What's the difference between the two sentences? i.e. what is in use, an apple or an orange, in the below two sentences?
1) Replace apple with orange.
2) Replace apple for orange.
1) Use orange to replace the apple

2) the thing to replace apple is orange
Can you tell me what is the difference between subtitute for and replace by?
Hmm, from my observation ' substitute ' is used on persons whereas ' replace ' is on things. Actually there are no rules governing this I believe, it is just that people tend to use it that way.

with = involve the person and his action

by = just only as a means to achieve one's objective or motive.

eg. I settle the bill with/by cash. ( with shows your action to pay )

for = for a purpose, you do something because of another

eg. I substitute him for the post, since he has no interest in it.
Can you clarify when to use "with" and when to use "for" after verb "replace"?
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1) You have an apple, you take it away and put an orange in its stead.
2) You're replacing the apple because orange wants you to.