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Should I cite R or RStudio?
I ran my data analysis and created my graphs in RStudio, but RStudio is just a platform for R. In my paper should I cite R or RStudio?

I have never seen anyone cite Rstudio. It would be like citing Word

Just to be clear to readers who don't know R, the OP didn't "create their graphs in RStudio," there is no functionality to do that in RStudio besides using R and its packages. Yes, it displays them for you, but that's it.

RStudio is an IDE for R — essentially an editor and debugger packed together. Your work is made possible by statisticians who developed the language R and graphical packages for it. If you want to cite R in your publication, here is the explanation how to do it.

You can also type citation() in the console to get the current citation information:
It works for packages too -- citation("packagename")

Google Scholar is probably not doing a great job of tracking these software citations compared to journal articles that fit standard citation formatting better, but RStudio has ~1,800 citations whereas R has over 100,000 using the most common citation aggregate for each.
Many people cite neither and instead cite particular packages that they use, but by far it is more common to cite R which includes all of the base libraries, etc. RStudio is only an IDE, and although it could be useful and you are free to cite it as having been helpful in your development, anyone can take your R code written with the help of RStudio and run it with only R and get the same result.

To follow on, if my PI and I collaborate on an R script, and I use RStudio and she uses emacs, should we cite both? It would seem wrong to cite emacs, so by extension, I see little reason to cite Rstudio.

@AzorAhai I agree that it is not typical to cite text editors, IDEs are a bit more involved but you don't typically cite those either. When someone cites something like Matlab or SAS or Stata, they aren't just citing the IDE and GUI but the underlying algorithms that have been tested, validated etc; the equivalent for that would be R, not RStudio.

Cite what you use. RStudio has a collection of developers who have made your work possible. Cite them. R is a language so it is, perhaps, less important to cite it. But if it has features that are important to your work, cite it. If you had used Python to do data analysis it might not be necessary to name it if there was nothing special about Python, but R is specialized for statistics so more likely that it should be cited.
Cite what you use. It is a courtesy to those who enable your work if nothing else. Citing RStudio

What is the downside to citing RStudio? Why the downvotes for this excellent answer (as usual from @Buffy)?

@JeremyC Probably coming from the suggestion that citing R is less important and perhaps the misunderstanding that R is "just" a language whereas RStudio is what "made your work possible."

@BryanKrause You may well be right, but one would hope that a downvote would be more carefully considered than that (and, of course, explained in a Comment.

@JeremyC More carefully considered than that? I do agree that a comment would be useful to explain but I think disagreement with an entire answer is a suitable reason to downvote if someone thinks that following the answer would mislead the OP or others with a similar question.

I did not downvote this, but I 100% defend the right to downvote if one thinks that the content of an answer is wrong / unwise, without need for further comments.

FWIW, I have no issue with downvotes. But comments are more useful as they can indicate where the writer may be wrong. I seldom downvote unless a post is literally dangerous to the OP, preferring comments if I disagree. OTOH, "cite what you use" seems to be a pretty good rule IMO.

@Buffy To make more clear, I think the thing that's wrong/dangerous in your answer possibly is that it makes it sound like RStudio is the thing that brings all the code and R is just the language, which is not the case. People that are "using" RStudio are mostly only using it as a text editor/for debugging tools. It is almost certainly more important to cite R than to cite RStudio. OP understands all this, but someone else might not.

@BryanKrause, the OP has said that he used it to create graphs for a publication. As such it was a tool that enabled his work. I based my answer primarily on that. Wrong? Dangerous?  Honor those who make your work possible.

@Buffy That's R, and possibly other 3rd party libraries, not RStudio.

@Buffy Have you used R? Your answer makes it sound like you have not.

@Buffy In my personal opinion, this and many your other answers sound like someone forced you to answer a question on a topic you know very little about. SE is not an exam. If you are not sure of a right/helpful answer to a question, it is quite appropriate to refrain from answering it.

I agree with Dmitry, I've found myself downvoting you more often than upvoting recently as your answers have sounded very speculative, or how you would expect things to be, rather than with personal experience.


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How to gracefully exit my postdoc position with 1 year left in contract
This is my 2nd year in the lab with 1 year remaining in the contract. The PI is a nice guy and well-funded, but he has completely shifted his focus to his business and clinic trials. For example, I just waited a month for him to start revising my manuscript. I'm unable to get any instructions or ideas from him.  Now I've finished the only paper and have no promising project in hand, I want to quit and find a new postdoc. But I don't know how to ask my PI for a reference letter. What should I do to avoid burning the bridge? I think he even expects me to extend the contract for another 2 years. I don't have any job offer yet, but I feel like I should tell my PI before sending out resumes.

Tell him you want scientific variety, geographic variety, etc.  I wouldn't get into the "he doesn't have time for you".  Just indicate you are interested in new things.  Tell him this is a natural break point since you wrapped one thing up, so it's not even like there is a huge dislocation.  Tell him you plan to continue working on current contract but looking for other things, very actively, at same time.
[Keep soaking up the current salary. Do some things to keep him/you happy, but it doesn't sound like there is huge supervision, expectations, anyways.  Assuming there is no new major project, figure out how to dust off some minor aspects and get some "cheaper" papers done that pad out your resume, build off of last project.  Helps you out and the advisor at least sees some pub count even though you aren't solving more Millennium Prize problems. If he gives you a new big project, I would be OK doing that, but keep looking for next spot and be willing to ditch it if you need to hop to another assignment.  Be able to write up incomplete work...there is an art to this and it is not as sleazy as it sounds.  In fact a lot of work is wasted because people don't write up incomplete work and it sits for years instead or gets redone.]
Ask for his assistance.  He'll either give it or won't give it.  I suspect he will at least give his blessing.  In any case, once you have told him, you just execute your plan and start looking for things.  2:1 anything you come up with ends up needing some time to develop and there is a natural dovetail with current contract end and new contract start.
Personally, I think a postdoc (or senior grad student) should be relatively independent and capable of starting, executing projects on own.  And of writing papers that just need a rubber stamp from the advisor who attaches his name to pad his CV.  (Definitely work on your paper writing...publications are how people keep score in academia and a PI is expected to be able to write a paper without someone above them.)

Thank you very much, your suggestion helps a lot. I will say something like I wanna try new research topics. I've been working independently here most of the time, but I feel I can be a lot more productive if there's good supervision.

source: Stack Exchange

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/

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Reusing part of my thesis within the same thesis
Doing an engineering thesis, and I have presented a detailed summary of my data in the abstract.  Is it ok for me to copy/paste entire paragraphs of my abstract to my conclusion without changing a word?

Yes, but do be advised that the abstract and conclusion serve different purposes, and you are missing an opportunity to expand upon ideas and build upon the main body in the conclusion.

Yes, of course. There are no issues with this at all. Self plagiarism only occurs when you don't cite your own words from other publications. Within a single document there is no problem. The reason that we self-cite is to let readers easily find the original source. But that doesn't apply here.
OTOH, make sure that it doesn't read "awkwardly" when you do this. It is just a style consideration, though.
I'm assuming that your abstract is actually part of the thesis, say a preamble.
However, if the abstract is to be published separately from the thesis, you should cite the thesis in the abstract. But you would do that in any case.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


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getting a job with a PhD in (pure) mathematics
Probably this concern has been addressed several times here but I will give a try to get other people's perspective from my situation. I am feeling sort of hopeless these times.
I am in my last year of my PhD in mathematics and doing my dissertation soon, my research was mainly devoted to algebraic topology and I made some progress in my advisor's particular area. However, I faced some problems during my studies (personal issues) and I never built a strong relationship with my advisor; so I could not finish all the initial research proposal intended for my PhD thesis.
I recently had a sincere talk with my advisor about my future, and he said that my progress is worth for a PhD thesis but it is not anything very surprising that is worth publishing, so I will be graduating with zero publications. He said that my chances of getting a PostDoc positions are really low and that I can not expect a strong recommendation letter from him. My advisor has a few collaborators (from overseas mainly) and none in the local department. He also never supervised another Master or PhD student while I was under his supervision, then I never got a chance to network or engage properly with other classmates. My advisor kindly suggested to explore other options in the job-market besides academia.
I like to explore new things, and in my free time during my studies I attended several teaching workshops, seminars and courses (I got a small degree in "university teaching"), and I am also familiar with Python, R, Matlab and Sage; however, I learn those things for fun and I have never really worked in
a big project using any of that.
I do not know what to focus on and what kind of job should I look for after I finish my PhD
I would like to keep doing research in Math, but my area is not very popular lately and I feel that I have no chances of succeed getting a PostDoc; I also feel that I do not have (demonstrable) skills to perform a job with "real-life" applications so probably my chances getting there are also low. And I do not really know the Teaching job-market, I think that those positions are temporary and it would be hard to find a place that is willing to sponsor a work visa (I am not a US-citizen, and the job market in the third-world country that I am from is nonexistent for PhD's in this area)

Learn to program.

Probably much too late for the original poster, but maybe helpful to some others: have you heard of topological data analysis? Not saying being good at TDA would get you a job on its own, but could be a stepping stone to applied areas if you already know algebraic topology.

