I am a new user of the R spatstat package and am having problems creating a polygonal observation window with owin(). Code follows:
library("maps")
library ("sp")`
library("spatstat")
mass.map <- map("state", "massachusetts:main", fill=T) # This returns a data frame includding x and y components that form a polygon of massachusetts mainland`
mass.win <- owin(poly=data.frame(x=mass.map$x, y=mass.map$y)
Error in if (w.area < 0) stop(paste("Area of polygon is negative -", "maybe traversed in >wrong direction?")) : missing value where TRUE/FALSE needed
I tried things like reversing the order of the polygon and got same error.
mass.win <- owin(poly=data.frame(x=rev(mass.map$x), y=rev(mass.map$y)))
Polygon contains duplicated vertices
Polygon is self-intersecting Error in owin(poly = data.frame(x = rev(mass.map$x), y = rev(mass.map$y))) : Polygon data contain duplicated vertices and self-intersection
Then I figured that maybe the polygon returned by map() is not meant to be fed to owin(). So I tried loading a massachusetts shape file (I am totally taking guesses at this point).:
x <- readShapePoly("../Geog/OUTLINE25K_POLY") ## The shape file for MASS, loaded from MassGIS website
mass.poly <- x <- readShapePoly("../Geog/OUTLINE25K_POLY", force_ring=T, delete_null_obj=T) ## I got following error whether or not I used force_ring
mass.owin <- as(mass.poly, "owin") Checking 1006 polygons...1, Polygon 1 contains duplicated vertices [Checking polygon with 91844 edges...] 2, 3, .. [etd 1:21:52] ....10 [etd 36:12] ..... [etd 23:10] ....20 [etd 16:59] ..... [etd 13:22] ....30 [etd 11:01] ..... [etd 9:21] ....40 [etd 8:06] ..... [etd 7:09] ....50 [etd 6:23] ..... [etd 5:46] ....60 [etd 5:15] ...[Checking polygon with 2449 edges...] .. [etd 4:49] ....70 [etd 4:27] ..... [etd 4:07] ....80 [etd 3:50] ..... [etd 3:36] ....90 [etd 3:22] ..... [etd 3:11] ....100 [ etc.
I got messages complaining about intersecting vertices, etc. and it failed to build the polygon.
Some context on problem: I am trying to use functions in spatstat for spatial relative risk calculations, ie, the spatial ratio of denstity of cases vs. controls. For that I need an observation window and point plot within that window. I could cheat and make the observation window a rectangle around massachusetts but that would presumably distort values near the coast. In any case, I'd like to learn how to do this right for any future work I do with this package. Thanks for any help you can provide.
EDIT 2021-02-04: I had this clockwise/anti-clockwise problem again and found my own answer the only one addressing the issue for spatstat. The answer was not very helpful. Have improved it to make it useful for a wider range of applications.
spatstat
package wants owin
object coordinates specified anticlockwise . A quote from the documentation of version 1.36-0:
single polygon: If poly is a matrix or data frame with two columns, or a structure with two component vectors x and y of equal length, then these values are interpreted as the cartesian coordinates of the vertices of a polygon circumscribing the window. The vertices must be listed anticlockwise. No vertex should be repeated (ie do not repeat the first vertex).
library("maps")
library ("sp")
library("spatstat")
mass.map <- map("state", "massachusetts:main", fill=T)
First, you'll need to find out whether your polygon is running clockwise or anticlock-wise. The approach here can be used to find out the answer. Formulate it as a function:
#' @title Check whether points for an owin are clockwise
#' @param x a dataframe with x coordinates in the first column and y coordinates in the second.
#' @details Similarly to owin, the polygon should not be closed
#' @return A logical telling whether the polygon is arranged clockwise.
#' @author The idea has been scavenged from https://stackoverflow.com/a/1165943/1082004
clockwise <- function(x) {
x.coords <- c(x[[1]], x[[1]][1])
y.coords <- c(x[[2]], x[[2]][1])
double.area <- sum(sapply(2:length(x.coords), function(i) {
(x.coords[i] - x.coords[i-1])*(y.coords[i] + y.coords[i-1])
}))
double.area > 0
}
Now, see whether the coordinates in mass.map
are clockwise:
clockwise(data.frame(x=mass.map$x, y=mass.map$y))
#> TRUE
They are. Turn the coordinates anti-clockwise by usingrev
function, which reverses vectors for x
and y
:
mass.win <- owin(poly=data.frame(x=rev(mass.map$x), y=rev(mass.map$y)))
plot(mass.win)
I'm quite familiar with the problem you have. If I understood right, you desire to get a polygonal object of class owin. Following codes will help you to acquire what you wanted.
#Loading the required packages
library (sp)
library(maps)
# Reading the dataset
mass.map <- map("state", "massachusetts:main", fill=T)
IDs <- sapply(strsplit(mass.map$names, ":"), function(x) x[1])
# converting can be done by loading the powerful package "maptools"
library(maptools)
# Converting into SpatialPolygons-object
mass.poly <- map2SpatialPolygons(mass.map, IDs = IDs)
# Converting by coercing into owin-object
mass.owin <- as.owin.SpatialPolygons(mass.poly)
The original question was posted 7 years ago (2014). The spatstat
package has changed vastly since then.
The error messages about duplicated vertices and self-intersecting polygons do not occur anymore , because the code now automatically corrects these flaws in the polygon data.
The error message Area of polygon is negative - maybe traversed in wrong direction?
still occurs . This is because owin
requires polygon vertices to be listed in anticlockwise order around an outer boundary (and clockwise order around the boundary of a hole). If your window is a single polygon rather than a collection of polygons, the fix is to simply reverse the order of the coordinate vectors using rev
:
library(maps)
library(sp)
library(spatstat)
mass.map <- map("state", "massachusetts:main", fill=TRUE)
mass.win <- owin(poly=lapply(mass.map, rev))
We can't make this happen automatically because it is not always what the user wanted.
For more information, see Chapter 3 of the spatstat book , which you can download for free from here .
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