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I am writing a publication-based PhD thesis, and the thesis will not be publicly accessible once has been finished due to classified data included. The thesis is not the traditional sandwiched thesis, it is supposed to be a commentary on my own publications.

I will use three papers in my thesis, two have been published in journals and another one is still under review. I have obtained permission to reuse the content of the two published papers for my thesis. I have two questions:

  1. Dose reuse mean that I can use exactly the same words? like I can copy and paste the content of the two published papers? or do I need to rephrase the content?

  2. The third paper has not been published yet. If I use the data in my thesis, can I still publish it in a journal? if so, can I copy and paste the same content?

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When compiling a dissertation, copying parts or entire sections from published papers is perfectly fine and standard behaviour.

If a section is (mostly) identical with a published paper, it should say so clearly at the start. If the paper is submitted, but not yet published, you could either just treat it as published, and cite the submitted version; or you could use the text in the dissertation without further comment, and then add a note to the article that it is based on Section X of the dissertation.

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Since you have the publisher's permission to use the words of the original you can quote freely. But make sure that it is a quote and that you actually cite the original.

Simply reusing the words without quoting will confuse any future reader. You avoid self-plagiarism by quoting the work as you would any other. You avoid copyright infringement by getting permission as you have done. You can quote longer passages from the papers than would normally be the case due to not having copyright issues. Alternatively you can rephrase and cite if you like, but don't avoid the citation. That is what lets a reader connect, properly, to the original work as is necessary for future research.

As to the third paper might be a bit different. If your thesis is not published and that paper is based on what is in the thesis, rather than the other way round, then the third "paper" that forms a part of the theses is really just a draft of any future paper and so you would normally be free to use it as you like. But your advisor could give you the best interpretation of that. The only issue I see is that while you don't intend to publish the thesis, things might change in the future. If that is a concern, then you could quote and cite just as in the other papers, avoiding self-plagiarism. You currently hold copyright yourself so you have no issues with that. But you are probably about to give up copyright since it is under review. So quote and cite seems the better path.

One worry I have is your use of the term classified data. If the work was done for a client, they may have some claims to the data and what is done with it that you will have to deal with.

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    Classified theses are a thing. You just don't stumble across them very often! But there are accredited institutions that serve the armed forces (e.g. Air Force Institute of Technology) where a masters or PhD thesis may be an analysis of classified stuff. – Jon Custer Oct 25 '19 at 17:55

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