R_Extracting coordinates from SpatialPolygonsDataFrame

Question

Is it only me who have the problem with extracting coordinates of a polygon from SpatialPolygonsDataFrame object? I am able to extract other slots of the object (ID,plotOrder) but not coordinates (coords). I don't know what I am doing wrong. Please find below my R session where bdryData being the SpatialPolygonsDataFrame object with two polygons.

> bdryData
An object of class "SpatialPolygonsDataFrame"
Slot "data":
  ID GRIDCODE
0  1        0
1  2        0

Slot "polygons":
[[1]]
An object of class "Polygons"
Slot "Polygons":
[[1]]
An object of class "Polygon"
Slot "labpt":
[1] 415499.1 432781.7

Slot "area":
[1] 0.6846572

Slot "hole":
[1] FALSE

Slot "ringDir":
[1] 1

Slot "coords":
         [,1]     [,2]
[1,] 415499.6 432781.2
[2,] 415498.4 432781.5
[3,] 415499.3 432782.4
[4,] 415499.6 432781.2



Slot "plotOrder":
[1] 1

Slot "labpt":
[1] 415499.1 432781.7

Slot "ID":
[1] "0"

Slot "area":
[1] 0.6846572


[[2]]
An object of class "Polygons"
Slot "Polygons":
[[1]]
An object of class "Polygon"
Slot "labpt":
[1] 415587.3 432779.4

Slot "area":
[1] 20712.98

Slot "hole":
[1] FALSE

Slot "ringDir":
[1] 1

Slot "coords":
           [,1]     [,2]
  [1,] 415499.6 432781.2
  [2,] 415505.0 432781.8
  [3,] 415506.5 432792.6
  [4,] 415508.9 432792.8
  [5,] 415515.0 432791.5
  [6,] 415517.7 432795.6
  [7,] 415528.6 432797.7
  [8,] 415538.8 432804.2
  [9,] 415543.2 432805.8
 [10,] 415545.1 432803.6
 [11,] 415547.1 432804.7
 [12,] 415551.7 432805.8
 [13,] 415557.5 432812.3
 [14,] 415564.2 432817.1
 [15,] 415568.5 432823.9
 [16,] 415571.0 432826.8
 [17,] 415573.2 432828.7
 [18,] 415574.1 432829.7
 [19,] 415576.2 432830.7
 [20,] 415580.2 432833.8
 [21,] 415589.6 432836.0
 [22,] 415593.1 432841.0
 [23,] 415592.2 432843.7
 [24,] 415590.6 432846.6
 [25,] 415589.0 432853.3
 [26,] 415584.8 432855.3
 [27,] 415579.7 432859.8
 [28,] 415577.7 432866.2
 [29,] 415575.6 432868.1
 [30,] 415566.7 432880.7
 [31,] 415562.7 432887.5
 [32,] 415559.2 432889.1
 [33,] 415561.5 432890.7
 [34,] 415586.2 432889.7
