"Everyone around us seems to agree by the way they fiddle with their phones, even without a signal underground."
I consulted the dictionary, but could not find a suitable explanation. Is there such a phrase as "agree by"? What does "by" mean here?
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I think this is quite a casual sentence structure so the grammar is relaxed a bit. The sentence may be more clear to you if we rephrase it:
"I can tell that everyone around us seems to agree by the way they fiddle with their phones"
The definiton of by used here is: "used to show how something is done"
The 'something that is being done' here is noticing that everyone agrees. The how it is done is "the way they fiddle with their phones". The 'by' is used to show this relation.
"Agree by" is not a set phrase. 'Agree' is just the verb that happens to appear in this sentence.
So the 'by' here is used to convey the following meaning: The way they fiddle with their phones is how I have inferred that everyone seems to agree
Another example of a similar structure with a different verb:
"Well, you can tell by the way I use my walk I'm a woman's man, no time to talk"