In un messaggio del Monday 10 December 2012, Mathieu Basille ha scritto: > 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 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. > > 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.
Thank you, Mathieu!
Neat solution, R-style!
> >> 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
--
Shading within a garment may occur.
----------------------------------------------------------
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
-----------------------------------------------------------
Please consider the environment before printing this email
Please do not send attachments in proprietary formats
http://www.gnu.org/philosophy/no-word-attachments.html
Use the UNI CEI Standard ISO/IEC 26300:2006
-----------------------------------------------------------
O< stop html mail - http://www.asciiribbon.org
signature.asc
Description: This is a digitally signed message part.
_______________________________________________ AniMov mailing list [email protected] http://lists.faunalia.it/cgi-bin/mailman/listinfo/animov