Your supervisor is honest, blunt, and very helpful because by ruling out the academic path he's saving you a lot of time.
The bad news is it sounds like you screwed up your PhD. Not getting strong research results, not having diversified your PhD experience (e.g. lack of teaching experience makes it harder for you to get a teaching job), and not having a firm idea of what you want to do after the PhD means you sound lost right now. The good news is, chances are you learned more than you think you did, and those things are applicable to the job market.
First: don't think you have to do research. It is what you've been doing for the PhD, but it's not what you have to do in the future. Just consider this: if you like research + are good at it, why didn't you do better in the PhD? Why weren't you able to complete the initial research proposals, why weren't you able to get publishable results, why weren't you able to impress your supervisor such that he can write a strong letter of recommendation? You might have good reasons for these, and it's up to you to convince yourself that yes, you still want to do research, and yes, you are talented + motivated enough to succeed in it.
If I were you, I'd start examining the possibility that I am not actually good at research and / or it is not what I want to do. Do some serious soul-searching here. You are making a life-altering decision. If it makes you feel bad that by leaving academia you are "failing", don't worry too much about it: there's a good chance that by leaving academia you'll have a more successful life (in terms of material possessions).
Second: go to your local jobs portal (use Google if you don't know what these are) and search for jobs that require a PhD in mathematics. Do you find anything that catches your fancy? For example searching on indeed.com for "phd math", I get this job among many others. Note the requirements:

Preferred qualifications:
  MBA, Master's or PhD degree in a quantitative field.
Experience with stakeholder management and ability to influence senior stakeholders.
  Demonstrated knowledge of statistics and data analysis including R programming or other statistical software packages.

I highlighted the most relevant parts. You say you are familiar with R. That means you are in business! You can potentially do this job! If you further have experience with statistics and data analysis (do you?) you're in an even better position.
It's up to you to search the jobs portal for jobs you can do, and then it's up to you to apply. It's true that visa issues might sink your candidacy, but it's also true that because PhDs are relatively rare, you might have skills nobody else will have and therefore the employer is willing to sponsor you. You will not know unless you try.
Do remember that even if you can't find a US employer, you can still work elsewhere. It's a big world out there, and it's not true that third-world countries don't need your skills. Example of such a job in India (admittedly they're not looking for PhD-level candidates, but you could still apply).
Third: once you have an idea about what the options in industry are like, then you can start thinking about what you want to do. Are you sure you still want to do math research? If so I'd talk to your supervisor again about what options are available to you. He's already told you your prospects are not good, so you'll need all the help you can get from him. For example, perhaps you could find a position as a teaching assistant somewhere and do research in your spare time. This will not be easy - doing research while holding a full-time job is very difficult - and it's not likely to be well-paid, but if it's what you want to do, you can try.
On the other hand if you think industry will serve you better, then finish up your thesis & defense and start applying for jobs. Be sure to visit your university's career center as well; they'll be able to help you a lot.

This question is  a year old, but it matched my own experience enough (including the specialization in algebraic topology) that I felt obliged to comment. Getting an academic math position is a crapshoot under the best of conditions. The field is glutted with other highly competent applicants (pretty much everyone going into pure math does so with the intention of doing pure math research); the field doesn't have the money of, say, computer science; and there really aren't any opportunites to do pure math research outside of academia and maybe a single-digit number of industry labs. With a great publication record and glowing recommendations from well-established professors, you have an outside shot at it. Without them, it's vanishingly likely to happen. It's unfair, especially if you wind up with a useless or abusive advisor, fall into a field that isn't the cool new thing, choose (or get saddled with) a research project in your limited time to prove yourself that doesn't work out, and so on. What's even worse is that (unlike some other fields) there's really no way to burnish your credentials; there's nothing you can do outside of academia that academic mathematicians would care about.
So, unfortunately, there's probably nothing you can do. It should be relatively easy for you to find some job in industry, though; the tricky part is finding one you like. Just being able to think rigorously and scientifically is a prized skill in industry, while it's taken as given in academia. (Conversely, some interpersonal and organizational skills work the opposite way. On the other hand, there are more opportunities to pick up the latter, whereas there's really no place to pick up pure math skills outside academia.) I don't see anything in your post to suggest that you aren't employable, so at least you should have some breathing room to take a look at what's out there and see if there's anything that might be, if not exciting, at least acceptable.

While a position at a top research institution may not be in your immediate future there are things you can do, up to and including proving that your advisor is wrong.
You don't actually need a faculty position to do research or publish in math but, in my experience, you do need a circle of collaborators. You indicate that you don't have that, but it would be good to start to develop it. Attendance at conferences is a good way in computer science, at least. Meet people, speak with them about ideas, and such.
There are also many teaching colleges around the world that value good math teaching over research. Almost all will require some, but many emphasize teaching the next generation over serious research. The MAA, for example, is full of people who, while doing research, focus much of their efforts on teaching.
And, of course, teaching at pre-college level is also open to you. You may find yourself overqualified for this, but it can make a satisfying life if you value teaching.
But, you can put it together if you have the willingness to do so. A lower level position, while developing mathematical ideas within a circle of collaborators can put you on a path to a better position, proving your advisor wrong in the long term if not immediately.
If your advisor is actually inexperienced at this he may be making a mistake in his analysis and also in his general advising. In particular, his assessment that you can't publish what you've done might just be wrong. You won't know unless you try.
Your life is what you make it.

Unfortunately, the visa issue is a serious one for US jobs.  Academic positions at colleges and universities are not subject to the H-1B quota, but pre-college teaching and industry jobs are, and, even if one can get a position, one has less than 50% chance of getting an H-1B and being able to accept the position.

The OP should be aware of the "Optional Practical Training" program that allows recent graduates in STEM fields to work in the US for a period of time (up to 3 years as I recall) after completing their degrees.  Teaching at a community college on OPT is sometimes a viable option for new PhD's who have acquired enough teaching experience to obtain such a position.

I know it's too late but for someone in the future, there are some folks in machine learning / AI (or more generally applied/engineering) community who are interested in the intersection with pure math, e.g., Topological data science employing the concept of Homology from Algebraic topology or homotopy methods in computational aspects of polynomials.
So, considering these directions and finding positions in industry might be interesting!
** In these directions, people likely do not appreciate the advancement in theoretical direction like the way you used to research on though...

Forks or folks?

@MoisheKohan thank you!


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Best tool for digitally marking assignments?
I was wondering if anyone could recommend a good piece of software for marking digital (PDF) assignments. Specifically, I am marking a first-year mathematics course, and need to do the following for each assignment:

Open student's PDF assignment
Make annotations (really, the only two tools I use are red pencil/pen and text comments). I am using a Wacom pen tablet for this.
Save a copy of the marked assignment in the original directory.
Repeat x many.

I am currently using Foxit and was using Xodo previously, but neither tool feels quite right for the job. I would favour something that:

Makes the above process quick and easy
Interacts nicely with the Wacom tablet (Adobe Reader doesn't, for example)
Is lightweight and easily usable (really only need pen and text tools, and possibly rotating pages every now and then. Everything else is clutter)
Has a good workflow so I can mark as efficiently as possible.

What problems are they solving? Could you have a “quiz” with calculations and have interim answers so you trap the detail?

What platform (operating system) are you using? If you're on a Mac, you can annotate PDFs in the Preview application that comes with the OS.

@shoover: I'm using Windows.


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PhD in computer science, jobs in mathematics?
Related to this question. I am a mathematician interested in doing a PhD in areas such as categorical logic, homotopy type theory, constructive math, etc. In the UK and Europe, most of the people studying this kind of stuff live in Theory groups in CS departments, rather than math departments. As a result, I would have to study in a CS department, and work towards a PhD in computer science, rather than mathematics.
What impact would this have on my intended future career plans as a research mathematician? e.g. would it be harder to secure jobs in mathematics departments with a PhD in computer science?

What evidence do you have for "most of the people..."? Seems a bit suspect.

The answer is in the question:  It is a rarer path to a job in a math department, so it is probably harder.

Why don't you want to do this research in a computer science department after your PhD?  I suspect the answer to this matters.

@Buffy: just my own research - I've found many in CS departments but barely any in math. In North America it seems to be the other way round.

@AlexanderWoo: I suppose I could, but I really consider myself a mathematician (logician) rather than a computer scientist, and would want to be appointed as such for teaching, supervising, etc...

How well have you looked in math departments? Have you considered looking for professors/groups in math that do "neighbouring" things but may be open to supervise a project of the kind you'd like to do?

@Lewian: I've looked pretty extensively for the schools I have looked at (of course there are many schools I haven't looked at). Good suggestion about math professors in "neighbouring" areas.

@AnonymousPhysicist: do you think it would be easier for a PhD in mathematics to get a job in a CS dept?

Yes, because there is more demand for computer scientists than for mathematicians.

First-rate people attract other first-rate people, but second-rate people tend to hire third-raters, and third-rate people hire fifth-raters.