 [35,] 415587.1 432888.6
 [36,] 415588.5 432890.2
 [37,] 415598.2 432888.7
 [38,] 415599.1 432887.7
 [39,] 415601.2 432886.7
 [40,] 415603.1 432885.7
 [41,] 415605.2 432884.7
 [42,] 415606.1 432882.7
 [43,] 415607.2 432880.7
 [44,] 415608.3 432878.3
 [45,] 415612.2 432874.8
 [46,] 415614.7 432871.9
 [47,] 415617.1 432870.7
 [48,] 415622.4 432868.2
 [49,] 415622.0 432862.4
 [50,] 415624.2 432855.4
 [51,] 415633.2 432845.3
 [52,] 415639.0 432841.1
 [53,] 415642.8 432832.9
 [54,] 415647.5 432828.7
 [55,] 415654.3 432820.3
 [56,] 415654.1 432816.5
 [57,] 415658.2 432812.8
 [58,] 415661.9 432808.6
 [59,] 415663.5 432808.7
 [60,] 415668.1 432803.5
 [61,] 415676.5 432801.3
 [62,] 415679.1 432802.7
 [63,] 415680.1 432802.7
 [64,] 415681.1 432802.7
 [65,] 415682.2 432802.7
 [66,] 415685.8 432804.7
 [67,] 415691.8 432802.2
 [68,] 415693.6 432798.9
 [69,] 415696.2 432777.0
 [70,] 415689.8 432773.5
 [71,] 415683.7 432771.6
 [72,] 415680.2 432766.7
 [73,] 415679.0 432765.6
 [74,] 415676.8 432753.7
 [75,] 415671.4 432747.7
 [76,] 415662.7 432747.2
 [77,] 415658.7 432750.0
 [78,] 415657.0 432746.3
 [79,] 415654.1 432743.7
 [80,] 415652.3 432739.8
 [81,] 415649.6 432739.6
 [82,] 415648.0 432739.7
 [83,] 415641.9 432736.4
 [84,] 415633.4 432736.9
 [85,] 415630.2 432734.7
 [86,] 415622.3 432733.6
 [87,] 415614.4 432726.5
 [88,] 415617.1 432719.1
 [89,] 415612.5 432718.1
 [90,] 415610.0 432720.9
 [91,] 415606.2 432716.6
 [92,] 415603.2 432713.9
 [93,] 415601.4 432710.0
 [94,] 415580.3 432708.7
 [95,] 415545.1 432709.7
 [96,] 415543.5 432711.5
 [97,] 415534.0 432715.7
 [98,] 415527.1 432713.7
 [99,] 415521.1 432711.6
[100,] 415505.6 432710.6
[101,] 415501.3 432710.9
[102,] 415499.3 432708.7
[103,] 415495.6 432711.6
[104,] 415482.6 432726.2
[105,] 415477.2 432734.0
[106,] 415478.1 432737.7
[107,] 415479.2 432739.7
[108,] 415480.9 432743.4
[109,] 415486.5 432751.2
[110,] 415493.2 432760.7
[111,] 415494.1 432762.7
[112,] 415498.1 432767.9
[113,] 415497.2 432770.7
[114,] 415490.6 432773.2
[115,] 415493.2 432775.6
[116,] 415496.0 432778.7
[117,] 415499.2 432779.7
[118,] 415499.6 432781.2



