Try
library(sp)
S@coords[,'roadtype'][S@coords[,'jointcount']!=1] <- NA
S
# SpatialPoints:
# jointcount roadtype
#[1,] 1 3
#[2,] 4 NA
#[3,] 3 NA
#[4,] 1 1
#[5,] 1 4
data
jointcount = c(1,4,3,1,1)
roadtype = c(3,2,5,1,4)
S <- SpatialPoints(data.frame(jointcount,roadtype))
solved Replace Values in a column wiht NA if values from another column are not 1 [closed]