There are within the plan of God those areas that God effects by His own immediate agency, without the aid or input of his creation, such as creation and regeneration. Although God has planned all, there are other areas of the plan of God that God brings about by secondary causes, that is by the actions of his creation rather than directly by himself, though He has rendered them certain.

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WCF 5.2 Although, in relation to the foreknowledge and decree of God, the first Cause, all things come to pass immutably, and infallibly; yet, by the same providence, He orders them to fall out, according to the nature of second causes, either necessarily, freely, or contingently. <hr>

WCF 5.3 God, in His ordinary providence, makes use of means, yet is free to work without, above, and against them, at His pleasure.

While not without its limitations this example may help:

God is the primary cause of the secondary causes that we observe in the world. For example, consider a man cutting wood with an axe. What is cutting the wood? One can say that the axe (secondary cause) is cutting the wood. Or one can say that the man (primary cause) is cutting the wood by using the axe. The difference between this example and the world is that God has created a very sophisticated axe: the secondary causes (physical laws) can act on their own, unlike the axe wielded by the wood-cutter.

Reformed and Always Reforming,