This is a quote from Paul Halmos, who attributed the idea to Andre Weil.
Outside of the top universities, relatively few US research universities have significant Theory groups in CS departments at all, because people doing theory research don't tend to bring in million dollar grants.
Outside of a few clusters, mostly at top universities, relatively few US research universities have logicians in mathematics departments, because the perception amongst most mathematicians is that logicians work in a completely disconnected area of no interest to mainstream mathematicians.  (Logicians have not helped themselves in this regard.)
EDITED TO ADD: My impression is that categorical logic, homotopy type theory, and related areas have been somewhat exempted from the difficulties logic has as a subfield because a lot of the interest in it comes from people who were trained, and in many cases first earned tenure, as algebraic topologists or algebraic geometers.  However, this doesn't help someone coming into the area whose background is in logic rather than algebra.
Outside of top universities, it is hard to get hired into a permanent position at a mathematics department in the US without some North American teaching experience.  You can get this experience as a postdoc, but you'd have to first get a postdoc.
If it turns out that you really are first-rate, and first-rate in logic usually means being at least arguably the single best logician on the job market that year, then I think it doesn't matter much.  Part of being a first-rate department and hiring first-rate people is understanding that the title on your degree doesn't mean much.
If it turns out that you're not first-rate, then the job market for logicians in the US has been terrible for many years - it's easily been the worst among the major subfields of mathematics - and the economic crisis associated with the pandemic can only have made it worse.  In the general mathematics job market, doing a PhD in Europe and not having US teaching experience as part of your PhD puts you at a disadvantage, and not having mathematics teaching experience (as part of your PhD or afterwards) also puts you at a disadvantage.  (CS works somewhat differently because administrators love those million dollar grants.)

Thanks, this is all good to know. Seems I certainly haven't picked the easy path - oh well. Perchance, does anyone know what the average mathematician thinks of reverse mathematics? It is effectively logic applied to "normal mathematics", so they might see it as more useful / interesting / relevant to their work.

Exaggerating a bit, I have particular problems I am interested in, and I am interested in the work of other mathematicians only if this work gives insight that helps solve the problems I am interested in.  There isn't much history as far as I know of reverse mathematics helping to solve mainstream mathematics problems.  Model theory is probably the subfield of logic with the most applications to mainstream mathematics.


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Automatically updating ORCID, etc, from arXiv?
Generally, whenever I write an article, I will always upload it to arXiv first. So, my list of publications on arXiv is essentially the most official version of my publication record.
Is there a way to automatically update my profiles from other websites (ORCID, Google Scholar, ResearcherID) directly from my arXiv record? (I do have an arXiv author identifier). i.e. whenever I upload a new article to arXiv, it will automatically be populated on those other platforms I mentioned.

I don't know the answer, sorry. I known that Zenodo does this, through DataCite. https://about.zenodo.org/principles/ https://blog.datacite.org/explaining-the-datacite-orcid-auto-update/

Does anyone have advice about how to write a small script to do such things for me?

Google scholar will add anything it finds to your profile automatically. Usually it is more necessary to clean up (e.g. if a name of a preprint does not match the published version exactly) than to add more.
ORCID only lists papers that are published by journals - no preprints. But it also does this automatically (and does a good job - you can help if you use your ORCID during submission).
I don't know about research gate.

ORCID allows me to add preprints from arXiv, which I have done. Should I not be doing this?

Oh, I did not know this. In most cases, preprint get published at some point. Then you should clean up the ORCID page to avoid duplicates.


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How to deal with sexual harassment by a senior colleague without jeopardizing my tenure case?
I apologize in advance that I cannot write about details, as they contain identifying information about the senior colleague in question.
The low-down is that I am a tenure-track professor at a US institution, and one of the tenured professors (married with children) in my department (and in fact, in my research group) has been harassing me for the past month.
He sends me personal emails commenting on my personal life and asking about my weekend plans, he shows up to academic events in the department that I organize (but has no academic interest in these events), and "paces" the hallway in front of my office whenever I have my door open (once I counted him pace by my door at least 10 times in an hour, and my office is located in a quiet corner and he had no reasons to be there). He also visits my office and tries to come up with excuses (department politics and gossip that I have no interest in hearing) to chat with me in the evenings. These visits have gotten increasingly creepy, although I cannot describe them without going into personal details. So far, there has not been any physical touch. (It's naturally a lot more creepy than what I've written, but I'm trying to keep out any identifying information and stick to general statements.)
So far, I have been playing it safe in an attempt to not escalate the situation by responding in monosyllables and hinting at every opportunity that I am busy. I ignore all personal emails. However, this colleague in question clearly doesn't understand social cues, and being cold and disengaging from non-necessary interaction hasn't worked so far.
I am also documenting these interactions since about 2 weeks ago. I am thinking about getting a recording app to record our conversations (I live in a one-party consent state).
The problem is that as he is a senior colleague who understands my research area, I am worried about my tenure case that if I directly tell him off, he may turn vengeful and make my life difficult. But I would like this to stop, and I would like to hear some suggestions on how to handle this.

Addendum (which involves some of my personal opinions): I spoke to close friends in academia (but no one in my department knows yet; I was hoping that the situation would die down, but it hasn't so far). Interestingly enough, the advice I got was clearly divided based on gender.
My male friends were very cautious, and convinced me to not send direct emails telling my colleague that I do not want any interactions other than a professional one. They thought that until I was 100% sure that he was making advances, I should not escalate it and wait for things to die down.
My female friends thought that I should establish boundaries early on, and directly tell him no, because a single faculty cannot strongly affect tenure cases. Sadly, most of them experienced something similar, and they said that once you establish boundaries, these kinds of people tend to fear you a little bit, and they back off quickly.
I found one question somewhat related to my case (although in this case, the OP did not have tenure on the line). It saddened me to read the answers, however. A lot of the suggestions, coming from males and females alike, insinuated that somehow the OP was at fault, in the following instances.

The OP is a "fresh meat" so people are going to be interested, so just wait it out: I felt that being a fresh face was not something wrong; I wished that the answerers would focus on the fact that the behavior of OP's colleagues was inappropriate, and talk about how to change their behaviors instead of placing the burden of "bearing with the unwanted advances until the male colleagues got tired of her".
Some answers suggested that the OP dresses down (and at least one answer suggested that OP's hemlines must be elevated). I object to this answer, because the OP should not have to change her behavior or clothes if it's not wrong. I felt that this answer was the academia-equivalent of telling a rape victim that she had it coming because she was wearing revealing clothes.
Another answer suggested that the OP should just bear it out and establish good working relationship with these people. Again, I did not agree with this answer, as it puts the burden of reconciling with her aggressors on the OP, who is the victim here (you would never tell a rape victim to reconcile with her attacker, right?)

So, I understand that questions of this type can often bring out very biased answers (and even women can have the same type of bias as men), that it can bring out charged reactions, and that despite all of our advances as a society, victim-blaming can seep through our answers.
But the answers that I am looking for here is the kind of things that I can do that doesn't blame me for the current situation, and that doesn't force me to bow down to my senior colleague in order to repair the relationship at some point. I am not afraid of fights, I am not afraid of going public, I don't care if everyone in the department knows about this, and I am not afraid of giving up my job if it comes to that (this is neither here nor there, but my family is rich enough that I don't really need a job; obviously I find fulfillment and enjoyment from my job and I'd like to keep it, but not in a toxic environment such as this.) I just want him to stop and acknowledge that what he did was wrong, and that he should fear for his job if he ever does anything like this again, preferably while not jeopardizing my chances at tenure. And I'd like my future female colleagues to feel safer about my department.

I'm voting to close this question. Although we don't support duplicate questions (the fact that the OP doesn't agree with the answers is immaterial), my main reason for the close vote is that the question in current form can't be objectively answered in a way that could be useful to other individuals (i.e. depends too much on personal factors and preferences).

Comments are not for extended discussion; this conversation has been moved to chat and future comments will be deleted without warning.

Have you had any contact with his wife? Even if the university might not have a limited ability to discipline him thanks to his tenure, I’m sure that his wife would be able to make his life a living hell if she wanted to - and if she were to find out that her husband was perving on women at his work and trying to cheat on her, she very well might.

Sadly there is no evidence on sex-related advances. Suppose that you two come to a court he can say that he just want to make a friend. Coming to your seminar, pacing over your door, or chatting about policies are not explicitly harassment. You could try to get a ring and wear it whenever you see him. Did he repeated send you more than two personal emails/message/calls even if you are not replying? Do you have new updates for 2020? I think WFH might just resolve this issue.

How did the story end?

I would recommend to set a boundary, e.g. by responding to an inappropriate e-mail with e.g.

Dear xxx, thank you for your e-mail, but I have to tell you, that I feel uncomfortable with such kind of e-mails and they are inappropriate. I really appreciate your professional expertise and support, but I would like to stick to a working relationship.

If he ignores this, you at least tried to tell him your point of view (which could help in case of an escalation).
Incorporating comments:
I gave this answer because you wrote that he did not react to subtile indications. I know from many males that they "did not notice that their behaviour was regarded as inappropriate". It is helpful to be very clear at least once. On the other hand, I'm not resided in the US and maybe my answer would sound rude in your ears. You should modify it in a way that shows respect and appreciation for the professional experience and support, but makes clear that there is no further private interest.
Regarding the tenure: If you feel there is any kind of problem arising, you can contact an ombudsperson and show your (and his) mails and ask him to be excluded from the process.