Slot "plotOrder":
[1] 1

Slot "labpt":
[1] 415587.3 432779.4

Slot "ID":
[1] "1"

Slot "area":
[1] 20712.98



Slot "plotOrder":
[1] 2 1

Slot "bbox":
       min      max
x 415477.2 415696.2
y 432708.7 432890.7

Slot "proj4string":
CRS arguments:
 +proj=tmerc +lat_0=49 +lon_0=-2 +k=0.9996012717 +x_0=400000 +y_0=-100000
+datum=OSGB36 +units=m +no_defs +ellps=airy
+towgs84=446.448,-125.157,542.060,0.1502,0.2470,0.8421,-20.4894

Subsetting second polygon from bdryData

> bdryData@polygons[[2]]
An object of class "Polygons"
Slot "Polygons":
[[1]]
An object of class "Polygon"
Slot "labpt":
[1] 415587.3 432779.4

Slot "area":
[1] 20712.98

Slot "hole":
[1] FALSE

Slot "ringDir":
[1] 1

Slot "coords":
           [,1]     [,2]
  [1,] 415499.6 432781.2
  [2,] 415505.0 432781.8
  [3,] 415506.5 432792.6
  [4,] 415508.9 432792.8
  [5,] 415515.0 432791.5
  [6,] 415517.7 432795.6
  [7,] 415528.6 432797.7
  [8,] 415538.8 432804.2
  [9,] 415543.2 432805.8
 [10,] 415545.1 432803.6
 [11,] 415547.1 432804.7
 [12,] 415551.7 432805.8
 [13,] 415557.5 432812.3
 [14,] 415564.2 432817.1
 [15,] 415568.5 432823.9
 [16,] 415571.0 432826.8
 [17,] 415573.2 432828.7
 [18,] 415574.1 432829.7
 [19,] 415576.2 432830.7
 [20,] 415580.2 432833.8
 [21,] 415589.6 432836.0
 [22,] 415593.1 432841.0
 [23,] 415592.2 432843.7
 [24,] 415590.6 432846.6
 [25,] 415589.0 432853.3
 [26,] 415584.8 432855.3
 [27,] 415579.7 432859.8
 [28,] 415577.7 432866.2
 [29,] 415575.6 432868.1
 [30,] 415566.7 432880.7
 [31,] 415562.7 432887.5
 [32,] 415559.2 432889.1
 [33,] 415561.5 432890.7
 [34,] 415586.2 432889.7
 [35,] 415587.1 432888.6
 [36,] 415588.5 432890.2
 [37,] 415598.2 432888.7
 [38,] 415599.1 432887.7
 [39,] 415601.2 432886.7
 [40,] 415603.1 432885.7
 [41,] 415605.2 432884.7
 [42,] 415606.1 432882.7
 [43,] 415607.2 432880.7
 [44,] 415608.3 432878.3
 [45,] 415612.2 432874.8
 [46,] 415614.7 432871.9
 [47,] 415617.1 432870.7
 [48,] 415622.4 432868.2
 [49,] 415622.0 432862.4
 [50,] 415624.2 432855.4
 [51,] 415633.2 432845.3
 [52,] 415639.0 432841.1
 [53,] 415642.8 432832.9
 [54,] 415647.5 432828.7
 [55,] 415654.3 432820.3
 [56,] 415654.1 432816.5
 [57,] 415658.2 432812.8
 [58,] 415661.9 432808.6
 [59,] 415663.5 432808.7
 [60,] 415668.1 432803.5
 [61,] 415676.5 432801.3
 [62,] 415679.1 432802.7
 [63,] 415680.1 432802.7
 [64,] 415681.1 432802.7
 [65,] 415682.2 432802.7
 [66,] 415685.8 432804.7
 [67,] 415691.8 432802.2
 [68,] 415693.6 432798.9
 [69,] 415696.2 432777.0
 [70,] 415689.8 432773.5
 [71,] 415683.7 432771.6
 [72,] 415680.2 432766.7
 [73,] 415679.0 432765.6
 [74,] 415676.8 432753.7
 [75,] 415671.4 432747.7
 [76,] 415662.7 432747.2
 [77,] 415658.7 432750.0
 [78,] 415657.0 432746.3
 [79,] 415654.1 432743.7
 [80,] 415652.3 432739.8
 [81,] 415649.6 432739.6
 [82,] 415648.0 432739.7
 [83,] 415641.9 432736.4
 [84,] 415633.4 432736.9
 [85,] 415630.2 432734.7
 [86,] 415622.3 432733.6
 [87,] 415614.4 432726.5
 [88,] 415617.1 432719.1
 [89,] 415612.5 432718.1
 [90,] 415610.0 432720.9
 [91,] 415606.2 432716.6
 [92,] 415603.2 432713.9
 [93,] 415601.4 432710.0
 [94,] 415580.3 432708.7
 [95,] 415545.1 432709.7
 [96,] 415543.5 432711.5
 [97,] 415534.0 432715.7
 [98,] 415527.1 432713.7
 [99,] 415521.1 432711.6
[100,] 415505.6 432710.6
[101,] 415501.3 432710.9
[102,] 415499.3 432708.7
[103,] 415495.6 432711.6
[104,] 415482.6 432726.2
[105,] 415477.2 432734.0
[106,] 415478.1 432737.7
[107,] 415479.2 432739.7
[108,] 415480.9 432743.4
[109,] 415486.5 432751.2
[110,] 415493.2 432760.7
[111,] 415494.1 432762.7
[112,] 415498.1 432767.9
[113,] 415497.2 432770.7
[114,] 415490.6 432773.2
[115,] 415493.2 432775.6
[116,] 415496.0 432778.7
[117,] 415499.2 432779.7
[118,] 415499.6 432781.2



Slot "plotOrder":
[1] 1

Slot "labpt":
[1] 415587.3 432779.4

Slot "ID":
[1] "1"

Slot "area":
[1] 20712.98

Extracting slots

> bdryData@polygons[[2]]@ID 
[1] "1"

> bdryData@polygons[[2]]@plotOrder
[1] 1

But problem with coordinates

> bdryData@polygons[[2]]@coords
Error: no slot of name "coords" for this object of class "Polygons"

