How to keep track of line numbers in response to reviewers?

This is always a pain, but I find it's not actually hard to deal with, just somewhat tedious. My method for doing so is rather low-tech: I keep a copy of the old document to be able to track the old line numbers, then leave all of the line numbers in the response as XXX until I am done with the revision. Then, for each entry, you just cross-index in both places and write both line numbers, e.g.,

'co-occur' was replaced with 'correlate' in line 245 [prev. 243]

For minor wording/grammar edits, however, I usually don't actually respond in such detail, but simplify both my life and the reviewers by just saying something like: "thank you, fixed"

Just refer to the line numbers mentioned in the comments. There is no need to go through the pain of also checking where the changes occur in the new document. If you work in Word you can keep the track changes and provide both a file with all the changes visible and one which is a clean version of the new version. If you work in LaTeX you could possibly put all changes in, for example, bold (since bold is usually not used anywhere else in a manuscript, still retaining a version without any highlighted changes. There are a few attempts for revision tools in LaTeX as well but as far as I have seen require intervention with a script or external software.

In any case, I do not know of any journals, including "my own", that would require such extensive reporting so as to keep track of both old and new line numbers for minute changes. This does not mean they do not exists but is is usually way over what will be required.

When it comes to small changes such as rephrasing of the type you mention, it would be more than sufficient to provide a letter itemizing all changes and just say "changed 'to occur' on l. 243 to 'correlate'". In fact your can also consider lumping all your made minor changes into one statement to the fact that you have made the changes and then follow up on the ones where you have decided not to do so or have done something differently.

My preference where the journal allows is to avoid making references to page and line numbers. It's a time consuming process and can generally be avoided.

• If the change is really simple (e.g., fixing a typo; changing one word), I'll just acknowledge that the change has been made.
• If a sentence or paragraph has been substantially reworded, I'll first paste a copy of the original paragraph and then a copy of the updated paragraph into my response document, possibly highlighting new text in bold.
• If text has been added to a paragraph, I'll paste the updated paragraph into the response document with added text in bold.

The general logic of the approach is to make the reviewer's task as simple as possible. The reviewer generally wont want to have to perform complex cross-referencing of responses with page and line numbers in the manuscript. Instead, I think it's easier for the reviewer to make such responses self-contained in the response document. If the reviewer really wants to check that the changes have actually been made, there's enough text in the response document to enable a quick search on the manuscript PDF to find the location.