Holes in polygons disappear after performing checkPolygonsHoles from maptools

On Fri, 3 Apr 2015, Grigory Alexandrovich wrote:

Am 02.04.2015 um 22:24 schrieb Roger Bivand:

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.

|Thank you for your answers guys. But I am still not fully convinced
that it is an issue of the plot function,
because the object shape_with_hole edited with checkPolygonsHoles
before, continues to behave in a strange way:

# we check which polygons are flagged as holes.
# The flags are still set properly,
# although the plot() function didn't recognize them:
sapply(shape_with_hole at polygons[[1]]@Polygons, slot, "hole")

[1] FALSE  TRUE  TRUE  TRUE

# load library rgdal for reprojection
library(rgdal)

# reproject with spTransform, just for testing
shape_with_hole <- spTransform(shape_with_hole, CRS("+proj=longlat
+ellps=WGS84 +datum=WGS84"))

# after reprojection all flags are set to FALSE
sapply(shape_with_hole at polygons[[1]]@Polygons, slot, "hole")

[1] FALSE FALSE FALSE FALSE


So it is still something wrong with shape_with_hole, or?

Please provide the output of sessionInfo(), rgeos::version_GEOS(), and 
rgdal::getGDALVersionInfo() with rgdal::getPROJ4VersionInfo(). I 
cannot reproduce the degradation of hole status following a no-op use 
of spTransform() with:

sessionInfo()

R version 3.1.3 (2015-03-09)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Fedora 21 (Twenty One)
...
attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods base

other attached packages:
[1] rgdal_0.9-3     maptools_0.8-34 sp_1.0-17

loaded via a namespace (and not attached):
[1] foreign_0.8-63  grid_3.1.3      lattice_0.20-31 rgeos_0.3-8
[5] tools_3.1.3

rgeos::version_GEOS()

[1] "3.4.2-CAPI-1.8.2 r3921"

rgdal::getGDALVersionInfo()

[1] "GDAL 1.11.2, released 2015/02/10"

rgdal::getPROJ4VersionInfo()

[1] "Rel. 4.9.1, 04 March 2015, [PJ_VERSION: 491]"

Roger

Best

Grigory|