You can perform an inner join
df <- data.frame(
lon = c(-105.3125, -105.4375, -105.3125, -105.4375),
lat = c(39.9375, 39.9375, 40.0625, 40.0625),
value = c(21L, 10L, 16L, 11L))
df_include <- data.frame(
lon = c(-105.3125, -105.4375),
lat = c(39.9375, 40.0625))
library(dplyr)
df %>%
inner_join(df_include)
#> Joining, by = c("lon", "lat")
#> lon lat value
#> 1 -105.3125 39.9375 21
#> 2 -105.4375 40.0625 11
Created on 2019-04-28 by the reprex package (v0.2.1.9000)