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Creating and combining polygons in R with sf

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0

I'm getting a bit confused by a few supposedly basic tasks involving polygons in R. I'm tying to keep everything in sf, but if I need to switch to sp that's ok.

Firstly, I'm creating some polygons from scratch using coordinates (lat/long). I'm calling st_polygon on each table of coordinates and joining the results into a list. If we call that list polys then

class(polys[[1]])

 [1] "XY"      "POLYGON" "sfg"



polys[[1]]

 POLYGON ((-68.48597 -54.50921, -68.46605 -54.50971, [...]

I'm also reading in another polygon from a shapefile:

external_polys <-  st_read("C:/.../shapefile-polygons.shp")



class(external_polys)

 [1] "sf"         "data.frame"



external_polys

 Simple feature collection with 4711 features and 28 fields

 geometry type:  MULTIPOLYGON

 dimension:      XY

 bbox:           xmin: -179.9196 ymin: -50.75335 xmax: 179.2308 ymax: 83.73

 epsg (SRID):    4326

 proj4string:    +proj=longlat +datum=WGS84 +no_defs

 First 10 features:

[...]

Ultimately I want to be able to write a shapefile which simply combines all these polygons. It will be used simply as a masking layer, so I don't really care about carrying attributes forward. There are overlapping areas, and I will want to dissolve these (just want to know whether any particular place is covered by a polygon or not). However, I'm struggling to do this.

At the moment I've got:

polys_combined <- reduce(polys, c) %>% st_combine() %>% st_set_crs(4326)



# Add these to external polygons



all_polygons_combined <- st_union(polys_combined, external_polygons)

But this throws an error Input geom 0 is invalid: Self-intersection at or near point 12.500000000000057 32.080000000000041 at 12.500000000000057 32.080000000000041.

Thoughts? I'm sure there's better ways of doing each step... I'd particularly like a neater way of going from the coordinates to a simple features collection of polygons.

r polygon polygonize sf

share|improve this question

asked 4 hours ago

Tim KTim K

1734

• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  It's hard to tell what the problem is without the actual data, but judging from the error message you have invalid geometries in your data. Running sf::st_buffer(x, dist = 0) could possibly solve your problems (see also gis.stackexchange.com/questions/163445/…)
  
  – karpfen
  4 hours ago
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  I don't know if this is relevant, but I can plot/write to shapefile both polys_combined and external_polygons fine, so separately their geometries seem to be ok?
  
  – Tim K
  4 hours ago
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  I wouldn't rely on that. You could also check your polygons with st_is_valid and work from there. (cran.r-project.org/web/packages/sf/vignettes/sf3.html)
  
  – karpfen
  4 hours ago
  

  
  
  
  

add a comment | 

0

I'm getting a bit confused by a few supposedly basic tasks involving polygons in R. I'm tying to keep everything in sf, but if I need to switch to sp that's ok.

Firstly, I'm creating some polygons from scratch using coordinates (lat/long). I'm calling st_polygon on each table of coordinates and joining the results into a list. If we call that list polys then

class(polys[[1]])

 [1] "XY"      "POLYGON" "sfg"



polys[[1]]

 POLYGON ((-68.48597 -54.50921, -68.46605 -54.50971, [...]

I'm also reading in another polygon from a shapefile:

external_polys <-  st_read("C:/.../shapefile-polygons.shp")



class(external_polys)

 [1] "sf"         "data.frame"



external_polys

 Simple feature collection with 4711 features and 28 fields

 geometry type:  MULTIPOLYGON

 dimension:      XY

 bbox:           xmin: -179.9196 ymin: -50.75335 xmax: 179.2308 ymax: 83.73

 epsg (SRID):    4326

 proj4string:    +proj=longlat +datum=WGS84 +no_defs

 First 10 features:

[...]

Ultimately I want to be able to write a shapefile which simply combines all these polygons. It will be used simply as a masking layer, so I don't really care about carrying attributes forward. There are overlapping areas, and I will want to dissolve these (just want to know whether any particular place is covered by a polygon or not). However, I'm struggling to do this.