Do you believe that this will not jeopardize my tenure case, or destroy my professional relationship with him? (I'm guessing I have about 30 years to go, although given the current climate, I can see myself wanting to move soon). Your answer feels a little bit one-dimensional to me, in the sense that it is definitely the correct one, but not the one that is simple to follow.

I gave this answer because you wrote that he did not react to subtile indications. I know from many males that they "did not notice that their behaviour was regarded as inappropriate" and maybe this happens to me as well and I don't know it (I hope this is not the case...). It is helpful to be very clear at least once.
On the other hand, I'm not resided in the US and maybe my answer would sound rude in your ears. You should modify it in a way that shows respect and appreciation for the professional experience and support, but makes clear that there is no further provate interest.

Regarding the tenure: If you feel there is any kind of problem arising, you can contact an ombudsperson and show your (and his) mails and ask him to be excluded from the process.

IIf I were the colleague, I would feel better if you deliver the message personally than via a third person (e.g. dean, seniour colleague, ...)

@OBu Aha! I did not know that an ombudsperson has this kind of power, but that is a very helpful piece of information (perhaps it varies by institution, so obviously I'd verify this first). Possibly the best course of action (based on the information given so far) is to make an appointment with the ombudsman office, since it's also a little bit removed from the departmental politics. I'm not planning to act on it immediately, but I'll keep this in mind, thanks.

@OBu I think you should include your comment in the answer. Keeping records and getting an ombudsperson on bord may indeed be a good strategy to keep the incriminated person out of the tenure decision. I don't know. In any case, the solution must be some combination of (1) setting boundaries and (2) removing the person from a position of influence and/or finding strong allies

This sounds like an appropriate tone in the US to me.

The power of an ombudsperson varies considerably from one institution to another. At my institution, I don't think that an ombudsperson could exclude a senior colleague from from participating in a tenure decision, but a dean (or perhaps even an associate dean) could.

I'm going to assume you are in the US.
Every college and university in the US that accepts federal financial has a sexual harassment policy. The first thing you should do is read the policy so that you know who the main official actors are and what would be involved in talking to them. However that doesn't mean that I would follow them immediately. This is because, as you know, in some institutions going the formal route will backfire, while in others it will not. However, sometimes you have the option to say "I am not making a formal complaint at this time, however I want to establish a contemporaneous record of what is happening."  Nonetheless it may be that the office will have little choice in the actions it takes. If anything you could email them and ask hypothetical questions about the process rather than discuss your specific case.
However, at my institution "responsible employees" such as deans and chairs must report to that office. But until you make a formal report the office can't do anything but give advice to the reporter, look at whether there is a history with the person doing the harassing, and be prepared for if a report from you or someone else comes in. So what I would do is make a report to a responsible employee and tell them you do not want to make a formal report at this time, but you want them to be aware and help you to get the behavior to stop. You could even mention that you know that despite this that they will have to make a report to the Title IX officer. Make sure you document this report with a follow up email so that if there is a problem at tenure time you have that. If it turns out that the person you reported to didn't do their mandatory reporting that will help you. Similarly the fact that your chair or dean was informed of the situation will help you if in the unfortunate situation you have to appeal a negative decision from your department or if you end up having to go to court.  I know it is unpleasant to think about, but you should think of the ways things could play out.
Do you have an annual official meeting with your chair?  This is also a place where you can express your concerns and talk about how dealing with this situation is undermining your work. You could also mention that you are concerned that he will advocate for you to be denied tenure. Of course this puts your chair in a position of having to assure you that this will not be allowed to happen.
You did a good thing in accessing your networks, but I'm going to suggest that you activate your on campus networks of other women especially somewhat more senior women. If you don't have those networks, think about who you might have met at an event or meeting and just email them and say "could I come talk to you about about a question about our institution that I feel I can't talk to my chair about"  and then ask them what they know about how these cases have been handled and what their advice is. Do not assume that if the first one you talk to is unsympathetic that others will also be.  Do you know the famous thing that Mr. Rogers said about what to do in an emergency, "Look for the helpers. You will always find people who are helping.”
So all of that is to say that it is essential that you get what is happening on the record so that if there is a future problem you have already documented the situation and that you get some local help.  This problem could be that this person argues against your tenure or that the situation escalates. Currently you don't sound like you are being physically threatened, but that could happen.
If you follow the responses to sexual harassment cases in the news you will notice that there is a repeated pattern of victim blaming where "why didn't she follow channels?" is one thing that is said, but also that contemporaneous documentation is extremely important.
Basically it will be a lot harder for him to cause problems for your tenure case if you have good records and people know about them, since they can discount anything he says about you and also make sure not to have any outside reviewers who are known to be his friends. The "don't do anything" advice is, therefore, not helpful.
The other thing I wanted to mention is that if this is a sudden change it could be that your colleague is having mental health problems. That's another reason to take steps locally.

Great answer, and especially the advice to “read the policy.” (The OP says they are tenure-track at a US institution. It is extremely unlikely that an institution with tenure is not required to have a policy.)

From what you have described, I don't think his behavior has crossed the line into sexual harassment. Not that I'm an expert, but it might fall under "creating a hostile work environment".
I would talk to your department chair, if that is safe, or the Dean, just to get advice. At the minimum, that will create a record that you felt uncomfortable. I am not sure it is in anyone's best interest to file a formal complaint at this time, but it is certainly good to let your chair/dean know about the situation and let them take some responsibility about how it is solved. They might take full responsibility for it! Like: "Sorry you had to deal with that, I know Jeff can be a bit unaware of social cues, let me talk to him and if you don't think there in an improvement in the next week, let me know."
It's their job to handle things like this, so I certainly recommend sharing the burden of how to proceed with them.

Based on how you phrased your question and especially your addendum it feels like you are very strongly leaning towards directly telling your colleague to stop and potentially further escalating this if he does not react. It's also clear you understand and can deal with potential negative consequences for your career.
An escalation will be a lot more effective if you already know how well your institution handles harassment cases. It will also help to know what the general sense is in your institution about your harasser. If you know that, you can better determine how to escalate, how much material you need to convince other people, who to go to and who not to go to, etc.
You mention you'd like to have your harasser "to stop and acknowledge that what he did was wrong". That's a very natural desire but the chances of him doing that voluntarily are probably very small. So maybe don't prioritise that too highly.

Thanks, you're right that it would be good to know what I'm getting into by looking at precedents etc. I would probably talk to some young female faculty in my department (imo it's really unfair that the women tend to get burdened with all these things, but I guess that remark is really for another thread...) Just to clarify, though: I do want to keep my job, and walking out to get involved in a legal battle would be my absolute last resort! If this can be resolved without escalating, even better. Maybe there's some magic phrase that's not rude but will let him see that he's inappropriate...

@user-2147481856 Yes, I rewrote my answer to be a bit more clear about what I meant by 'escalating' (i.e. first telling him to stop, and if he doesn't react, take it further). In terms of a magic phrase, I can't do better than what OBu suggested. It might be more magic when spoken by someone who's higher in the hierarchy.

My male friends were very cautious, and convinced me to not send direct emails telling my colleague that I do not want any interactions other than a professional one. They thought that until I was 100% sure that he was making advances, I should not escalate it and wait for things to die down.
My female friends thought that I should establish boundaries early on, and directly tell him no, because a single faculty cannot strongly affect tenure cases. Sadly, most of them experienced something similar, and they said that once you establish boundaries, these kinds of people tend to fear you a little bit, and they back off quickly.

I'm going to agree with your female friends here; that it is best to establish boundaries early on.  However, I also think that it is best to avoid accusations of misconduct in the first instance, and make your first move with a simple conversation, rather than an email or a report to HR.  I would recommend that you have a frank conversation with this man, establish the things he is doing that make you uncomfortable, and give a clear indication of the boundary you would like to set in your relationship.  I think this would be better done with a polite and gentle conversation in the first instance.
Some men show interest in women in a way that is not malicious, but which is discomforting to them.  Such men are often not terribly good at reading subtle signals of disinterest or discomfort, and so they benefit from being told that they are making you uncomfortable.  As a general rule, males are very explicit communicators, so if you would like a change in your relationship with this man, that can probably be obtained by having a conversation to that effect.  Unless he is a particularly strange man, he will probably be quite mortified once he finds out he is making you uncomfortable.
If you take this approach, there is always the possibility that it will go badly --- e.g., a hostile response to your conversation, or some kind of petulant cessation of the entire professional relationship.  However, I would estimate that nine times out of ten this will get you the best result.

The OP could seek support from a trusted member of their department (e.g., a senior colleague, the head of department, ...) to deliver an anonymous (verbal or written) message---outlying boundaries---to the inappropriate colleague, rather than the OP setting boundaries themselves (e.g., as female friends of the OP have suggested and as suggested in an answer).
If handled well, this approach has the advantage that the inappropriate colleague need never know the OP's identity. Of course, they may have their suspicions, but acting upon them could be outright dangerous for the inappropriate colleague, since there's an established record of inappropriate behaviour (known to the trusted department member) and the inappropriate colleague may fear that vengeance could lead to dismissal for sexual harassment.

