Answer for Simple Features:

sf package draws on Geometry Engine Open Source, and as such can access the list of commands such as st_within etc.

One such command, st_difference, will do the job:

    require(sf)
    
    # make a square simple feature
    s <- rbind(c(1,1), c(1,5), c(5,5), c(5,1), c(1,1))
    s.sf <-st_sfc(st_polygon(list(s)))
    s.pol = st_sf(ID = "sq", s.sf)
    
    # make a smaller triangle simple feature
    s2 <- rbind(c(2,2), c(3,4), c(4,2), c(2,2))
    s2.sf <-st_sfc(st_polygon(list(s2)))
    s2.pol = st_sf(ID = "tr", s2.sf)
    
    # find the 'difference', i.e. reverse of st_intersection
    t <- st_difference(s.pol,s2.pol)
    
    plot(t)

also see towards the bottom of [this article][1]

can also be done by coercing Sp to sf with st_as_sf. Heed the warnings as attributes can be tricky to manage!


  [1]: https://cran.r-project.org/web/packages/sf/vignettes/sf3.html