Create SpatialPolygonsDataFrame indicating the polygons in a single source SpatialPolygonsDataFrame that overlap with the new polygons?

I figured out how to achieve this  in raster, however for the real data the
raster files and array exceed my availible 16gb memory.

I would still be interested in any suggestions on how to achieve directly
with the SpatialPolygons

For the record here is the raster/ array approach I figured out:
rm(list=ls())
library(rgdal)
library(raster)
library(sp)
library (plyr)
p1<-Polygons(list(Polygon(cbind(x=c(0,2,2,0,0),y=c(0,0,2,2,0)))),1)
p2<-Polygons(list(Polygon(cbind(x=c(1,3,3,1,1),y=c(1,1,3,3,1)))),2)
p3<-Polygons(list(Polygon(cbind(x=c(0,2,2,0,0),y=c(1,1,2,2,1)))),3)

mypolys<-list(p1,p2,p3)


SDF<-SpatialPolygons(mypolys)
plot(SDF)
ext<-(extent(SDF))

xy <- abs(apply(as.matrix(bbox(ext)), 1, diff))
n <- 1
r <- raster(ext, ncol=xy[1]*n, nrow=xy[2]*n)
for(i in 1:length(SDF)){
 rr<-rasterize(SDF[i,],r)
 if(exists("S")) S<-stack(S,rr) else S<-stack(rr)
}
A<-as.array(S)

C<-apply(A,3,as.numeric)
U<-unique(C)
C<-data.frame(C)
U<-data.frame(U)
ID<-as.numeric(rownames(U))
U<-cbind(ID,U)
Vals<-matrix(join(C,U)$ID,dim(S)[1],dim(S)[2])
Vals<-setValues(r,Vals)
Vals<-ratify(Vals)
levels(Vals)[[1]]<-U
names(levels(Vals)[[1]])<-c("ID","p1","p2","p3")
plot(Vals)
plot(SDF,add=T)
print(Vals)



On Thu, Jul 3, 2014 at 4:17 PM, nevil amos <nevil.amos at gmail.com> wrote:

I am trying to create a polygon dataset that creates a new polygon for
each unique combination of location and overlap of polygons in an input
polygon dataset, and is attributed with the input polygons underlying each
of the derived polygons, and th output does not contain any overlapping
polygons.


#trivial example
#single layer with three partially overlapping polygons
library(sp)
p1<-Polygons(list(Polygon(cbind(x=c(0,2,2,0,0),y=c(0,0,2,2,0)))),1)
p2<-Polygons(list(Polygon(cbind(x=c(1,3,3,1,1),y=c(1,1,3,3,1)))),2)

p3<-Polygons(list(Polygon(cbind(x=c(1.5,3,3,1.5,1.5),y=c(1.5,1.5,3,3,1.5)))),3)
mypolys<-list(p1,p2,p3)
mydata<-data.frame(Name=c("p1","p2","p3"),row.names=c(1,2,3))

SDF<-SpatialPolygonsDataFrame(SpatialPolygons(mypolys),mydata)
par(mfrow=c(3,4))
plot(SDF)


#the desired result is a SpatialPolygonsDataFrame with a single separate
polygon for each of the six areas deifined by the interection of the
boundaries of the three input polygons
text(.5,.5,1)
text(1.25,1.25,2)
text(1.75,1.75,3)
text(2.5,2.5,4)
text(1.25,2.5,5)
text(2.5,1.25,6)

# such that the data frame lists the input polygons (p1,p2,p3) that
overlap at the location of each of the output polygons (1:6) and the output
has no overlap between the polygons
# the results would be the six unique polygons shown in the plot and so
the attributes would look like:
data.frame(polys=c("p1","p1 p2","p1 p2 p3","p2 p3","p2","p2"))
# or alternatively

data.frame(cbind(c("p1","p1","p1","p2","p2","p2"),c(NA,"p2","p2","p3",NA,NA),c(NA,NA,"p3",NA,NA,NA)))
# or alternatively
data.frame(cbind(p1=c(1,1,1,0,0,0),p2=c(0,1,1,1,1,1),p3=c(0,0,1,1,0,0)))


#This last plot shows the "apparent polygons" I want in separate colors (
because you cannot see the overlapping portions)
Outpoly<-union(SDF,SDF)
plot(OutPoly,col=1:9)

plot(SpatialPolygons(list(Polygons(list(Polygon(cbind(x=c(2,2,3,3,2),y=c(1,1.5,1.5,1,1)))),1))),col=12,add=T)
text(.5,.5,1)
text(1.25,1.25,2)
text(1.75,1.75,3)
text(2.5,2.5,4)
text(1.25,2.5,5)
text(2.5,1.25,6)
#The nearest I could get was raster::union however this requires two ( and
only 2) SpatialDataFrames as input , what I need is union with a single
input union(SDF,SDF) results in 9 polygons not 6, these are all simple
rectangles of overlapping pairs (union(union(SDF,SDF)SDF)) results in 27
polygons - all again just the simple rectangular overlaps and original
polygons
union(SDF,SDF)@data

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