It seems to be generally considered poor programming practise to use variable names that have functions in base R with the same name.
For example, it is tempting to
R is very robust to this, but you can think of ways to break it. For example, consider this funcion:
foo <- function(x,fun) fun(x)
Which simply applies fun to x. Not the prettiest way to do this but you might encounter this from someones script or so. This works for mean():
> foo(1:10,mean)
[1] 5.5
But if I assign a new value to mean it breaks:
mean <- 1
foo(1:10,mean)
Error in foo(1:10, mean) : could not find function "fun"
This will happen very rarely, but it might happen. It is also very confusing for people if the same thing means two things:
mean(mean)
Since it is trivial to use any other name you want, why not use a different name then base R functions? Also, for some R variables this becomes even more important. Think of reassigning the '+' function! Another good example is reassignment of T and F which can break so much scripts.