[R] points rejected as lying outside the specified window

[Abby Rudolph]

Hello,

I am using the following code to create ppp files from csv data and map shape files, but I am getting some errors which I have been unable to fix by searching them online:


library(spatstat)
library(maps)
library(maptools)

NYC2<-readShapePoly("nybb.shp") # this is a map of the NYC boroughs without waterways and no census tract divisions (but it does include lines separating the 5 boroughs)
plot(NYC2)

NYBorough<-readShapePoly("NYBoroughsShapeMerge.shp") # this is a map of the NYC boroughs with census tract divisions
plot(NYBorough)

myfile<-read.csv("myfile.csv")
# my csv file contains 4 columns (ID, variable_type, X, Y)
# my goal is to determine whether individuals of variable_type=1 are spatially distributed more than what would be expected due to chance, if individuals of variable_type=0 are spatially distributed more than what would be expected due to chance, and finally if the spatial distribution of variable_type=1 differs from that of variable_type=0.

x<-NYBorough at polygons[[1]]@Polygons
# ppp(x.coordinates, y.coordinates, x.range, y.range)
coords<-slot(x[[1]],"coords")
coords
coords<-coords[19:1,]
coords<-coords[-1,]
coords

u<-myfile$type==0

Type_0<-ppp(myfile$X[u],myfile$Y[u],
                window=owin(poly=list(x=coords[,1],y=coords[,2])))
Type_1<-ppp(myfile$X[!u],myfile$Y[!u],
                window=owin(poly=list(x=coords[,1],y=coords[,2])))

ERROR Message:
Warning message:
In ppp(myfile$X[u], myfile$Y[u], window = owin(poly = list(x = coords[,  :
  217 points were rejected as lying outside the specified window
Warning message:
In ppp(myfile$X[!u], myfile$Y[!u], window = owin(poly = list(x = coords[,  :
  435 points were rejected as lying outside the specified window

# I only have 652 points, so all of my points are rejected as lying outside the specified window

Can someone please tell me what I am doing wrong.  The code I was using as a template was only looking at one county so it had a defined border which was somewhat rectangular.  Could it be because the shapefile I am using for NYC has too many borders?  Is it the coords code that is incorrect?

Any advice or suggestions would be greatly appreciated.

In case it is helpful, the code that follows is:
qtype_1<-quadratcount(type_1,10,10)
plot(type_1,pch="+",main=Title")
plot(type_1,add=TRUE,col="red",ltw=2,cex=1.2)
polygon(coords,lwd=2)
points(type_1,pch=".")

Thanks,
Abby