106

Actually changing the name because someone might be offended by a sound that comes from a completely different domain and is completely separate from the history of racism would be condescending, in my view. And, as you say, the term is in common use. Changing it would also confuse some people. Leave it be. There was no intention to do harm and the acronym ...


103

In physics we deliberately do not prove the series converges, because we are not interested in teaching concepts like convergence. Physics courses are not intended to be mathematically rigorous. It just is not one of the goals.


86

I agree with the other answers that this may be an artifact of the histogram. May I humbly offer a few alternative ways to plot these grades? All of these essentially show that your effects are likely due to small n and possibly an essentially discrete underlying data generating process. R code: require(hdrcde) require(Hmisc) require(denstrip) require(...


85

If you are at all unsure about causing offense, you could always use the full name in your paper "Normal-Inverse-Gaussian distribution". It won't be any less readable for that. In your code pick a different prefix that still clearly identifies the distribution, e.g. ninvg_foo().


75

Let me add a thought following the other post, which asserts that this is not a mistake, pedagogically. Take this as a given: you don't need to "call out" the professor for failing to teach "properly." It is, however, still the case that you personally are wanting to dig into the mathematical foundations of these concepts more deeply, and find it important ...


62

I would suggest approaching your colleague in a humble and inquisitive way (especially since you're a junior member of the team). If you start the conversation with "your conclusions are wrong and here's why" you're going to set a combative tone for the rest of the meeting. There may be reasons that they interpreted the data the way they did that you're not ...


46

Yes. I would have a separate section of your paper entitled something like "Further exploratory analysis", report what you did and what you found, and note that until a study has been design to specifically test your hypothesis, it remains a hypothesis, but suggest that it might be an attractive target for further study.


42

You will not have a paper rejected for poor coding style. Particularly not in bioinformatics. Unless the paper is a tool development paper, the chance that a reviewer even looks at the code is not that high, and if they do, it will just be to check that its reasonable. In the outside case a reviewer might spot a bug, or poor assumption that actaully makes ...


40

General feedback rules apply. Here are some of them: There is no need to criticize any person. Stick to facts. Describe things, especially describe what you think about things, e.g. don't write "the assertion is not justified by the data" but "I can't see how this is explained by the data" (and probably give an example of some claim which you find equally "...


37

There are several possible factors here: given the relatively small number of points available, lumping can skew how grades are distributed, particularly if they're also awarded in whole number increments. (That is, there's not enough refinement in the model to separate things out.) Another issue is that the sample size is relatively small; twenty-four ...


37

Let me bring up a more serious issue that you don't ask about. Poor coding "style" can also mean poor "coding". And poor coding can hide errors, affecting the results. If your research results don't depend on the coding then it may not be an issue and there is probably no need to publish the code itself, beyond some description of it. But ...


35

YES. There are lots of reasons to and no reasons not to (unless you're under some kind of strange space/ink constraint). Here is an important and underappreciated reason why: Most of the people who make the kind's of R packages, in fact the people who made R itself, are other academics. Meaning: They didn't get paid specifically for the time they spent ...


33

Overall, I would suggest you err on the side of rather citing too many packages (with version numbers, please!), although odd quite probably is a borderline case. I'd rationalize this tendency as a bit of balance for all the people who use packages extensively but do not cite them. In general, I would certainly cite anything that saved me a non-trivial ...


33

Don't do this. Here is some random data with 21 experiments A-U, each one repeated 3 times. In both cases, the experimentwise means (indicated using red crosses) are identical, but the within-experiment standard deviations are very different (1.0 in the top graph and 0.2 in the bottom one). R code is below. Just seeing the experimentwise means is very ...


31

Echoing parts of the other answers, and some of the comments: first, it is inaccurate to declare omissions such as "proof of convergence" a "mistake". There simply is no absolute obligation to verify that all parts of the mathematics work as a physicist expects for other reasons. Yes, you or I and others might want to see the proof, that is, mathematical ...


29

I think you have a big misconception of what plagiarism is. Passing other people's work as your own is plagiarism; doing something and later discover that it was done before is not. It is not even unethical. The worst case is that your work is rendered redundant, but this depends on how different your settings and results are.


28

I did a Kernel density estimate plot of your data, shown below. You have a central lump of candidates with 4-5ish and a second lower lump of students who've done pretty badly.


26

It would be nice if statistics was always about the truth, and there was a right answer or method to every question. That simply isn't the case though, and many elements have room for debate. I'm an economist, and I've seen this first-hand in three different areas. First, I did some interdisciplinary empirical research where I worked with a sociologist ...


26

I'm sorry this happened to you. It is, unfortunately, all too common for those of us that have vital skills that are asked to contribute to research initated by others. What can be done at this stage? There are only realistically three options: The paper is retracted. Its possible it could be submitted for publication again with you as an author, but this ...


24

Yes (but it's usually an unconscious bias, and not openly stated). Many academics consider failing to become a professor actual "failure". An academic career is supposed to be a vocation. PhD students are supposed to be passionate about the topic, so much so that they'll want to continue to work on it after graduating. The best graduate students go ...


23

This is not an easy question, as are many other questions about coauthorship. To an extent, all answers will be opinion-based. I am in a similar position. I work in industry but advise many of my wife's clinical & biological psychology students on statistical matters. My personal cutoff point is somewhat later than yours seems to be. I'll happily ...


23

One major pitfall is going into analyzing the data without an a priori protocol to deal with outliers. Time to time, tension rises between analysts and investigators on whether a point should be removed or not. Investigator may wish to keep it because it drives the significant result; analyst may be anxious to keep it because, well, it drives the significant ...


21

"If I were a reviewer..." The easiest way to accomplish this is to frame the critique as something a reviewer would want to know. In this way, you are positioning yourself as a very valuable team player, who is protecting the team from an imaginary adversarial reviewer. I frequently give critiques like this: "if I were a reviewer, I would want evidence ...


21

Nearly all PhD students will never be professors. Some PhD programs might prefer to recruit PhD students who intend to become professors, but sensible PhD programs will realize that students who wish to work in industry are students capable of making a realistic plan. That is a good thing. Stating your intent to work in industry is unlikely to hurt your ...


20

Change the name if you like. Point it out prominently in your paper and code, possibly more than once (e.g. first mention in the main text and in the methods / supplement, of course also in the function documentation, etc.). The names of even common objects are changed for a variety of reasons. It happens, and people should be aware that names are usually ...


18

Males have historically outnumbered their female counterparts in the field of psychology, but this has changed in recent years. According to the American Psychological Association Psychology, once a man's profession, now attracts mostly women. Data from the 1986 APA report, "The Changing Face of American Psychology," and the National Science Foundation ...


18

If you want to present science as new, it has to be new. If the setting is sufficiently different, then you can present it as new, but you still need to cite the research that took part in other countries. For example, if there has been research in the relation between air quality and chocolate consumption in Canada, nothing stops you from performing the ...


17

Just adding to the other statistical analyses here...you can't really be sure that this sample doesn't come from a normally distributed population of grades from similar students in similar classes. Here's some more R code for analyses and their output: x=c(1.2,1.4,1.4,1.9,2.0,2.3,2.6,2.6,3.4,4.2, 4.2,4.3,4.6,4.6,4.8,4.8,4.9,5.3,6.0,6.2,6.4,7.1,7.8,7.8);...


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