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Should I cite a paper that I deem of bad quality just because it is among the only two papers that use the same methodology I'm using in my research?

I'm writing a paper that uses a relatively new computational tool. There are ONLY two studies that use the same tool in similar research contexts. One did it superbly (Paper A). The other didn’t (Paper B). I have to make the reader aware I am not the first using this software in my field, but the scope of my paper is clearly defined and does not include delivering opinions on the other two papers (both papers are in my same field, but their research questions are so different to mine that, on behalf of directness, there is no point in discussing their results and wasting precious space in an already dense paper). In other words, a plain sentence of the sort “Software X has been use in rocket science before (Cite A; Cite B)” must do. But I feel a little uncomfortable for not differentiating between the disparate quality of the papers, perhaps sounding like I am endorsing Paper B at the same degree I am endorsing Paper A, and implying that readers should view both as having equally meaningful information. As a clarification, I do not see any wrongdoing by the authors of Paper B; it is just a flawed paper that made it into a top journal.

Is it ethical to skip citing a paper that I consider of bad quality? To what extent does citing means endorsement if no further evaluation of the cited paper is included?

Consider that the problem is more nuanced that it might seem. If the software was of customary use, no citation would be needed, but these two papers and mine are the only studies using the software, and I want to make the reader aware I am not a crank for trying this approach.

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    If the only reason for citing papers A and B is to say that you're not the first to use software X, then I think you could safely cite only A provided you don't give the impression that it's the only prior use of X. You might write "Software X has been used in rocket science before, for example (Cite A)." By saying "for example" you make it clear that it's only an example of prior use, not a complete catalog of prior use. – Andreas Blass Mar 18 '17 at 22:20
  • From your title, I thought you were asking if anyone has an objection to you omitting mention of the mediocre paper. But in your question, it sounds like you're on the fence. Are you, in fact, leaning one way or the other at this point? Is space at such a premium that the proposal by @JeffE would not be workable? – aparente001 Mar 19 '17 at 22:40
  • @aparente001 The space is really a premium and I don't want to open a discussion that, due space constrains, it's going to be unsatisfactory at the end. Nonetheless, I want the readers to know, even unconsicusly, that I am reviewing the correct literature. For the very same reason, JeffE opinion, that I should cite and then remain silent, isn't satisfactory to me. – j91 Mar 20 '17 at 0:11
  • Let's just make sure we're on the same page here about Jeff's answer. You could cite both papers extremely briefly, fairly early in the paper, in 25 words or less. In a separate place in the paper, you can speak more specifically about the good paper. By not speaking more specifically against the more mediocre paper, a careful reader will understand that the one you were quiet about did not have anything in it that was worthy of specific comment. – aparente001 Mar 20 '17 at 4:45
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To which extent citing means endorsement if no furher evaluation of the cited paper is included?

None at all.

By citing the paper as using the software, you are acknowledging that the paper exists, and that it used the software, and that is the only thing you are doing. Citation is not a sign of approval or agreement or endorsement; it is merely acknowledgement of existence and relevance. Citations are not statements about the quality of any result, either positive or negative. If you want to state an opinion about the quality of a result, either positive or negative, you must actually state your opinion in the text, using English words.

I suggest initially citing both papers, and then giving more details about how paper A used the software to derive interesting results, and then remaining conspicuously silent about paper B.

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    I disagree with the 'conspicuously silent' part. It will look obvious and as a reviewer, I will wonder why didn't the authors mention paper B? Is it because it is similar? Are they trying to hide something? I would talk about A and B simultaneously if the only point is to highlight past works that use method X. Let the reader judge what is good or bad. – Prof. Santa Claus Mar 19 '17 at 22:18
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You are not obliged to cite work that is accepted as badly sub standard. In fact the job of an academic, as with all research, is to filter, to choose the best parts of what is out there. Research is inherently a filtering process, and therefore you want to show your reader that you are good at filtering, that you have vetted the material you choose to cite, otherwise you lose respect of the reader. Ironically if you do not filter properly, you yourself will be filtered by other academics who see that you waste the reader's time.

That may be a bit harsh for one citation, I'm just expressing the general rule, and the more exceptions we make the more likely our own work's quality will be questioned.

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    I disagree with this comment. Give credit where credit is due. Papers are supposed to talk about ideas/concepts/solutions, not evaluate the quality of papers. It is very easy to 'filter' info to make yourself look great; e.g., Trump. – Prof. Santa Claus Mar 19 '17 at 23:01
  • There seems to be a misunderstanding. Of course credit has to be given where it is due, and that is always given even in cases where we credit bad work. My understanding of the question is that it is asking about citing entire articles in a kind of literature review (in this case a short one since there were only two articles). When doing a review the author must only present the best works, there is no reason to include unhelpful work in any part of one's research because part of expertise is knowing what is valuable and what is not. – Ootagu Mar 20 '17 at 2:08
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    @Ootagu, "when doing a review the author must only present the best works" is not correct, to my perception, especially when there is very little prior art. After all, if the second paper is not merely "worst" (or "worse", for just two), but is also second-best, how is it possible to not mention it? And, after all, mention/citation is not the same as endorsement, it is merely recounting facts, not judging them. – paul garrett Jul 26 '18 at 22:53

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