At the moment I've got:

polys_combined <- reduce(polys, c) %>% st_combine() %>% st_set_crs(4326)



# Add these to external polygons



all_polygons_combined <- st_union(polys_combined, external_polygons)

But this throws an error Input geom 0 is invalid: Self-intersection at or near point 12.500000000000057 32.080000000000041 at 12.500000000000057 32.080000000000041.

Thoughts? I'm sure there's better ways of doing each step... I'd particularly like a neater way of going from the coordinates to a simple features collection of polygons.

r polygon polygonize sf

share|improve this question

asked 4 hours ago

Tim KTim K

1734

• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  It's hard to tell what the problem is without the actual data, but judging from the error message you have invalid geometries in your data. Running sf::st_buffer(x, dist = 0) could possibly solve your problems (see also gis.stackexchange.com/questions/163445/…)
  
  – karpfen
  4 hours ago
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  I don't know if this is relevant, but I can plot/write to shapefile both polys_combined and external_polygons fine, so separately their geometries seem to be ok?
  
  – Tim K
  4 hours ago
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  I wouldn't rely on that. You could also check your polygons with st_is_valid and work from there. (cran.r-project.org/web/packages/sf/vignettes/sf3.html)
  
  – karpfen
  4 hours ago
  

  
  
  
  

add a comment | 

I'm getting a bit confused by a few supposedly basic tasks involving polygons in R. I'm tying to keep everything in sf, but if I need to switch to sp that's ok.

Firstly, I'm creating some polygons from scratch using coordinates (lat/long). I'm calling st_polygon on each table of coordinates and joining the results into a list. If we call that list polys then

class(polys[[1]])

 [1] "XY"      "POLYGON" "sfg"



polys[[1]]

 POLYGON ((-68.48597 -54.50921, -68.46605 -54.50971, [...]

I'm also reading in another polygon from a shapefile:

external_polys <-  st_read("C:/.../shapefile-polygons.shp")



class(external_polys)

 [1] "sf"         "data.frame"



external_polys

 Simple feature collection with 4711 features and 28 fields

 geometry type:  MULTIPOLYGON

 dimension:      XY

 bbox:           xmin: -179.9196 ymin: -50.75335 xmax: 179.2308 ymax: 83.73

 epsg (SRID):    4326

 proj4string:    +proj=longlat +datum=WGS84 +no_defs

 First 10 features:

[...]

Ultimately I want to be able to write a shapefile which simply combines all these polygons. It will be used simply as a masking layer, so I don't really care about carrying attributes forward. There are overlapping areas, and I will want to dissolve these (just want to know whether any particular place is covered by a polygon or not). However, I'm struggling to do this.

At the moment I've got:

polys_combined <- reduce(polys, c) %>% st_combine() %>% st_set_crs(4326)



# Add these to external polygons



all_polygons_combined <- st_union(polys_combined, external_polygons)

But this throws an error Input geom 0 is invalid: Self-intersection at or near point 12.500000000000057 32.080000000000041 at 12.500000000000057 32.080000000000041.

Thoughts? I'm sure there's better ways of doing each step... I'd particularly like a neater way of going from the coordinates to a simple features collection of polygons.

r polygon polygonize sf

share|improve this question

asked 4 hours ago

Tim KTim K

1734

class(polys[[1]])

 [1] "XY"      "POLYGON" "sfg"



polys[[1]]

 POLYGON ((-68.48597 -54.50921, -68.46605 -54.50971, [...]

external_polys <-  st_read("C:/.../shapefile-polygons.shp")



class(external_polys)

 [1] "sf"         "data.frame"



external_polys

 Simple feature collection with 4711 features and 28 fields

 geometry type:  MULTIPOLYGON

 dimension:      XY

 bbox:           xmin: -179.9196 ymin: -50.75335 xmax: 179.2308 ymax: 83.73

 epsg (SRID):    4326

 proj4string:    +proj=longlat +datum=WGS84 +no_defs

 First 10 features:

[...]

polys_combined <- reduce(polys, c) %>% st_combine() %>% st_set_crs(4326)



# Add these to external polygons



all_polygons_combined <- st_union(polys_combined, external_polygons)

share|improve this question

asked 4 hours ago

Tim KTim K

1734

share|improve this question

asked 4 hours ago

Tim KTim K

1734

asked 4 hours ago

Tim KTim K

1734

asked 4 hours ago

Tim KTim K

1734