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Recently I had a paper accepted by a major journal in discrete mathematics. Now the paper is going through the final stages of publication. The publisher sent me a link in which I have to specify the access policy for the paper. I can choose to either pay a fee (which I won't), and make my paper publicly available from the publisher website, or I can choose to self-archive, and then make my paper publicly available after a period of 24 months of embargo. More precisely, the text for the self-archiving is the following:

I wish to self-archive my accepted author manucript , which is my draft version of the article and which may include any author-incorporated changes from the peer review process. I can post this author manuscript on my institutional or subject-orientated repository immediately for internal use and make it publicly available after a journal specific embargo period has expired.

The problem is that I have already posted the revised version of my paper at arxiv much before receiving this access form from the publisher. So I have some questions concerning this paragraph.

  1. The paragraph says that I can post the manuscript at a subject-oriented repository immediately for internal use. As mentioned before I already posted it to arxiv, which I think can be considered as a subject-oriented repository. Is that allowed? What do they mean by internal use?
  2. What do they mean about making the manuscript publicly available after the embargo? I have a link at my homepage pointing to the arxiv page. Is this considered to be publicly available?
  3. What is the difference between posting it to a repository and making it public?
  4. Can I get in trouble if they find the link to the paper at my homepage?
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    Did you tell the journal that your manuscript was already available on arxiv upon submission? I hope you did... – Cape Code Oct 19 '15 at 9:57
  • You should also check the policies of the body that funded this work. Some will pay for open access (in fact some require that you take the paid open access option, and make funds available through your institution). – Chris H Oct 19 '15 at 15:42
  • @CapeCode: Public distribution of preprints---either on the arxiv or personal websites---is common bordering on universal in mathematics. There's no need to report it to a journal, because the journal should assume that's the case. – Henry Oct 19 '15 at 16:06
  • @Henry So I've heard, but I'd thought a journal that has en embargo policiy would surely care about whether it's already online before submission. – Cape Code Oct 19 '15 at 16:11
  • @CapeCode: They might care, but they don't need to be told, because the answer is "yes, of course it is". – Henry Oct 19 '15 at 16:14
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The text you quote is from Elsevier, and their policy on hosting articles says that "arXiv and RePEc can update a preprint immediately with the accepted manuscript and a DOI link to the formal publication" (while the embargo period applies only to other organizations), so you haven't violated the agreement in updating the arXiv posting. You can add the DOI via the arXiv's journal reference feature once it is available.

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I can post this author manuscript on my institutional or subject-orientated repository immediately for internal use […]

[…]

The paragraph says that I can post the manuscript at a subject-oriented repository immediately for internal use. As mentioned before I already posted it to arxiv, which I think can be considered as a subject-oriented repository. Is that allowed? What do they mean by internal use?

This respective sentence is not very well phrased and probably misphrased. “Subject-orientated repository” sounds very much like ArXiv but contradicts “internal use” (unless they have a very wide definition of internal). Having a “subject-orientated repository“ for “internal use” would have to be institutional and thus already be covered without adding “subject-orientated repository“.

To be sure you should check other information by the publisher, in particular the copyright agreement (or similar) you probably agreed to already. Sherpa/Romeo may also help. If all that fails, you need to (and should) ask the publisher to clarify this.

If needed to guess, I would say that that line originally read “I can post this author manuscript on my institutional immediately for internal use” and then somebody inserted “or subject-orientated repository”.

What do they mean about making the manuscript publicly available after the embargo? I have a link at my homepage pointing to the arxiv page. Is this considered to be publicly available?

The ArXiv is already publically available, linking it does not change this. Making publically available means exactly that, so, e.g., it would cover putting the manuscript directly on your homepage.

What is the difference between posting it to a repository and making it public?

A repository may be not public. For example, our group has its own private paper repository.

Can I get in trouble if they find the link to the paper at my homepage?

If they find out about your ArXiv publication only that way, perhaps. But given that the ArXiv is public and easily searchable, that’s very unlikely.

What you can get in trouble for is publishing the paper on ArXiv. However, if the journal is general open to ArXiv publishing (see the first point), it is unlikely that they only allow it after they published the paper themselves. Again, what you should do is to take a look into the copyright agreement and similar and what they say about prior publication on public repositories and ask them if the information is unclear.

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