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
>From the kernelkc help, seems to me I should be able to do the same thing:
grida 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$Date,for
mat="%y%m%d")), id=puechData$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
cell: 978-857-8266
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