clip a SpatialPolygonsDataFrame
On Fri, 6 Aug 2010, Laetitia Blanc wrote:
Can the KDE be run with the correct coordinates in the specified projection on the input data, so that thw window matches the outlines? Can you re-write the code making res to generate a SpatialGridDataFrame? The input points must have a projection. Without a shared projection (CRS, coordinate reference system) this is not possible. Roger
I have taken into account your advice. I have loaded my input data with the correct CRS (lambert II) in order to
match with the map :
d <- read.csv('total.csv', header = TRUE) #, sep = ",", quote="\"",
dec=".",fill = TRUE, comment.char="", ...)
d <- d[-(1:10),]
d2 <- data.frame (d)
spd2 <- d2
#transformation into SpatialPointDataFrame
coordinates ( spd2 ) <- ~ x + y
proj4string ( spd2 ) <- CRS("+init=epsg:27572")
Then, i have realised my KDE :
source("stkde2.txt")
res <- array(0,c(20,20,length(unique(spd2$an)))) # cr?er 30
(length(unique(d$an))) tableaux de 20x20.
for (i in 1:length(unique(spd2$an))) {
spd3 <- subset(spd2,spd2$an == 1979+i) # r?sum? en conservant que 1973+i o?
i=30 donc en gardant que 2009
lynxkde<-stkde(xlong=spd3$x, ylat=spd3$y, ztime=spd3$an,
xgrids=20,ygrids=20,bwmethod="cv.ml")
res[,,i] <- lynxkde$dens
}
At that moment, the window where the KDE is running has te correct unit
(meters) (xrange : >from 823 000 to 981 000 ; yrange : from 2 079 500 to 2 305 500)
No, this is a misunderstanding. Until you get this right, please forget the simulation, make sure everything is correct for a single period first. I am pretty sure that lynxkde$dens is a matrix, and if you take the trouble to read help(image), you'll see that if the first argument is a matrix, then the window is set to 0,1. You need to pass the cell centres of the xgrids and ygrids to the image call. Beware that if the spd3$x and spd3$y change by i, the grid will be different each time, evenj though it is 20x20, it will start somewhere else, and have a different cell dimension. I think that you are using a function from the stam package - you need to adapt it to pass the x.seq and y.seq values now generated internally in as arguments, which will permit you to make sure that you have full control of the location of the output grids. If you then pass the same x.seq and y.seq to image() as the first two arguments, and the matrix as the third argument, it will use them to specify its axes, giving you the correct window. You need to be sure that your x.seq and y.seq contain all of the xlong and xlat for all periods. If stkde took a GridTopology object as a grid definition, the output could easily be used to create a SpatialGridDataFrame object, which would be very easy to plot in register with your boundaries, but this is something for the package maintainer. Hope this helps, Roger PS. CC-ing the stam maintainer.
But then, when i create my animation, the window has the x and y ranges :
0:1. I think the >probleme comes from my animation. Moreover, when i try to insert my map in my animation, i still >have an alternation between the map and the kernel >rather than the kernel ON the map (like
overlay/superposition...) :
library(animation)
library(MASS)
# create a HTML page from my animation :
pres.ani <- function()
{
for (i in 1:length(unique(spd2$an))) {
image(res[,,i],xlab='',ylab='',main=unique(spd2$an)[i])
contour(res[,,i],add=T)
plot(france,xlim=range(823000:981000),ylim=range(2079500:2305500),add=TRUE)
Sys.sleep(.5)
}
}
ani.start(interval=.5,title = "movie presence lynx", outdir = getwd())
pres.ani()
ani.stop()
I think i must solve the problem by changing my animation but i don't know
how. Do you have an >idea ? Do you think that it can be because i have spatial objects ? -- View this message in context: http://r-sig-geo.2731867.n2.nabble.com/clip-a-SpatialPolygonsDataFrame-tp5376909p5379892.html Sent from the R-sig-geo mailing list archive at Nabble.com.
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Roger Bivand Economic Geography Section, Department of Economics, Norwegian School of Economics and Business Administration, Helleveien 30, N-5045 Bergen, Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43 e-mail: Roger.Bivand at nhh.no