I had a very unpleasant R debugging experience this morning: when is what you see not what you actually have?
The screenshot at left reproduces what I was seeing: inds1 and inds2 both are shown as the vector 2, 4, but inds2 selects the 2nd and 3rd array elements, not the 2nd and 4th, as expected.
The code I used to create inds1 and inds2 makes the problem clear - the second number is just a bit larger than 4 in inds1, but just a bit smaller than 4 in inds2:
inds1 <- c(2, 4.00000001);
inds2 <- c(2, 3.99999999999);
So, what happened?
The inds1 and inds2 arrays are type numeric (double), but they are shown on the screen rounded, in this case, not showing any numbers past the decimal. They look like integers, but are not. When used to specify array indices R coerces the arrays to integers. as.integer() does not round, but rather truncates. Thus, inds2 becomes 3.
I will now be including tests in my code to be sure what I think are integers are actually integers, such as all.equal(inds, as.integer(inds)).