1. “by” + place : The meaning is " beside " , at the side of, next to, close to
examples: The house is by a river.

2. “by” + method of transport : This structure describes how you travel somewhere.
examples: David went to Manchester by train.

3. “by” + method of communication : This structure describes how you communicate with someone.
examples: I spoke to her by telephone.

4. “by” + method of payment : This structure describes how you pay for something.
examples: We paid for the computer by cheque.