By has many meanings, among them "beside" or "at
the side of," "handy" or "in an easy-to-reach place,"
"not later than," and (with a "self" pronoun) "alone"
or "without help." By is also used to show manner
of transportation and the method of doing something.

There are still other meanings / uses for by, however.

For example, by is also used with measurements:

He's renting a car by the week until his own car
is repaired. (He's renting a car one week at a time.)

We'd like to hire temporary help by the month.
(We'd like to hire temporary help one week at
a time.)

Eggs are usually sold by the dozen.
(Eggs are usually sold a dozen [12] at a time.)

Flour and sugar are usually sold by the pound.
(Flour and sugar are usually sold a pound at a time.)

The costs of mailing a package vary by weight.
(The costs are different for different weights.)

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In addition, by can be used to show agents (doers of
actions)--and are very common in passive sentences
when the object and the action are emphasized more
than the subject.

Examples:

Was that sonata written by Beethoven?

The agreement will be signed by the presidents of
three different countries.

The highest mark was scored by Leonardo.

The operation is going to be performed by a team
of surgeons.

"Dave's ESL Cafe" is visited by thousands of
people every day.

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By can also be used to show extent or amount:

That car almost hit us! It missed us by only
a few inches!

Mehdi is heavier than his twin brother by at least
twenty pounds.

Johnson won the election by more than 20,000 votes.

The game was close. The Comets won by just
two points.