R help - Feb 2012 - using shapefiles in adehabitat/ converting shapefile to spatial pixel data frame

Hello
I wonder if anybody can help,
I am using the package adehabitatHR to estimate the potential distribution of a
species using the command "domain"

In the example given in the AdehabitatHS manual a map containing elevation
information is loaded (class= spatial pixels data frame) as well as the GPS
points of the animals being tracked, these are then plotted on each other and
estimation of habitat suitability performed.

I have a map containing sea depth information in the form of a shapefile which I
want to relate to some GPS tracks I have, however I believe that the shapefile
with my sea depth information has to be of the class spatial pixels data frame
before I can perform many of the analysis in AdehabitatHS,

I have tried converting the shapefile to a spatial pixel data frame using the sp
package by exporting the data from the attribute table in my depth shapefile
then importing it into R as a csv file (see my attempts below)
>depth<-read.csv("depthmap.csv")
>pts = depth[c("x", "y")]
>y = SpatialPixels(SpatialPoints(pts))
suggested tolerance minimum: 1
Error in points2grid(points, tolerance, round) :
 dimension 1 : coordinate intervals are not constant
> depth<-read.csv("a.csv")
> coordinates(depth) <- c("x", "y")
> points2grid(depth)
suggested tolerance minimum: 1
Error in points2grid(depth) :
  dimension 1 : coordinate intervals are not constant

Bur these do not seem to work, does anyone have any ideas?

Many thanks
Louise Soanes


School of Environmental Sciences
University of Liverpool
Brownlow Hill
L69 3GP

http://sites.google.com/site/puffinislandseabirdresearch/


	[[alternative HTML version deleted]]

The error you are getting says that the coordinates provided do not
define a regular grid (within the tolerance allowed).

Are the points in your CSV file really a regular grid, or do they
represent a surface by way of irregular points? You could check this
manually by plotting:

depth<-read.csv("depthmap.csv")
plot(depth$x, depth$y)

(Otherwise, this is a text file - csv is "comma separated values" and
has nothing to do with an ESRI Shapefile. )

If your points really are a regular grid, or "near enough" to one you
can use the tolerance argument to SpatialPixels, see

library(sp)
?SpatialPixels
vignette("sp")

for some introduction to these data structures and tools.

Also, R-Sig-Geo is a better target list for these topics so please use that.

Cheers, Mike.

On Thu, Feb 23, 2012 at 11:06 PM, Soanes, Louise
<Louise.Soanes at liverpool.ac.uk> wrote:
> Hello
> I wonder if anybody can help,
> I am using the package adehabitatHR to estimate the potential distribution
of a species using the command "domain"
>
> In the example given in the AdehabitatHS manual a map containing elevation
information is loaded (class= spatial pixels data frame) as well as the GPS
points of the animals being tracked, these are then plotted on each other and
estimation of habitat suitability performed.
>
> I have a map containing sea depth information in the form of a shapefile
which I want to relate to some GPS tracks I have, however I believe that the
shapefile with my sea depth information has to be of the class spatial pixels
data frame before I can perform many of the analysis in AdehabitatHS,
>
> I have tried converting the shapefile to a spatial pixel data frame using
the sp package by exporting the data from the attribute table in my depth
shapefile then importing it into R as a csv file (see my attempts below)
>
>>depth<-read.csv("depthmap.csv")
>>pts = depth[c("x", "y")]
>>y = SpatialPixels(SpatialPoints(pts))
>
> suggested tolerance minimum: 1
> Error in points2grid(points, tolerance, round) :
> ?dimension 1 : coordinate intervals are not constant
>
>> depth<-read.csv("a.csv")
>> coordinates(depth) <- c("x", "y")
>> points2grid(depth)
> suggested tolerance minimum: 1
> Error in points2grid(depth) :
> ?dimension 1 : coordinate intervals are not constant
>
> Bur these do not seem to work, does anyone have any ideas?
>
> Many thanks
> Louise Soanes
>
>
> School of Environmental Sciences
> University of Liverpool
> Brownlow Hill
> L69 3GP
>
> http://sites.google.com/site/puffinislandseabirdresearch/
>
>
> ? ? ? ?[[alternative HTML version deleted]]
>
> ______________________________________________
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> PLEASE do read the posting guide
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-- 
Michael Sumner
Institute for Marine and Antarctic Studies, University of Tasmania
Hobart, Australia
e-mail: mdsumner at gmail.com