I would shut it down hard and in an email.
If you have a spouse or boyfriend, it can be helpful to mention that you are off the market and that you don't like someone else hitting on you when you are with someone else.
Really, I think there is probably enough here to go ahead and go to HR department now.  It's not like you want to kill the guy.  But get him warned and that will back him off.
I am male and had a sexual harassment situation in grad school.  It wasn't even flattering (like someone who likes you and you just turn it down) but a just a strange older lady who kept bugging me.
I am very far from litigious or touchy or sensitive.  But at a certain point, you just have to stick up for yourself or you are letting people walk on you.  Didn't want to end up with a bunny in the pot and this lady wasn't just smitten, she was creepy.  I ended up taking it to the HR department and they got her shut down.
[Print all the emails.]
I wouldn't just ignore it until tenure.  Yeah, there is some danger it could affect your case.  But so what.  Do you really want to put up with Mr. Weirdo if that gets you tenure?
Just reading between the lines, I don't get the impression that you are they type who is trying to instigate grievances.  Get the impression that Mr. Weirdo is the one at fault.

Your second paragraph is bullshit. Saying no should be sufficient. We shouldn't have to say that we already belong to some other man to get someone to back off.

Oh, I remember now, belonging to another man is the only valid reason in the minds of other men to stop coming on to somebody. sarcasm off

Commenters are absolutely correct that you shouldn't have to say you belong to some other man.  @penelope it's not that belonging to another man equals a valid reason to stop coming on to somebody, it's the fear that the other man will respond physically, ie, it's just a threat. Outside of that point - which is almost just an aside to the rest of the post ('it might be helpful if ...') - this is actually a pretty good answer:  "Take action to stop the behaviour either directly (email) or indirectly (HR).  Document correspondence. And for your own sake, don't let it continue".

Not a specialist but sexual harassment perhaps has certain connotations that aren't evident from the Q text. It could also be a case of bothering/boring behaviour and no more. In both cases abd even if perhaps others have already suggested this:
Make clear to him/her that the behaviour is uncomfortable to you by viva voce as well as keep records of emails already received and or exchanged.
This will be useful in case escalating the situation will be unavoidable.
But it is quite possible that s/he realise that is wrongly behaving, if clearly informed. Sometimes we really need of someone opening our eyes.
It is somehow forced to think of retaliation. Academia is not much different from the life outside, and the vast majority of the times people do elaborate refusal without much of vengeance desire.
I would perhaps escalate just after, if the pressure from that person doesn't cease and/or that person will complicate your work in response.

Why would orally be better than in writing?

Perhaps is the same. One should know the email already sent. A clear mail should work as well. But anyway, if the relationship was ok before, it seems to me better to take a couple of minutes to clearly say what is OP situation. . "I am not interested in discussing such things" in an email and something to explain that a behaviour is cause of discomfort are two different things, at least it could be. @Azor Ahai

I like how this answer starts; and while I don't think it's really OPs duty (or the duty of anybody who feels harassed) to educate their harasser, or open their eyes, but informing the person to stop is an important step that should be taken first, and nothing wrong hoping the behaviour will stop then. Sadly, you follow that by only a very vague suggestion to "(perhaps) escalate it later" for the case it does not stop, with no suggestions how to do this considering tenure is on the line and the other person involved is a senior tenured colleague from the same department and discipline.

@penelope I do not wish to anyone be harassed - sexually or not - at work place, and especially by a senior. I do not have a nice answer to that except that academia can still be one of the most protected places. I wanted to make sure that OP frankly try to stop this with a brief and mature discussion that might take a couple of minutes. Already feeling sexually harassed instead of just bothered (it might be indeed a lot bothering) suggest to me that she has somehow circumvented a decise but polite discussion.


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Impact of a C+ grade in a graduate course
I'm planning to apply to competitive PhD programs in theoretical physics. Unfortunately, I received a C+ grade in one relevant graduate-level course. I really don't know how I got this grade, because I think I did well in the final examination. The final exam was worth 100 % of the total grade. Now, I received 5 A's, two B+, and two B's in the 10 graduate courses that I took. Unfortunately, my undergraduate degree is unrelated to the field I intend to do a PhD in. I didn't even attend undergraduate courses in calculus. I taught myself math and physics from calculus up to algebraic topology and Quantum field theory. I have also scored high in the subject GRE test.
I would like to know if these grades would have negative impact on my PhD applications. Should I attempt to do anything about this C+ grade?

Can you add your country and the meaning of the grades in your countey?

Do you have a master's degree? In the US, it is very unusual for undergrad students to have completed ten graduate courses -- seems like you've likely already finished the coursework requirement for your PhD....

Did you unknowingly forget to answer some questions in the final examination (e.g. the questions were printed on two sides of the paper and you only answered questions on the first side)? If so, that could explain the C+.

I lost 14 points out of 50 in the second semester examination. This was not because I did not know the answer to one of the questions. In fact, I think the professor was not fair in his marking because the questions did not really require any thinking. It is basically repeating the derivations in the textbook for the course, which I did.

In the first semester, I lost 19 points. In that test, however, I didn't have time to finish writing answers to all the questions in the test even if I knew how to answer them. This is stupid as well. The exam was too long really for 3 hours. I think this is sensitive to how fast I can write or something stupid like that.

@csguy  If you give those answers to a Ph.D. admissions committee, or in your written material, you're going to come across as a whiner.  In general, whiners are not looked upon with favor.

One bad mark is unlikely to have much if any effect. Especially if it isn't the most recent. People are looking for indicators of success, so you have to provide plenty of that in your admissions package. Someone may ask you why you got a poor grade, but most will accept a reasonable answer. But your record is what it is and you can't change the past. Apply to the programs that interest you and make your best case.

Clearly, if they were A+'s, it would be much better, but it is still better than not having taken that course; even if we think the worst that you didn't get the material from that course, you are at least familiar to that material compared to a student who haven't taken it.
Plus, you have the chance to explain that "bad grade" in the statement of purpose if there was some exceptional situations, or you can argue as

since I had a lack of the material from that course, I did this, this
  and this to compensate those missing pieces later etc.

of course, if you do such thing; this might even be better who knows!.

what is the reason for the down vote?


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Stuck with an advisor who is unprofessional
I'm a Masters student in computer science. My current advisor is completely un-professional. He doesn't only write bad letters of recommendations for his students in order to keep them working for him, he even wrote bad letters of recommendations for students who did not ask him for these letters. I think this is egregious. I don't really know why. It might be psychiatric issues. Now, he is the only one in my school doing research. I don't know how to deal with it. Any suggestions would be really appreciated.

This is very confusing. How can a professor write a recommendation letter which was not requested? How do they know where the student is applying to?

Sounds strange that there's only one professor doing research in your school. Maybe you can get a supervisor from a different school?

He would ask other professors about the place someone is applying to. It is really strange. He wants people to work for him.

Sounds like you have to ask the professors who you ask for reference letters to treat your application and request for reference strictly confidential (including other faculty in the school). Apart from that, time to say goodbye to that school. Really, writing nasty references unbidden is pretty much at the very bottom of behavioural patterns, that's not just unprofessional, it's basically a form of academic swatting.

Don’t walk. Run.

How does OP know what's in the letters of recommendation? They are not generally public. They may also be correct about the candidates, even if they are unflattering.

This is a troll post; and if not, it is very, very confused.

It is not trolling. The advisor I'm working with is really terrible. Basically, he isn't happy with M.Sc students leaving him to do PhD studies abroad. He is also terrible in the subject matter. He depends on other collaborators and students in his work. He doesn't even understand the details of the papers he has his name on.

Run away! The most important thing to success in your graduate education is your desire to succeed and your advisors desire for you to succeed. I've had friends and family with advisors who were immoral or emotionally unstable, and they are much happier now that they switched institutions/advisers or left the field entirely.

I think the answer largely depends on your particular circumstances. You mention bad recommendation letters. Okay, this is awful, but apart from this issue it seems you don't have any other complaints. Thus your course of actions depends on whether (1) you need recommendation letters while you are doing your masters and (2) these letters have to be from your supervisor.
If changing your supervisor and/or school is not an option, think about these questions. In a sense, your original question begs the trivial answer: if your supervisor writes bad and unwanted letters, you have to get these letters elsewhere and somewhat quietly.

In computer science you can build a reputation without your advisor. Get on github and start contributing to open source projects related to your interests. Go to conferences and network.
People probably know this guy is not honest and discount his letters (assuming what you say is true).

You can't get a degree from GitHub.

@Buffy you don’t need a degree to be a software engineer

Software engineering and computer science are not the same thing.

"...probably know this guy is not honest..." - only in their own department, not if the students apply elsewhere. The lightning has to strike twice in the same place for flags to start becoming red. In the meantime, the student's future has been damaged.

@anomaly of course you are right. It isn’t clear what the OP’s long term goals are. If he wants to stay in academia he has a bigger problem.

It seems my answer is quite unpopular. I appreciate that CS and software engineering are not the same, but there are CS projects (especially computer vision and machine learning) that are open source and accept contributions. My point is that the OP should network outside of his school.

I don't understand all the downvotes either. Perhaps people are thinking about PhD students. Most Masters' students don't even have advisors. Just get recommendations from a couple professors who liked you instead.


