Removing columns in a SpatialPolygonsDataFrame in R?

Use the syntax object_ name[,-(1:5)] to remove columns 1 to 5 or object_name[,-c(1,5)] to drop columns 1 and 5. See the example below (with comments):

require(maptools)

#load shapefile from maptools package to make a reproducible example.
xx <- readShapeSpatial(system.file("shapes/sids.shp", package="maptools")[1],
                   IDvar="FIPSNO", proj4string=CRS("+proj=longlat +ellps=clrk66"))

class(xx) #check the object class
#[1] "SpatialPolygonsDataFrame"
#attr(,"package")
#[1] "sp"

head(xx@data,3) #print first three rows from the slot 'data'

       AREA PERIMETER CNTY_ CNTY_ID      NAME  FIPS FIPSNO CRESS_ID BIR74 SID74
      0.111     1.392  1904    1904  Alamance 37001  37001        1  4672    13
      0.066     1.070  1950    1950 Alexander 37003  37003        2  1333     0
      0.061     1.231  1827    1827 Alleghany 37005  37005        3   487     0

      NWBIR74 BIR79 SID79 NWBIR79
         1243  5767    11    1397
          128  1683     2     150
           10   542     3      12

xxx <- xx[,-(1:5)] #remove columns 1 to 5

head(xxx@data,3) #print the subsetted data frame

     FIPS FIPSNO CRESS_ID BIR74 SID74 NWBIR74 BIR79 SID79 NWBIR79
     37001  37001        1  4672    13    1243  5767    11    1397
     37003  37003        2  1333     0     128  1683     2     150
     37005  37005        3   487     0      10   542     3      12

To use the names of columns, you can implement Joris Meys' solution here, which consists in creating a list of names and using it to drop the columns.

For example:

drops <- c("AREA","PERIMETER") # list of col names
xxx <- xx[,!(names(xx) %in% drops)] #remove columns "AREA" and "PERIMETER"

Here is one alternative using the select function from package dplyr:

library(dplyr)

SPDF@data <- SPDF@data %>% 
select(1, 3) #keeps column 1 and column 3 in the spdf object.