Holes in polygons disappear after performing checkPolygonsHoles from maptools

On Thu, 2 Apr 2015, Roger Bivand wrote:

On Thu, 2 Apr 2015, Edzer Pebesma wrote:

 On 04/01/2015 08:03 PM, Grigory Alexandrovich wrote:

 Hello all,

 I encountered the following unexpected result using 

checkPolygonsHoles:

 # attach the worldmap as SpatialPolygonsDataFrame from the 

package >  maptools

 library(sp)
 library(maptools)
 data(wrld_simpl)

 # get a polygon with a hole

 shape_with_hole <- wrld_simpl[5,]

 # plot it (hole is left white, surrounded by blue color)

 plot(shape_with_hole, col = "blue")

 # perform checkPolygonsHoles

 shape_with_hole at polygons <- lapply(shape_with_hole at polygons,
 checkPolygonsHoles)

 # plot again, now holes aren't recognized as such

 plot(shape_with_hole, col = "blue")

 # and even the original SpatialPolygonsDataFrame object is 

changed !?

 plot(wrld_simpl[5,], col = "blue")

 One irritating side effect here is that the original object 

wrld_simpl

 is also changed. This result looks to me like a bug, or have I 

missed

 something?

 It looks as if it is related to rgeos, as

 avoidGEOS = FALSE
 library(sp)
 library(maptools)
 data(wrld_simpl)
 x = wrld_simpl

 shape_with_hole <- wrld_simpl[5,]

 if (avoidGEOS)
     gpclibPermit()
 shape_with_hole at polygons <- lapply(shape_with_hole at polygons,
 checkPolygonsHoles,
  avoidGEOS = avoidGEOS)

 data(wrld_simpl)
 all.equal(x, wrld_simpl)

No, but:

library(sp)
library(maptools)
data(wrld_simpl)
x = wrld_simpl
shape_with_hole <- wrld_simpl[5,]
pls <- slot(shape_with_hole, "polygons")
pls1 <- lapply(pls, checkPolygonsHoles, avoidGEOS = FALSE)
isTRUE(all.equal(pls, pls1))
# TRUE
gpclibPermit()
pls1 <- lapply(pls, checkPolygonsHoles, avoidGEOS = TRUE)
isTRUE(all.equal(pls, pls1))
# FALSE

where the Polygon objects are re-ordered and plotted out of order, so 
the deprecated gpclib code may be broken here. However, this isn't 
the problem,

The gpclib code is OK, it re-orders the Polygon objects, but the plot 
order is correct. The problem is as described below.

Roger

but rather (perhaps) graphics::polypath. If it is used (by default it 
is), and with the default path fill mode:

plot(x[5,], col="blue", usePolypath=TRUE, rule="winding")

does not whiten the holes. However:

plot(x[5,], col="blue", usePolypath=TRUE, rule="evenodd")

does. Using:

plot(x[5,], col="blue", pbg="white", usePolypath=FALSE)

also works by overpainting the island with the holes in white.

Please summarise the your SO thread.

By the way, in R it is unusual for changes in one object to propagate 
in an unintended way to another object, and this is not happening 
here. The visual impression is being driven by polypath doing 
different things depending on its rule setting. Look at ?polypath for 
details.

Well, this doesn't clarify, but it explains what is happeing, I hope ...

Roger

 returns a difference, but TRUE if avoidGEOS = TRUE.