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Academic Affiliation - Paper will be Resubmitted during PhD but published as an AP in another institution
I have a paper that needs to be resubmitted by the end of the week. It should be the last round, and I strongly expect the paper to be accepted for publication after that.
I am still employed as a Ph.D. student in institution A, but will move to institution B as an assistant professor at the beginning of May.
Thus, the paper will be published while I am working for institution B. Institution B provide financial incentives for such publication, and it would, therefore, be beneficial for me to put the affiliation "B" on the paper.
What is the proper affiliation to put? I would tend to list both A and B as my affiliations, with a short footnote explanation.

Academia varies more than you think it does.  (The answer to this question depends on your field of study, and, in some cases, even your subfield.)  https://academia.meta.stackexchange.com/questions/1203/welcome-to-academia-se

Some journals allow you to give both an affiliation (where the work in the paper was done) and a current address (where people can find you when it's published).

Affiliation is primarily so that people can contact you and so that names can be disambiguated. On the other hand, you probably need to honor the institution that enabled your work. List an email and and affiliation that will be useful to people after publication. But in the acknowledgements you can indicate the prior affiliation with appropriate thanks.
However, their are some scientific fields in which work is only possible in a lab funded by some entity that must be credited. In those fields, the PI is generally also listed as a co-author of the work, even if s/he does little of the actual research. In those fields it may be necessary, largely for political reasons, to use an affiliation under which the work was done. In such a case, it will be a bit of a dance to do something in the paper that helps readers find you if necessary. Or else you can arrange to have all attempted contacts forwarded to you in the future.

This answer is correct for my field (mathematics), but I have learned in various places that it is not correct for some other fields.

@AlexanderWoo, I've completed the answer.


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Will EasyChair preprints be automatically indexed by Google Scholar?
Is anyone aware if a preprint uploaded to EasyChairs preprint server will automatically be indexed by Google Scholar, or do I need to manually add the citation to my profile?


text:
Should I quit Master's after 2 months into the program? Please help!
I completed my Bachelor's in Electrical engineering last year in a foreign country. I already had a job pending in that country when I finished but due to visa concerns, I would only be able to start working after 7 months. To keep myself busy and use my time productively, I decided to enrol into a 1-year Master's program in Statistics and Data Science in the same country.
Two months into the program, I realize that I have not been putting my heart and mind into studies. I am only going to lectures for the sake of it, and I will probably not use most of the knowledge gained in my courses in the career path I want to pursue.
I was just able to obtain my work visa from within the country, so I can start working after one month in the position I had secured last year. However, if I push it through for the next 5 months, I will be done with my coursework and I can start working while I complete my thesis on the side. On the other hand, if I decide to quit now, I will lose 50% of the fees I paid (on a loan).
So, basically, if I do not quit now and start work after 5 months, I will have a Master's degree by the end of next year, more career options and make some use of the fees I have already paid. But if I decide to quit now, I will have a month off to rejuvenate (the past few months have been very stressful for me), get an extra income of 5 months which I can use to start paying off my debt and save the other 50% of the fees. In addition, I may save myself the struggle of pushing through an intensive degree I am not too interested in or the risk of failing a few courses. The same knowledge can be gained online via a ton of resources available on the subject.
Could someone please guide me on what would be the right approach to my situation? I feel like I had made a hasty decision to enrol into the Master's program, but I do not want to make a hasty decision to drop out. Any advice and guidance would be greatly appreciated!

There is no right answer for this question but I can explain what my approach would be.
Question I would ask:

Does the content of the master study interest you?
Is the gained knowledge/degree useful for potential career paths?
How much money do you waste by quitting?
How much money can you make by working instead of studying?
How would quitting/continuing affect your mental health?
If you do already have a pending job offer how does quitting/continuing affect the offer?
Do you really want to write your thesis on the side will practicing a full time job? (stressful, long time)
Can you work half time at the job?
Will your potential employer support/endorse your expanded study?
What is the future intend of pursuing an academic career?(Quitting a Master's program can place barriers for acceptance into other master programs and PhDs in the future (suggested by@Mefitico))
How will quitting affect your CV?

For a "sober" look at all those question a decision matrix would be useful.
If the financial calculations are to complicated asking a question here may help.

Great answer. I'd suggest as well to consider future intent of pursuing an academic career. Quitting a Master's program can place barriers for acceptance into other master programs and PhDs in the future.

@Mefitico +1 I added it to the list


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Can I use published data by other authors in my study?
I'm in the process of publishing an article in the Engineering field. The manuscript got a preliminary acceptance, and should be published after few modifications. However, based on one comment I got, I need to evaluate my model's performance based on certain input data. I don't have such data, but such data has been published before in the literature. Is it OK to use the date published by other authors just to evaluate my model?
What am I going to do is to digitize the published figures and use the values. I'm going to cite the papers, but I'm not going to add the figures or the datapoints to my manuscript.

I cannot imagine any reason that prevents you to do that. You would be just using information publicaly available

Yeah, it is fine.  If anything, it is how the literature and scientific enterprise is supposed to work.  I would just be clear about attribution and that you haven't discovered the relationship (from first paper) but instead used existing info to validate your method.

You can almost certainly use the data that you find. Copyright restrictions only prevent you from republishing it. But if the originators make it available, they do so so that others can take advantage of it (as well as making verification of their own work possible).
Of course, the original authors may grant a non-restrictive license to the data in any case, in which case you are bound by that.
The same is true if you read something in a copyrighted book. You can use that information for any purpose, but you cannot republish it. But for your work all you really need to do is to cite it properly to avoid any charge of plagiarism.
Given the final comments in your question, you should be fine.

If the data is publicly available, yes, by all means, but don't forget to cite the source of the data (and any associated papers that introduce or describe it).


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Is verbatim copying a data collection plan with citation considered plagiarism?
Cheers, I am writing a thesis using secondary data and need to report on the sampling methods used to collect the data. Am I allowed to verbatim state what is listed in the study documentation? It is fairly complex and thus paraphrasing it changes the meaning.

This is all indeed helpful. Say I actually copy and pasted paragraphs from the documentation and sprinkled it throughout the thesis. I want to be honest about this and wonder how the best way to do that is? I have seen other thesis that copy verbatim but do not say they did (but do cite it once). That's another question I have. Do I need to cite the data source more than once? I have a few pages on it but it seems not right to cite it in every paragraph.

Your advisor should probably be able to offer concrete advice having looked at precisely what you intend to copy. He or she is probably familiar with what is considered acceptable.

See https://academia.stackexchange.com/help/merging-accounts  to merge your accounts so you can write comments.

It isn't plagiarism, but it may be a copyright violation. Plagiarism is claiming that something is due to yourself that is actually due to another. Your citation covers that. But it may still not be proper to quote it at too much length. Laws on that (copyright) vary by location. Look for any stated license on the work or contact the publisher to be sure.

If you are copying large chunks of material verbatim, and paraphrasing won't work, then you should give a direct quote with citation to the source and page number.  If the volume of material is too large for a block quote, or if you plan to refer to chunks of the text over and over again, it might be easier to add the entire document as an attachment in the appendix of your own work, and then refer to the parts you need with citation (but without giving the quote) in the body of your work.

Proper way to handle that would be to say you've used the methodology of Dude et al. (20XX), which you have reproduced here for convenience.  That wouldn't violate any copyright.  You dont need the their publisher's permission every time you quote someone. It only matters if you're using a published figure.

I think your statement "It only matters if you're using a published figure." is incorrect and possibly dangerous if the advice is followed. Some text can be quoted, but there are limits. "Here I have reproduced chapter 3 of Dune for convenience." Boom. Lawsuit. Don't give permissive legal advice if you are not a lawyer.


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How to find "original papers" on some topic?
Anyone know how to find an "original paper" (the first one or the few first ones where something appears)?
Is there some particular search methodology for this?
I saw some search engines have tags such as "follow-up study". Does this imply that some search engine might know how to find the original papers?

Pick one paper from the topic, look for the oldest references that still include what you are looking for and then repeat...

As much you deepen your read of papers on a topic, the "first papers" will be cited recurrently.
However, the first paper candidates could be extracted computationally. You could use scientometrics techniques that map most cited works, for example. The most cited works are good candidates to be considered an "original paper".
Another way is to map the history of a field using visualization techniques. You extract a relevant set of papers in a topic, and then draw citations networks. The papers on the root of the network probably are good candidates to be original papers. And not necessarily have many citations.
A good book to see these techniques is Mapping Scientific Frontiers, from Chaomei Chen. The author presents an interdisciplinary view on science study, focusing on found the scientific frontiers - including finding papers that are disruptive or initiated a whole study field.


text:
Do scientific methodological beliefs affect the topics that are investigated?
Do scientific methodological beliefs affect the topics that are investigated?
I've lately been led to this question, since I've wondered about what a difference would it be to do a "very empirical" vs "very definitional/mathematical" Ph. D. thesis. In e.g. image processing one can find applications and technique introductions. While technique introductions are often tested on empirical data, their results may not be like those of real empirical phenomena. On the other hand, doing empirical studies might require those methods. There are e.g. plenty of classification and segmentation algorithms that truly work well only in "specific types of data", when "in empirical sense" they should work on "data with broad variations". But on the other hand things like CNNs seem to approach this kind of "data as it is" -view.
But if "scientific methodological beliefs" for example assume that "empirical is hard", then could this motivate more studies on "easy approximations", rather than "phenomena themselves"? Intuitively they need to agree somewhere, but I was more thinking along the lines of:
Is it possible to produce a lot of research by researching "easy approximations" than "studying the real thing"? Does scientific belief justify this by making people "okay with easy approximations"?

