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.
First, I would recommend using rgdal for reading/writing shapefiles. It looks like you are trying to directly assign your owin object to your ppp object. This will not work in the way you are thinking. You can, in fact, specify the owin window object when creating the ppp object. This is detailed in the as.ppp help which can be accessed using: ?as.ppp
Is this a marked process problem (values associated with the points)? If so then you need to change the way you are coercing the point data, using ppp directly, so you can define the marks.
# Add required packages
require(sp)
require(rgdal)
require(spatstat)
# Set working directory and read shapefiles
setwd("C:/MyData")
Year1 <- readOGR(getwd(), "1983")
Studyarea <- readOGR(getwd(), "SA-R")
# Coerce study area to owin object
w <- as.owin(Studyarea)
# Coerce points to ppp object and pass the object the study area window
Year1 <- as.ppp(Year1, W=w)
# Alternate method with marks
Year1 <- ppp(coordinates(Year1)[,1],coordinates(Year1)[,2], window=w, marks=Year1@data$MyVar)
# Plot points with study area window
plot(Year1)
Best Answer
ok figured it out eventually myself