Any help is really appreciated. Thanks.

rm167 · Accepted Answer · 2015-04-23T15:24:25.773

15

Finally, I figured out that I didn't parse the output correctly. The correct way to do is bdryData@polygons[[2]]@Polygons[[1]]@coords. Mind the difference in command polygons(Polygons and polygons) and it took me ages to find out.

edited Apr 23 '15 at 15:24

answered Apr 23 '15 at 14:06

rm167

1,185
2
10
26

1

What polygon would this code be for? I can't understand the mismatch in the [[2]] and [[1]] reference. – LoveMeow Jun 08 '15 at 01:41
2

This is not generalizable and, like @Ms.Meow, I'm not sure where the 2 comes in. – forlooper May 24 '16 at 14:00
2

This worked perfectly for me. I only had 1 polygon in the list and so I replaced `[[2]]` with `[[1]]` and replaced `bdryData` with my SpatialPolygons object and it was able to extract the coordinates. – colonelforbin97 Dec 03 '20 at 21:22

score 6 · Answer 2 · answered Apr 22 '15 at 16:18

6

Use the coordinates() function from the sp package. It should give you the values in a list format.

You can also get the Polygon attribute from the shapefile.

mfile = readOGR(dsn=dsn,layer=layername)
polys = attr(mfile,'polygons')
npolys = length(polys)
for (i in 1:npolys){
  poly = polys[[i]]
  polys2 = attr(poly,'Polygons')
  npolys2 = length(polys2)
  for (j in 1:npolys2){
     #do stuff with these values
     coords = coordinates(polys2[[j]])
  }
}

answered Apr 22 '15 at 16:18

Max Candocia

4,294
35
58

Thank you. But the real problem was that I didn't parse it correctly and took me ages to solve it. please check my answer. – rm167 Apr 23 '15 at 14:00
1

coordinates() retrieves the labpt slot, not the polygon coordinates – cmbarbu May 26 '15 at 18:01
What @cmbarbu said is correct, coordinates() won't work. – forlooper May 24 '16 at 14:02

score 5 · Answer 3 · answered May 19 '16 at 19:25

This took me a while to figure out too. The following function I wrote worked for me. sp.df should be SpatialPolygonsDataFrame.

extractCoords <- function(sp.df)
{
    results <- list()
    for(i in 1:length(sp.df@polygons[[1]]@Polygons))
    {
        results[[i]] <- sp.df@polygons[[1]]@Polygons[[i]]@coords
    }
    results <- Reduce(rbind, results)
    results
}

score 2 · Answer 4 · answered Mar 23 '19 at 09:21

This question was also addressed on gis.stackexchange, here. I made an example below testing all the options mentioned here by @mdsumner. Also have a look here

library(sp)
library(sf)
#> Warning: package 'sf' was built under R version 3.5.3
#> Linking to GEOS 3.6.1, GDAL 2.2.3, PROJ 4.9.3
library(raster)
library(spbabel)
#> Warning: package 'spbabel' was built under R version 3.5.3
library(tmap)

library(microbenchmark)
library(ggplot2)

# Prepare data
data(World)
# Convert from sf to sp objects
atf_sf <- World[World$iso_a3 == "ATF", ]
atf_sp <- as(atf_sf, "Spatial")
atf_sp
#> class       : SpatialPolygonsDataFrame 
#> features    : 1 
#> extent      : 5490427, 5660887, -6048972, -5932855  (xmin, xmax, ymin, ymax)
#> coord. ref. : +proj=eck4 +lon_0=0 +x_0=0 +y_0=0 +datum=WGS84 +units=m +no_defs +ellps=WGS84 +towgs84=0,0,0 
#> variables   : 15
#> # A tibble: 1 x 15
#>   iso_a3 name  sovereignt continent area  pop_est pop_est_dens economy
#>   <fct>  <fct> <fct>      <fct>     <S3:>   <dbl>        <dbl> <fct>  
#> 1 ATF    Fr. ~ France     Seven se~ 7257~     140       0.0193 6. Dev~
#> # ... with 7 more variables: income_grp <fct>, gdp_cap_est <dbl>,
#> #   life_exp <dbl>, well_being <dbl>, footprint <dbl>, inequality <dbl>,
#> #   HPI <dbl>