Arguably, setting up empirical studies is easier than coming up with new mathematical models. You just need to gather the data and process it.

@nick012000 Not necessarily in e.g. classification. Isn't the point of big data that it's much faster than humans? For large data sets.

Who's beliefs, exactly. Those of an individual investigator or those held "generally". Note that "generally" doesn't mean universally.

Do scientific methodological beliefs affect the topics that are investigated?

The obvious answer to that is, of course, yes. Scientists are people, too, and while we try our best to conduct the actual research as objective and unbiased as possible (and sometimes we fail at that as well), lots of very subjective and "unscientific" factors go into the selection of concrete hypotheses, problems, and methodologies to work on / use.
These include perceived chance of success (nobody wants to spend a lot of time and money on a study they assume will fail in uninteresting ways), perceived importance, personal taste (if you hated mathematics the question you raise in your introduction would likely not even cross your mind), chances of writing a high-level publication (people are much more likely to commit to a study that could get into their favorite A* venue than one that is unlikely to), and many other factors.

But if "scientific methodological beliefs" for example assume that "empirical is hard", then could this motivate more studies on "easy approximations", rather than "phenomena themselves"? Intuitively they need to agree somewhere, but I was more thinking along the lines of:
Is it possible to produce a lot of research by researching "easy approximations" than "studying the real thing"? Does scientific belief justify this by making people "okay with easy approximations"?

"Perceived difficulty", especially in relation to expected impact and publication chances, are certainly one of these factors that make people choose which concrete problem to work on over others. However, I would argue that this is less about "beliefs" and more about fairly pragmatic cost/benefit estimations: if empirical works take a long time and are not valued highly, then fewer people will work on them. Again, researchers are people, too, and as a group researchers (just like anybody else) react to the incentives that are presented to them.


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How often are research domains "competitive"? In terms of results etc
How often are research domains "competitive"?
That is, is there often a competition within the field for the "most content" or "highest quality results"?
Is it always the case?
OTOH, I find that "competition for truth" is inherent to scientific method, particularly "criticality", but OTOH I find that as in other endeavors, having competitive interest might also lead to poorer quality papers, due to e.g. working faster.

I'd argue every field of work without hard-capped performance is competitive.
There is only so much one can do working as the customer support; it is a much needed job, yes, but the competition is limited to some extent by the reasonable "top achievable performance".
On the other hand, in academia people normally strive to do good science, so only non-competitive fields in terms of researchers aiming for great results are long studied ones when there is a consensus about how things work. It is usually the point to aim for amazing results when sky's the limit, is it not?
Somewhat paradoxically, however, there could be a period of overlap where the competition for the funding is cutthroat because of industry being interested in refining the technology but not as much room for the scientific (as opposed to engineering) breakthroughs left. From my point of view, the research on luxury yacht design is probably less competitive than the research on the Grand Unified Theory despite having more financial enticement attached to it... But that's probably just me not knowing enough about research on luxury yacht design :)

Research is always competitive. In STEM, and that's all I will discuss here, you compete against nature or the vagaries of mathematical structure. This competition, if you do seriously challenging research, is far outweighing, in my opinion, the competition of your peers.
Some people like to measure competition by counting how many papers get rejected in the conference you publish in or in the grants you receive. In my opinion, the first one is arbitrary (a conference with high rejection rate simply got a good reputation in the community, but after decades may simply stew in their own juice; tough to get in, but not really at the most innovative top of things); the second one is competitive in terms of funding, but ultimately it is not the funding that counts but what you do with it. If you can send an otherwise equivalent satellite to orbit for a tenth of the funding of another project, which of the grants is scientifically/engineering-wise more competitive?
Proving a theorem that no-one proved before, discovering a new type of reaction, or a new particle, that's the competition. You battle nature in the first place, and your peers only to a secondary degree.

"ultimately it is not the funding that counts but what you do with it." -- But if you don't get it then you can't do anything. And the lack of funding trickles down to competition for spots in PhD programs, postdoc jobs, pressures to publish frequently which can put a damper on riskier-but-higher-reward research... And even if faculty are not hired with grant funds, limited funding in general is a factor in the job market for tenure track positions, which I would classify as competitive in every field I am aware of.

@Andrew "If you don't get it then you can't do anything." - Well, this is trivially true, but not everywhere funding needs to be constantly competed for all the time. Not every place is the US, although it managed to push important aspects of its funding philosophy onto other countries. As for academic positions, I agree, this is competitive, but it is competitive everywhere, in STEM as well as in liberal arts, but there are simply far more people that have any hopes up to get one in STEM than in liberal arts. I interpreted OP to ask on content, not on job scarcity which is universal.

One definition of an academic field that would not have a lot of competition, would be one where there was sufficient funding that every high quality grant proposal in that domain got funded. If you find a field like that, let me know!


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How much of published papers is reasonable to expect to "fail" somehow? E.g. not having the impact you planned
How much of published papers is reasonable to expect to "fail" somehow? E.g. not having the impact you planned
Are there studies that would e.g. measure, how much of published papers become lesser than expected or become obsolete faster, than expected? Or the kinds of issues.

I don't know why this question is closed: while the question is subjective, I think it's a common X-Y question with an objective answer.

This is a question not about science, but about personal expectations.
Consider the following different perspectives on the same set of papers, some well received and some poorly received:

All of these papers have failed, because I am not famous yet.
Some of these papers have succeeded and some have failed, because my community embraced some and ignored others.
All of these papers have succeeded, because the response to them has given me an objective assessment of how interested my community is in these pieces of work.

I recommend taking the latter approach and considering the impact of a paper part of its effective peer review and feedback for you with regards to your research choices.

I think that Albert Einstein had to wait quite a while before his ideas became mainstream. I've heard it said that the scientific establishment of the day had to die or retire so that younger and more open researchers came to the fore.

@Buffy Planck's principle: "A new scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die and a new generation grows up that is familiar with it. . . . An important scientific innovation rarely makes its way by gradually winning over and converting its opponents: it rarely happens that Saul becomes Paul. What does happen is that its opponents gradually die out, and that the growing generation is familiarized with the ideas from the beginning: another instance of the fact that the future lies with the youth."

If "failed" means "not having the impact planned" then hell, it is probably close to one-hundred percent!
However, I think that's the wrong way to look at this.  You can control the quality of your paper, but you can't control its impact (though perhaps you can influence it with some good marketing).  If you write a high-quality paper that adds useful knowledge that is available to society, that is a great success in my view, even if no-one appreciates it.  Obviously it is unfortunate if your good paper has little impact, and that matters, but it is not a reason to consider the work a failure.

This is interesting, because I perceive that often people are positively biased prior to publishing. After all, why would they publish, if they weren't ascertained that it's "worthwhile". And sometimes publications may be glorified just because "they were published". W/o considering, whether their "impact" is significant. Obviously a paper that becomes cited a lot may be more useful than something that becomes not. OTOH count of citations is not necessarily a measure of quality, because the field/domain might be small.


text:
Ways to improve writing, so that one needs less time spent on proof reading?
Ways to improve writing, so that one needs less time spent on proof reading?
I've been a bit annoyed, because it seems that using a "write, then proof read" -approach seems ineffective, because then one must read full text. And the checking might become more complicated to handle, if one does not fully keep track of what one has checked.

You have unrealistic expectations about how much time proofreading (and writing) ought to require.  I spend several days proofreading each of my papers.

@AlexanderWoo I just find it a hassle. And I think there should be more effective methods for dealing with it. It reminds like having to manually check for something for which one'd expect there to be "efficient algorithms" already. Something that I've thought: progress in writing only after you've checked previous (does not work, since later observations might change earlier ones), proof read in "chunks" (does work, but cannot reveal e.g. content errors that exist relative to different parts in the text).

I used to be someone who could regularly write full conference papers in one fell swoop with only 1-2 proofreading rounds, and few fixes necessary. Conditions for that were: I had all results. I was the sole author. I had opportunity to get in the mood. I was fully concentrated and in the zone (i.e. no checking of internet/email/social media at all). I was super meticulous to write correctly right away, so that grammar and content were correct at sentence level and made sense immediately. I am no longer able to do so, as too many duties pull at me now. But the last point remains.

