, P100 = P100, P125 =
P125, P150 = P150, P200 = P200, pre = pre))
# You forgot to save the output of this, but in your case, that was not
# a problem
env_maps <- managNAkasc(env_maps) # just to check
presence <- read.csv("presence5.csv")
# I assumed that the second and third columns give X-Y coordinates. But
# it is somehow weird since many of them fall in the water -- assuming
# it's islands and water
octopus.hab <- data2enfa(env_maps, presence[, 2:3])
pca.octopus <- dudi.pca(octopus.hab$tab, scannf = FALSE)
Hope this helps,
Cheers,
Mathieu.
Consuelo Hermosilla a écrit :
Dear Mathieu,
Thanks for your quick reply!!! :)
I thought that too, but then, why I'm able to plot the imported map? It
makes no sense, I wouldn't be able to plot it if there was an error
there, would I?
This was my code:
library(adehabitat)
chl= import.asc("chl-box_qt.asc", type ="numeric")
sst = import.asc("sst-box_QT.asc", type ="numeric")
dep = import.asc("dep-box_QT.asc", type ="numeric")
euph = import.asc("euph-box_QT.asc", type ="numeric")
OX0 = import.asc("OX0-box_QT.asc", type ="numeric")
OX200 = import.asc("OX200-box_QT.asc", type ="numeric")
OX50 = import.asc("OX50-box_QT.asc", type ="numeric")
P0 = import.asc("P0-box_QT.asc", type ="numeric")
P100 = import.asc("P100-box_QT.asc", type ="numeric")
P125 = import.asc("P125-box_QT.asc", type ="numeric")
P150 = import.asc("P150-box_QT.asc", type ="numeric")
P200 = import.asc("P200-box_QT.asc", type ="numeric")
pre = import.asc("pre-box_QT.asc", type ="numeric")
env_maps = as.kasc(list(chl, sst, dep, euph, OX0, OX200, OX50, P0, P100,
P125, P150, P200, pre))
managNAkasc (env_maps) # just to check
presence <- read.csv("presence.csv")
octopus.hab <- data2enfa(env_maps, presence)
pca.octopus <- dudi.pca(octopus.hab$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
oooO
( ) Oooo
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Stop Gaza Massacre
On Tue, Apr 27, 2010 at 11:31 PM, Mathieu Basille
<basi...@biomserv.univ-lyon1.fr <mailto: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
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+ Centre d'Étude de la Forêt
Département de Biologie
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~$ fortune
``If you can't win by reason, go for volume.''
Calvin, by Bill Watterson.
--
~$ 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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