Crop for SpatialPolygonsDataFrame - r

Question

I have two SpatialPolygonsDataFrame files: dat1, dat2
extent(dat1)
class : Extent
xmin : -180
xmax : 180
ymin : -90
ymax : 90
extent(dat2)
class : Extent
xmin : -120.0014
xmax : -109.9997
ymin : 48.99944
ymax : 60
I want to crop the file dat1 using the extent of dat2. I don't know how to do it. I just handle raster files using "crop" function before.
When I use this function for my current data, the following error occurs:
> r1 <- crop(BiomassCarbon.shp,alberta.shp)
Error in function (classes, fdef, mtable) :
unable to find an inherited method for function ‘crop’ for signature"SpatialPolygonsDataFrame"’

Answer 1

Streamlined method added 2014-10-9:
raster::crop() can be used to crop Spatial* (as well as Raster*) objects.
For example, here's how you might use it to crop a SpatialPolygons* object:
## Load raster package and an example SpatialPolygonsDataFrame
library(raster)
data("wrld_simpl", package="maptools")
## Crop to the desired extent, then plot
out <- crop(wrld_simpl, extent(130, 180, 40, 70))
plot(out, col="khaki", bg="azure2")
Original (and still functional) answer:
The rgeos function gIntersection() makes this pretty straightforward.
Using mnel's nifty example as a jumping off point:
library(maptools)
library(raster) ## To convert an "Extent" object to a "SpatialPolygons" object.
library(rgeos)
data(wrld_simpl)
## Create the clipping polygon
CP <- as(extent(130, 180, 40, 70), "SpatialPolygons")
proj4string(CP) <- CRS(proj4string(wrld_simpl))
## Clip the map
out <- gIntersection(wrld_simpl, CP, byid=TRUE)
## Plot the output
plot(out, col="khaki", bg="azure2")

Answer 2

Here is an example of how to do this with rgeos using the world map as an example
This comes from Roger Bivand on R-sig-Geo mailing list. Roger is one of the authors of the sp package.
Using the world map as an example
library(maptools)
data(wrld_simpl)
# interested in the arealy bounded by the following rectangle
# rect(130, 40, 180, 70)
library(rgeos)
# create a polygon that defines the boundary
bnds <- cbind(x=c(130, 130, 180, 180, 130), y=c(40, 70, 70, 40, 40))
# convert to a spatial polygons object with the same CRS
SP <- SpatialPolygons(list(Polygons(list(Polygon(bnds)), "1")),
proj4string=CRS(proj4string(wrld_simpl)))
# find the intersection with the original SPDF
gI <- gIntersects(wrld_simpl, SP, byid=TRUE)
# create the new spatial polygons object.
out <- vector(mode="list", length=length(which(gI)))
ii <- 1
for (i in seq(along=gI)) if (gI[i]) {
out[[ii]] <- gIntersection(wrld_simpl[i,], SP)
row.names(out[[ii]]) <- row.names(wrld_simpl)[i]; ii <- ii+1
}
# use rbind.SpatialPolygons method to combine into a new object.
out1 <- do.call("rbind", out)
# look here is Eastern Russia and a bit of Japan and China.
plot(out1, col = "khaki", bg = "azure2")

Answer 3

You cannot use crop on sp polygon objects. You will need to create a polygon representing the bbox coordinates of dat2 and then can use gIntersects in the rgeos library.
Edit: This comment was in relation to the version available in 2012 and this is no longer the case.

Answer 4

see ?crop
corp(x, y, filename="", snap='near', datatype=NULL, ...)
x Raster* object
y Extent object, or any object from which an Extent object can be
extracted (see Details
You need to rasterize the first SpatialPolygon, using rasterize function from the raster package
I create some data to show how to use rasterize:
n <- 1000
x <- runif(n) * 360 - 180
y <- runif(n) * 180 - 90
xy <- cbind(x, y)
vals <- 1:n
p1 <- data.frame(xy, name=vals)
p2 <- data.frame(xy, name=vals)
coordinates(p1) <- ~x+y
coordinates(p2) <- ~x+y
if I try :
crop(p1,p2)
unable to find an inherited method for function ‘crop’ for signature ‘"SpatialPointsDataFrame"’
Now using rasterize
r <- rasterize(p1, r, 'name', fun=min)
crop(r,p2)
class : RasterLayer
dimensions : 18, 36, 648 (nrow, ncol, ncell)
resolution : 10, 10 (x, y)
extent : -180, 180, -90, 90 (xmin, xmax, ymin, ymax)
coord. ref. : +proj=longlat +datum=WGS84
data source : in memory
names : layer
values : 1, 997 (min, max)