In un messaggio del Wednesday 05 December 2012, Corrie Curtice ha scritto: > Hi folks. > > I have a question about how to supply a grid to the kernelkc method. In a > previous email > (http://www.mail-archive.com/[email protected]/msg00219.html) Damiano > recommended reading in an ASCII grid file to supply as input to kernelUD. > At that time, I did this using import.asc from the old adehabitat package > and I believe it worked fine. But now I'm working with kernelkc and > running into a problem
Well. that behaviour is possible (and in some way, expectable).
The "new" Adehabitat* now uses sp and raster classes.
This means no 'kasc' objects anymore. You must use sp* classes.
This may seem a little pain somewhere ;) but in fact is a great thing, since
now also adehabitat uses standard classes for geodata.
The trick should be importing the grid in -say- GeoTIFF format using raster
from
raster package. The problem is in the conversion into SpatialGridDataFrame.
>
> From the kernelkc help, seems to me I should be able to do the same thing:
>
>
> grid a number giving the size of the grid on which the UD should be
> estimated. Alternatively, this parameter may be an object of class asc, or
> a list of objects of class asc, with named elements corresponding to each
> level of the burst/id
>
> I've clipped my area and saved as an ASC file from ArcGIS. I've tried to
> read it in two ways, but get an error both times. One is an asc and one is
> a SpatialGridDataFrame.
>
> library(SDMTools)
>
> > antpen_asc <- read.asc('shapefiles/antpen500m.asc')
> > class(antpen_asc)
>
> [1] "asc"
>
> > uu <- kernelkc(t699_b2, h =
> > c(5000,5000,5*3600*24),grid=antpen_asc, tcalc= as.POSIXct("2012-01-27"))
>
> Error in `gridded<-`(`*tmp*`, value = TRUE) :
> gridded<- only works for SpatialPoints[DataFrame] or
> SpatialGrid[DataFrame]
> When I read it in w/ sp read.asciigrid, which produces a
> SpatialGridDataFrame I still get an error.
>
> > antpen_sgdf <- read.asciigrid('shapefiles/antpen500m.asc', as.image =
> > FALSE,
>
> + proj4string = CRS('+proj=utm +zone=20 +south
> +datum=WGS84'))
>
> > class(antpen_sgdf)
>
> [1] "SpatialGridDataFrame"
> attr(,"package")
> [1] "sp"
>
> > uu <- kernelkc(t699_b2, h =
> > c(5000,5000,5*3600*24),grid=antpen_sgdf, tcalc=
> > as.POSIXct("2012-01-27"))
>
> Error in as.vector(gr) : no method for coercing this S4 class to a vector
>
> The vignette example uses a SpatialPixelsDataFrame for the kernelUD method
> but doesn't show an example with kernelkc. I made an ltraj out of the
> data and tried to pass in the supplied map, but get the same error as when
> using a SGDF. Below is code that should reproduce what I'm seeing.
>
> > data(puechabonsp)
> > # regular kernel w/ grid
> > kudm <- kernelUD(puechabonsp$relocs[,1], grid=puechabonsp$map)
> >
> >
> >
> > # Try product kernel w/ grid. Need to get ltraj
> > class(puechabonsp$relocs)
>
> [1] "SpatialPointsDataFrame"
> attr(,"package")
> [1] "sp"
>
> > puechData<-puechabonsp$relocs@data
> > puechData$X <- puechabonsp$relocs@coords[,1]
> > puechData$Y <- puechabonsp$relocs@coords[,2]
> > puechTraj
> > <-as.ltraj(cbind(puechData$X,puechData$Y),as.POSIXct(strptime(puechData$
> > Date,format="%y%m%d")), id=puechData$Name) uu <- kernelkc(puechTraj, h =
> > c(1000,1000,72*3600), tcalc= as.POSIXct("1993-07-20"),
> > grid=puechabonsp$map)
>
> Error in as.vector(gr) : no method for coercing this S4 class to a vector
>
>
> Here's my session info...
>
> > sessionInfo()
>
> R version 2.13.1 (2011-07-08)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] C/en_US.UTF-8/C/C/C/C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] SDMTools_1.1-9 adehabitatHR_0.3 adehabitatLT_0.3.4
> CircStats_0.2-4 boot_1.3-2 MASS_7.3-13 [7]
> adehabitatMA_0.3.2 ade4_1.4-17 tripack_1.3-4 gpclib_1.5-1
> sp_0.9-84
>
> loaded via a namespace (and not attached):
> [1] grid_2.13.1 lattice_0.19-30 tools_2.13.1
>
> Am I just too out of date on something(s), or am I completing missing
> something obvious in how I should be proceeding?
>
> Thanks for any guidance.
>
> --corrie
>
> ---
> Corrie Curtice
> Research Analyst
> Marine Geospatial Ecology Lab
> Nicholas School of the Environment, Duke University
> http://mgel.env.duke.edu
> em: [email protected]
> ph: 252-504-7538
--
Besides, REAL computers have a rename() system call. :-)
-- Larry Wall in <[email protected]>
----------------------------------------------------------
Damiano G. Preatoni, PhD
Unità di Analisi e Gestione delle Risorse Ambientali
- Guido Tosi Research Group
Dipartimento di Scienze Teoriche e Applicate
Università degli Studi dell'Insubria
Via J.H. Dunant, 3 - 21100 Varese (ITALY)
tel +39 0332421538 fax +39 0332421446
http://biocenosi.dipbsf.uninsubria.it/
IRC: #prea skype: prea.net
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