I cannot as yet offer a complete solution, but the immediate issue is that the parcel object has invalid geometry. If you can fix the geometry, we should be able to get the intersections to work. As an example of problematic geometry, this expression is fine:
gIsValid(hr_kud, reason = TRUE)
But this one will consistently crash R:
gIsValid(parcel, reason = TRUE)
So, one or more of the 20,069 polygons in parcel appears to be broken in some way. I don't know how to validate geometry within R but Quantum GIS does have a tool for this. I assume that you have the original shapefile or other data source from which you created parcel but you can recreate this by using the writeOGR function from the rgdal library like so:
library(rgeos)
library(rgdal)
setwd("your_directory_name_here")
load("Data.RData")
class(parcel)
class(hr_kud)
object.size(hr_kud)
object.size(parcel)
parcel@proj4string
hr_kud@proj4string
gIsValid(hr_kud, reason = TRUE)
#gIsValid(parcel, reason = TRUE) # warning! this will crash R
writeOGR(parcel, ".", driver = "ESRI Shapefile", layer = "poly")
This should produce 4 files:
poly.shp
poly.shx
poly.dbf
poly.prj
In QGIS, first load your shapefile by going to the 'Layer' menu and clicking on 'Add Vector Layer..." then select the poly.shp file or the folder in which the file resides. Then go to the 'Vector' menu, click on the 'Geometry Tools' menu item then on the 'Check geometry validity' item. Then click OK on the next dialog box. With more than 20k polys this took quite some time (about half an hour I think), but the result was this:
[EDIT: I upgraded to QGIS 1.8 Lisboa with two results - a massive increase in validation speed and the discovery of other errors, as per the revised screenshot below.]
So, it looks like you have a number of issues there. Before you close the dialog box, click on the error in the dialog box list and QGIS will show you the offending polygon. I'm not experienced in this kind of GIS but the tips in this tutorial might help. Google QGIS and "self intersecting" for more ideas.