# Try various functions:

raster::geom(atf_sp)
#>       object part cump hole       x        y
#>  [1,]      1    1    1    0 5550200 -5932855
#>  [2,]      1    1    1    0 5589907 -5964836
#>  [3,]      1    1    1    0 5660887 -5977490
#>  [4,]      1    1    1    0 5656160 -5996685
#>  [5,]      1    1    1    0 5615621 -6042456
#>  [6,]      1    1    1    0 5490427 -6048972
#>  [7,]      1    1    1    0 5509148 -5995424
#>  [8,]      1    1    1    0 5536900 -5953683
#>  [9,]      1    1    1    0 5550200 -5932855

ggplot2::fortify(atf_sp)
#> Regions defined for each Polygons
#>      long      lat order  hole piece id group
#> 1 5550200 -5932855     1 FALSE     1  8   8.1
#> 2 5589907 -5964836     2 FALSE     1  8   8.1
#> 3 5660887 -5977490     3 FALSE     1  8   8.1
#> 4 5656160 -5996685     4 FALSE     1  8   8.1
#> 5 5615621 -6042456     5 FALSE     1  8   8.1
#> 6 5490427 -6048972     6 FALSE     1  8   8.1
#> 7 5509148 -5995424     7 FALSE     1  8   8.1
#> 8 5536900 -5953683     8 FALSE     1  8   8.1
#> 9 5550200 -5932855     9 FALSE     1  8   8.1

spbabel::sptable(atf_sp)
#> # A tibble: 9 x 6
#>   object_ branch_ island_ order_       x_        y_
#>     <int>   <int> <lgl>    <int>    <dbl>     <dbl>
#> 1       1       1 TRUE         1 5550200. -5932855.
#> 2       1       1 TRUE         2 5589907. -5964836.
#> 3       1       1 TRUE         3 5660887. -5977490.
#> 4       1       1 TRUE         4 5656160. -5996685.
#> 5       1       1 TRUE         5 5615621. -6042456.
#> 6       1       1 TRUE         6 5490427. -6048972.
#> 7       1       1 TRUE         7 5509148. -5995424.
#> 8       1       1 TRUE         8 5536900. -5953683.
#> 9       1       1 TRUE         9 5550200. -5932855.

as.data.frame(as(as(atf_sp, "SpatialLinesDataFrame"),"SpatialPointsDataFrame"))
#>     iso_a3                   name sovereignt               continent
#> 8      ATF Fr. S. Antarctic Lands     France Seven seas (open ocean)
#> 8.1    ATF Fr. S. Antarctic Lands     France Seven seas (open ocean)
#> 8.2    ATF Fr. S. Antarctic Lands     France Seven seas (open ocean)
#> 8.3    ATF Fr. S. Antarctic Lands     France Seven seas (open ocean)
#> 8.4    ATF Fr. S. Antarctic Lands     France Seven seas (open ocean)
#> 8.5    ATF Fr. S. Antarctic Lands     France Seven seas (open ocean)
#> 8.6    ATF Fr. S. Antarctic Lands     France Seven seas (open ocean)
#> 8.7    ATF Fr. S. Antarctic Lands     France Seven seas (open ocean)
#> 8.8    ATF Fr. S. Antarctic Lands     France Seven seas (open ocean)
#>                area pop_est pop_est_dens              economy
#> 8   7257.455 [km^2]     140   0.01929051 6. Developing region
#> 8.1 7257.455 [km^2]     140   0.01929051 6. Developing region
#> 8.2 7257.455 [km^2]     140   0.01929051 6. Developing region
#> 8.3 7257.455 [km^2]     140   0.01929051 6. Developing region
#> 8.4 7257.455 [km^2]     140   0.01929051 6. Developing region
#> 8.5 7257.455 [km^2]     140   0.01929051 6. Developing region
#> 8.6 7257.455 [km^2]     140   0.01929051 6. Developing region
#> 8.7 7257.455 [km^2]     140   0.01929051 6. Developing region
#> 8.8 7257.455 [km^2]     140   0.01929051 6. Developing region
#>                  income_grp gdp_cap_est life_exp well_being footprint
#> 8   2. High income: nonOECD    114285.7       NA         NA        NA
#> 8.1 2. High income: nonOECD    114285.7       NA         NA        NA
#> 8.2 2. High income: nonOECD    114285.7       NA         NA        NA
#> 8.3 2. High income: nonOECD    114285.7       NA         NA        NA
#> 8.4 2. High income: nonOECD    114285.7       NA         NA        NA
#> 8.5 2. High income: nonOECD    114285.7       NA         NA        NA
#> 8.6 2. High income: nonOECD    114285.7       NA         NA        NA
#> 8.7 2. High income: nonOECD    114285.7       NA         NA        NA
#> 8.8 2. High income: nonOECD    114285.7       NA         NA        NA
#>     inequality HPI Lines.NR Lines.ID Line.NR coords.x1 coords.x2
#> 8           NA  NA        1        8       1   5550200  -5932855
#> 8.1         NA  NA        1        8       1   5589907  -5964836
#> 8.2         NA  NA        1        8       1   5660887  -5977490
#> 8.3         NA  NA        1        8       1   5656160  -5996685
#> 8.4         NA  NA        1        8       1   5615621  -6042456
#> 8.5         NA  NA        1        8       1   5490427  -6048972
#> 8.6         NA  NA        1        8       1   5509148  -5995424
#> 8.7         NA  NA        1        8       1   5536900  -5953683
#> 8.8         NA  NA        1        8       1   5550200  -5932855