I understand your question is about the writing stage, but one way to make proofreading faster is to have a computer script flagging common issues, see for instance: matt.might.net/articles/shell-scripts-for-passive-voice-weasel-words-duplicates/

This depends to some extent on the kinds of errors that you tend to make while writing. If you are thoroughly  practiced in such things as sentence structure, punctuation, correct use of adverbs and such (as exemplified in The Elements of Style), then there are a lot of errors that will never appear (or rarely) in your work.
However, for the content of what you write it is almost impossible to keep errors out without several passes over the work. The problem is that we take a double view of what we write; an overall, strategic, view, and a microscopic, tactical, view. They sometimes conflict.
Often enough, when you are writing, your mind is in "strategic space" and you just write the wrong thing, thinking that you actually wrote something different - and consistent with the long view. The opposite can also occur.
Even proofreading isn't a panacea. In reading your own work, you often "see" what you thought you wrote, not what you actually wrote. This is partly (at least) of how the eye scans the  page and coordinates with the mind.
I've written quite a lot of textbooks and always make mistakes, often bone-headed mistakes; reversing mathematical operators, for example. They are hard for me to find, but another person, reading the book will find them quickly and they will be totally obvious. One of the things holding up a long-term project is that I don't have a proof reader. I've made several passes over the text and still find some head-slappers.
So, you can, with practice, avoid mechanical mistakes, but content is much harder to get right other than with several tries.
Even beyond the technical errors, of course, is that a writer has a certain context that the reader probably does not. It is therefore easy for the writer to make inappropriate assumptions about the understandability of the work. You need a special "hat" to wear to try to catch those sorts of mistakes. Again, an external proofreader has a different context and can usually help. A co-author once described my writing as "precise" but sometimes at the expense of understanding. It was enlightening.

Note that The Elements of Style is out of copyright and you can find a pdf on the web various places.

The Elements of Style is one of the 10 best books ever written. Every author should review it before sitting down to write.

@DavidSmith what are the other 9? ;-)

Let me add that the "hat" you mentioned is one that every teacher should wear when preparing for class. It's much too easy to talk to a class the same wayI talk to myself (but louder) and assume that I'll be understood.

I strongly encourage anyone who thinks of The Elements of Style as an authoritative source on English grammar to read this: http://www.lel.ed.ac.uk/~gpullum/LandOfTheFree.pdf

@Dan Romik. Personal choices depending on discipline. Strunk & White belongs on any writer's list.

@DavidSmith While I have no strong opinion about EoS, and it's certainly useful to read, claiming it is one of the best books ever written is a bit like claiming some finger practice studies to be superior to the bulk of Beethoven sonatas. I prefer the view that form follows function and that style supports substance. Charles Darwin is an classic example of well written science. OP should seek one or more scientific authors in their field whose style they admire and learn from the masters directly.


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Can any automatic citation checkers infer about the validity of the content?
Can any automatic citation checkers infer about the validity of the content?
Rather than just formatting?
I.e. if one writes something like
"abc has been studied by XYZ (2015, p. 25). In this study they made an observation about abc with 45% accuracy.".
Then the checker would check, whether the source XYZ actually talks about abc and whether at p. 25 of the linked document there is mention of this 45% accuracy thing.

Is there some reason you think such a thing might exist?

@AnonymousPhysicist Because it's useful for large citation counts?

I think it's called a 'grad student'.

If you are you talking about a software that would search the Internet and make inferences, than that's technically next to impossible. But perhaps you meant something like: you have all (or most of) your references in the same folder in the same format, and you want the software to perform a local search? Even that, though, would be an immense technical challenge to perform entirely automatically, as it's hard for a computer to extract meaning from a free-form English sentence. If such a thing exists, the best it could do is to show you the page so that you can check visually.

No, there is no such automatic citation checker. It would exceed what is technically possible at present.

Addendum: it would be a good research project for a PhD or even beyond that. There are now extractor solutions for medical and law papers. I do not know how good/reliable they are.


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Is there a systematic way to verify "textual quality" of submission at the time of submission?
Is there a systematic way to verify "textual quality" of submission at the time of submission?

Some older posts:
How accurate are published papers?
Why are there many typos and errors in publications?
Dealing with the inevitable presence of mistakes in paper submissions

It has seemed to me that 100% error freeness could be technically challenging.
However, is there some general "test of goodness" for "ready for submission"? Using n number of readers, something else?
When checking maths, citations, or grammar this is easier. Just see if it matches the rules. But in writing, the particular problem may also be about subjective factors like in:
https://link.springer.com/chapter/10.1007%2F978-94-007-4168-3_1

Note:
Dealing with the inevitable presence of mistakes in paper submissions
Has some answers like:
https://academia.stackexchange.com/a/171572/125350
https://academia.stackexchange.com/a/171578/125350
However, definitions such as:

"they make the paper unreadable"

seem ambiguous if the submitter believed it's readable. So how to decide how readable is it?
Tips like:

"you learn to make papers "better" by writing papers"

seem unclear for actual verification or measurement of quality for submission. Intuitively mere practice does not also guarantee enlightened experience.
There's one answer saying:

In summary, my recommendation is to try to point out the key areas in
your paper that are likely to be read by Reviewers and focus on having
those completely free of mistakes. Perfection is difficult to
guarantee, so at least focus on the big picture.

But this is contradictory for the process of writing. If the paper would be read in "glimpses", then shouldn't this suggest that one should aim to make short explanations in the first place? And then checking would be easier since there's less of it? However, is this the only way? OTOH, short texts may fail by being "too dense". And then the question would be "well how'd one know it's too dense?".
Further, this is contradicted by:
https://academia.stackexchange.com/a/171570/125350

More-narrative approaches can be more robust, and less sensitive to
typos and other errors.

Confusing the notion on whether the quality can be managed in an independent way. Making writing seem like a matter of taste, but which it cannot be if "quality" must be agreeable. And introducing hard-to-systemize aspects(?)

I’m voting to close this question because it asks for instructions to do something that is impossible.

Also possible duplicate.  https://academia.stackexchange.com/questions/41812/how-accurate-are-published-papers?rq=1

Please consult the help for information about asking questions.

No need for your question to be deleted; if you'd prefer it to be closed as a duplicate of one of these other questions rather than merely closed, you can reply to this comment (with "@BryanKrause") and I'll update it.

@BryanKrause I've put an honest effort into making it better and I still think it's a useful question.

@mavavilj I don't think it's a bad question overall, but I do think it's a bit naïve or opinion-based perhaps, which is possibly why others have downvoted or voted to close. What I do not understand is how your question remains after reading the answers in the questions you link, which seem to cover it pretty well.

@AnonymousPhysicist Isn't this about the goals of scientific publications? So are good, readable publications then impossible? Some sources say that many of them are hard to read though: https://www.nature.com/articles/nature.2017.21751

Published texts are virtually never 100% error-free. If it happens, it's because all the people involved proofread it very, very carefully.
For illustration, I once edited a book where the author's wife said she'll proofread the manuscript again and again until she can't find any more errors. She (and me) carefully checked all the proofs at every stage, and yet after we published it, we found a typo ...

When error free things appear in print it is, often enough, a combination of blind luck along with many eyes.
The luck part should be clear.
The many eyes means that several people have reviewed the work with an "eye" toward corrections. The different people have different concerns. Content reviewers are looking for errors of meaning. But copy editors are looking purely at the form. And that process of using several different people with different concerns is what publishers use to approach an error-free text even if it fails in some way. They also, often, publish errata, so that the reading public can help in the process of error correction with future printings taking account of the errors found and reported.
Donald Knuth has, in the past offered cash bounties for errors found in his CS works, though they are now symbolic "payments". So, the error free state is approached asymptotically in a sense.
An author is not the best person to find errors in their work because of the way the mind works. There are two aspects to this. One is that you, the author, often "see" on the page what you thought you wrote rather than what you did write. I've switched intersection and union in math formulae for example and it was only by accident that I noticed it.
The second aspect is that the mind uses a predictive process when you read (I don't have a reference handy) so that it predicts what is to follow immediately after what you have already read. This speeds up reading, but also lets you overlook errors. This second aspect applies to other readers than just the author of course, bringing us back to many eyes and luck.
And some copyeditors are just better at finding small errors than others, and some reviewers are better at finding big errors.
So, the process works even if imperfectly.
This is one of the big issues with self-publishing. You don't normally have many eyes, only (blind) luck.

So is standard that "sufficiently many eyes agree on it"? But this could vary by sample? I'm not also sure if it's about luck, since some may claim that writing is a formal endeavor. That is, by following "rules" the text should be golden. And a good test is how well it meets these rules? Like a grammar test (you compare to established grammar rules).

@mavavilj, it is more that the "many eyes" actually improve it, not just agree that it is ok.

But I'm asking for measures for deciding when the submission is "ready for primetime". So e.g. how many eyes? What kind of eyes? What if there are eyes that don't agree?

I think you've changed the question so that it is too dissimilar to the original. The editor decides when it is ready.

So is it then, when one has bounced it to the editor enough times? That's the measure? But this doesn't inform how one could improve systematically as a submitter.


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What are some examples of research papers that are very generally viewed as "well-written"?
What are some examples of research papers that are very generally viewed as "well-written"?
And by "generally" I refer to something which is not dependent so much on "subjective factors" of taste.

@Roland Is this such? I think this is a question about the perception of "well-written research paper".

Which field is of interest to OP?

@Aruralreader Any field, but intuitively such paper should not be "too easy", because easy topics are easy to write about.

The American Mathematical Society and the Mathematical Association of America give out some awards for papers and textbooks that are focused on the quality of exposition. Look at the winners, they will give some fine examples of what you’re looking for.