You could try and use the gDistance
function in the rgeos
package for this. As an example look at the below example, which I reworked from this old thread. Hope it helps.
require( rgeos )
require( sp )
# Make some polygons
grd <- GridTopology(c(1,1), c(1,1), c(10,10))
polys <- as.SpatialPolygons.GridTopology(grd)
# Make some points and label with letter ID
set.seed( 1091 )
pts = matrix( runif( 20 , 1 , 10 ) , ncol = 2 )
sp_pts <- SpatialPoints( pts )
row.names(pts) <- letters[1:10]
# Plot
plot( polys )
text( pts , labels = row.names( pts ) , col = 2 , cex = 2 )
text( coordinates(polys) , labels = row.names( polys ) , col = "#313131" , cex = 0.75 )
# Find which polygon each point is nearest
cbind( row.names( pts ) , apply( gDistance( sp_pts , polys , byid = TRUE ) , 2 , which.min ) )
# [,1] [,2]
#1 "a" "86"
#2 "b" "54"
#3 "c" "12"
#4 "d" "13"
#5 "e" "78"
#6 "f" "25"
#7 "g" "36"
#8 "h" "62"
#9 "i" "40"
#10 "j" "55"