# What about speed? raster::geom is the fastest
res <- microbenchmark(raster::geom(atf_sp),
                      ggplot2::fortify(atf_sp),
                      spbabel::sptable(atf_sp),
                      as.data.frame(as(as(atf_sp, "SpatialLinesDataFrame"),
                                       "SpatialPointsDataFrame")))
ggplot2::autoplot(res)
#> Coordinate system already present. Adding new coordinate system, which will replace the existing one.

^{Created on 2019-03-23 by the reprex package (v0.2.1)}

score 0 · Answer 5 · answered Dec 06 '19 at 18:28

0

ggplot2's fortify() function may be deprecated at some point so the broom package is now suggested

library(broom)
broom::tidy(atf_sp)

answered Dec 06 '19 at 18:28

PeterI

39
5

Birdflax · Answer 6 · 2022-11-15T18:06:13.343

The only valid answer on this posting was provided by the author "repres_package" above. See that author's recommended solutions if you want to get the right answer. If you want to obtain the geometry of a polygon dataset, you are seeking the long and lat for every single vertex in the polygon feature class. The author's suggestion of using raster::geom() or ggplot2::fortify(), for example, will give you the total number of vertices that are contained in the spatialpolygonsdataframe. That's what you want. The other author's fail to do so.

For example, in my spatialpolygonsdataframe of North Carolina counties (from US Census), I have a total of 1259547 vertices. By using raster::geom(NC_counties), I am given a dataframe that contains a long and lat for each of those 1259547 vertices. I could also use gglot2::fortify(NC_counties) to obtain coordinates for those 1259547 vertices. All of the valid options are given in the answer by "repres_package".

When I ran the recommended codes in the other answers on this posting, I obtained long and lat coordinates for only 672 vertices, 1041 vertices, or 1721 vertices, which is off by over one million vertices. I'm supposed to get long and lat coordiates for 1259547 vertices. I suspect that those codes are interpolating centroids for the polygons, which is not the geometry of the polygons.

This does not provide an answer to the question. Once you have sufficient [reputation](https://stackoverflow.com/help/whats-reputation) you will be able to [comment on any post](https://stackoverflow.com/help/privileges/comment); instead, [provide answers that don't require clarification from the asker](https://meta.stackexchange.com/questions/214173/why-do-i-need-50-reputation-to-comment-what-can-i-do-instead). - [From Review](/review/late-answers/33190494) — IRTFM, Nov 21 '22 at 23:15

R_Extracting coordinates from SpatialPolygonsDataFrame

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