Best, Mathieu.
Le 11/12/2012 15:40, Corrie Curtice a écrit :
Thanks for the suggestions everyone. Here's what I tried, and the error I'm still getting:antpen_2 <- readGDAL('shapefiles/antpen500m.asc')shapefiles/antpen500m.asc has GDAL driver AAIGrid and has 1555 rows and 1263 columnsimage(antpen_2) #displays fine class(antpen_2)[1] "SpatialGridDataFrame" attr(,"package") [1] "sp"uu <- kernelkc(t699_b2, h = c(5000,5000,5*3600*24),grid=antpen_2,+ tcalc= as.POSIXct("2012-01-27")) Error in as.vector(gr) : no method for coercing this S4 class to a vectorHappy to upload files somewhere if that would be helpful, or provide more detail on my antpen500m.asc file if that could potentially be the problem. Thanks all, Corrie On 12/10/12 11:40 AM, "Mathieu Basille" <[email protected]> wrote:Le 10/12/2012 06:10, Damiano G. Preatoni a écrit :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 problemWell. 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.Two solutions for this: 1) Either use readGDAL to import the raster into R as a SGDF (from almost any format); 2) Or convert a raster to a SGDF using 'sgdf <- as(raster, "SpatialGridDataFrame")'. Mathieu.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_______________________________________________ AniMov mailing list [email protected] http://lists.faunalia.it/cgi-bin/mailman/listinfo/animov-- ~$ whoami Mathieu Basille, PhD ~$ locate --details University of Florida \\ Fort Lauderdale Research and Education Center (+1) 954-577-6314 http://ase-research.org/basille ~$ fortune « Le tout est de tout dire, et je manque de mots Et je manque de temps, et je manque d'audace. » -- Paul Éluard _______________________________________________ AniMov mailing list [email protected] http://lists.faunalia.it/cgi-bin/mailman/listinfo/animov_______________________________________________ AniMov mailing list [email protected] http://lists.faunalia.it/cgi-bin/mailman/listinfo/animov
-- ~$ whoami Mathieu Basille, PhD ~$ locate --details University of Florida \\ Fort Lauderdale Research and Education Center (+1) 954-577-6314 http://ase-research.org/basille ~$ fortune « Le tout est de tout dire, et je manque de mots Et je manque de temps, et je manque d'audace. » -- Paul Éluard _______________________________________________ AniMov mailing list [email protected] http://lists.faunalia.it/cgi-bin/mailman/listinfo/animov
