You can use std.error() function of plotrix library or se() function of sciplot library to calculate the standard error of the mean in R.
Here is an example:
> a<-runif(20)
> a
[1] 0.77540313 0.22338489 0.93450655 0.42343861 0.84989759 0.06896429 0.28866681 0.79730126 0.71743547 0.22640911 0.69567960 0.68597593 0.04677569 0.90157480 0.57804623 0.21837233 0.33654928
[18] 0.11710434 0.64092480 0.28355924
> library(plotrix)
> std.error(a)
[1] 0.0663643
> library(sciplot)
> se(a)
[1] 0.0663643
If you do not want to use any of these libraries. You can calculate the SEM using the following formula:
SEM = standard deviation/sqrt(length(vector))
Here is an example:
> sd(a)/sqrt(length(a))
[1] 0.0663643