Selection and extraction of points (shapefile) within a polygon in R

Question

I have two shape-files; one is a point file (some information for world) and the other is a 21-countries shape-file.

I need to extract the points which falls with in a country. I have to repeat this step in 21 times in QGIS or ArcGIS.

Is there any way to do this in R and if is in batch processing, that would be really great as I have to repeat this for other 4 data sets as well. Thanks in advance

Answer 1

So as an example how to use over() consider the following simulated data.

library(raster)
library(sp)

#generate point distribution | with (x,y) coordinates
set.seed(42);pts <- SpatialPoints(data.frame(x = runif(30, 1, 5), y = runif(30, 1, 5)))

#create polygons
df<-data.frame(X = c(rep(1,5),rep(2,5),rep(3,5),rep(4,5),rep(5,5)),
               Y = c(rep(seq(1,5,1),5)))
df$cell<-1:nrow(df) #polygon identifier (for later)

#make into spatial object (probably better way to do this)
coordinates(df) <- ~X+Y 
rast <- raster(extent(df), ncol = 5, nrow = 5)
grid<-rasterize(df, rast, df$cell, FUN = max)
grid<-rasterToPolygons(grid) #create polygons

#plot to check
plot(grid); points(pts)

#and extract
pointsinpolygon = over(SpatialPolygons(grid@polygons), SpatialPoints(pts))

The last bit you can also do as

df$pointsinpolygon <- over(SpatialPolygons(grid@polygons), SpatialPoints(pts))

to write the results directly to the dataframe.

Answer 2

Here is an example polygons shapefile and how you can read it into R.

library(raster)
# example polygons filename
f <- system.file("external/lux.shp", package="raster")
pol <- shapefile(f)

I do not have a matching points file, so I generate some points for this example

pts <- spsample(pol, 5, type="regular")
crs(pts) <- crs(pol)

To see what area the points fall in you can use over or extract . They both return the values in the order of the points, but extract also adds the (sequential) "point id" --- this is primarily for when you have overlapping polygons, such that a point might fall in two polygons.

over(pts, pol)
#  ID_1       NAME_1 ID_2           NAME_2 AREA
#1    3   Luxembourg    9 Esch-sur-Alzette  251
#2    2 Grevenmacher    7           Remich  129
#3    3   Luxembourg   11           Mersch  233
#4    2 Grevenmacher    6       Echternach  188
#5    1     Diekirch    1         Clervaux  312

extract(pol, pts)
#  point.ID poly.ID ID_1       NAME_1 ID_2           NAME_2 AREA
#1        1      10    3   Luxembourg    9 Esch-sur-Alzette  251
#2        2       7    2 Grevenmacher    7           Remich  129
#3        3      12    3   Luxembourg   11           Mersch  233
#4        4       6    2 Grevenmacher    6       Echternach  188
#5        5       1    1     Diekirch    1         Clervaux  312

If you just want the intersection, say of the points that fall in "Grenmacher", like you may want to do with your countries, you can

g <- pol[pol$NAME_1 == "Grevenmacher", ]
i <- intersect(pts, g)
i
#class       : SpatialPointsDataFrame 
#features    : 2 
#extent      : 6.27111, 6.27111, 49.53585, 49.7887  (xmin, xmax, ymin, ymax)
#crs         : +proj=longlat +datum=WGS84 +no_defs 
#variables   : 5
#names       : ID_1,       NAME_1, ID_2,     NAME_2, AREA 
#min values  :    2, Grevenmacher,    6, Echternach,  129 
#max values  :    2, Grevenmacher,    7,     Remich,  188 

And perhaps write that back to disk like this

shapefile(i, "test.shp")