Friday, September 15, 2017

Career preparation for graduate students.

This is an important issue, and I have already spent 4 news items on this. A recent publication in PLOS ONE investigated some of the strategies and resources PhD students (and postdocs) use for non-academic jobs. This is very important because more than 80% of our graduate students end in these non-academic jobs (although these numbers also includes MSc students). I should not have been surprised, but there are sociological theories and active research programs around this issue, resulting in publications where I am only comfortable reading the abstract and discussion, and hoping that the reviewers did their job. The crux from the results section to me was this section:

Interestingly, our results also show that a trainee’s perception of high program support for career goals had direct and significant effects on their career development search efficacy, while perceived advisor support was not significant at all. It may be that perceived program support for career goals enables trainees to develop a broader support base within their graduate programs (as opposed to being driven by dissatisfaction with one’s advisor).
This presents a glass half full/empty perspective on career preparation: a grad student readiness does not depend on an advisor's experience that will vary wildly between faculty members, but more on the support provided by the department/college/university. And since universities are explicitly tasked to prepare their graduates for the job market, there is some incentive to address any shortcoming institutionally. The question, of course, still remains if Integrative Biology and the university as a whole provides sufficient support. So is your glass half full, or half empty? Let me know.

Thursday, August 24, 2017

Reviewers should (also) be paid by publishers

Stephen Heard touched on a controversial issue in his latest blog post: Can we stop saying reviewers are unpaid? This (contrarian?) point of view resulted in some push-back in the comments, and on other blogs (e.g. Let's keep saying it, and say it louder: REVIEWERS ARE UNPAID by Mick Watson). I agree with most of Stephen Heard's points, and also with his updated point "publishers (mostly) don't pay for reviews". Where I disagree with him (there has to be at least one disagreement, because why otherwise waste digital bandwidth on writing this?), is that "reviewers are (mostly) paid" is actually an important admission.

I struggled to find a useful analogy to explain my unease with his admission, and it suddenly dawned on me. Several years ago, I read a blog post by Alex Bond on Why volunteer field techs are a bad idea. I hope I summarize their (further developed with Auriel Fournier in a published opinion piece that received a lot of pushback) arguments correctly with these points:

  • it is an essential part of the research process, so it should be rewarded accordingly;
  • not paying reduces the field tech's value, and thus "the professionalism of science as a whole";
  • prevents underprivileged scientists from participating;
  • financial restrictions, tradition, and CV building for the field techs are not good enough justifications in light of these criticisms.
The analogy with peer review is immediately obvious in the first line: it is an essential part of the scientific process, so it should be rewarded. Stephen Heard's argument is that reviewers are being rewarded (paid). What the analogy with volunteer field techs exposes, though, is that it is important to look at who benefits from the work. In the field tech case, it is first the scientist who got funding for the study that benefits from the volunteer work, and then in a second step science as a whole. In the peer review case, what I think Stephen Heard overlooks is that publishers benefit first, and science as a whole only in a second step. 

And this benefit to publishers is important. A recent Science paper by Gretchen Vogel and Kai Kupferschmidt report on a quick back-of-the-envelop type of calculation:
"Collectively, the world's academic libraries pay some €7.6 billion in subscription fees for access to between 1.5 million and 2 million new papers annually, or between €3800 and €5000 per paper, according to an estimate by the Max Planck Society."
While the net benefit to the publishers will be lower, of course, nobody can argue that publishers do not benefit directly from the reviewers. And publishers do not pay reviewers, directly or indirectly. Yes, society as whole pays scientists partly for their many contributions, but eliminating the publishers from that argument is wrong. If we make the analogy with the volunteer field tech case again, that would be similar to imagining a PI flush with money saying that she will not pay her field tech because the "pay" provided by the experience will improve his CV and his changes for a scholarship or job. Or more succinctly: Volunteer field techs are (mostly) paid.

If that above scenario raises some problems, then arguing that reviewers are (mostly) paid, is not the "right" statement to ponder. If you agree that in the above scenario that the field tech should receive monetary compensation for his contribution (or be paid) from the PI, and that that is the important debate, then I think that "reviewers should (also) be paid by publishers" is the more important debate to have.

Tuesday, August 15, 2017

Science and passion

Since starting these news items, we have discussed themes related to mental health issues, their causes, and some solutions. Ardon Schnorr, a Biology PhD student at Carnegie Mellon University wrote a very powerful article around this theme that touches on a lot of issues surrounding this problem: It is a must read for any graduate student. And if you are inspired by the positive effects of science communication, but do not know where to start, you can always start with the University of Guelph Let's Talk Science outreach program.

Wednesday, July 19, 2017

Blaming the victim, follow-up.

As expected, I was not the only one providing some push back to the Nature Jobs article I discussed previously. Together, they make reasonable suggestions, both towards the supervisor, and the university. The first one by D. A. McDonald acknowledges that supervisors should be open aware of all aspects of their graduate students' lives ("what they do when they are not in the lab"). The second one by D. Mehta and K. Vavitsas point out institutional resources that can help tackle one of the root problems ("providing more courses and resources to train principal investigators in management and leadership"). I wonder what the participation rate would be for UoG faculty if the university would offer these types of courses?

Tuesday, June 13, 2017

Problem in R: how to create a .Rprofile that does not hide important information ...

... but still is specific to each R script file. For instance, a lot of R users in our group load their packages at the top of their R scripts. Often, these packages are the same, but sometimes they add a different one for a specific type of analysis. I use the tidyverse all the time, and in some analyses vegan. A school of thought would be to automatically add these package to the start up using a .Rprofile file. Others would argue that this makes the code less reproducible, since some essential pieces of information are hidden from the R script file.

But what if you could have both? All the boilerplate stuff such as loading packages at the top of each R script file, but execute them automatically when you open that script file? I think I have found a solution to that mythical beast. I googled for it, but could not find anything similar, so that is why I provide my code here. Hopefully somebody else will find this useful, or point me to other, more elegant, solutions that I can incorporate in my own code.

How to create a generic but specific profile file that reads the beginning of each R file  

Copy this profile file either in your home directory or in each working directory. A quick google on .Rprofile and your OS will help you out for the advantages/disadvantages of these two approaches. However, I created this profile file to ensure that it will read all your script files within a folder, and execute them until it finds the line "# Startup ends here".

I assume that this will be mainly for loading libraries, so I specified the script to only read the first 30 lines, but you can increase/decrease this for your coding practices. I also made it recursive, so it will read all the script files within the folder structure, but you can change this too.

And I have also added some encouragement, that has the secondary objective that you can see if the .Rprofile code worked correctly.

You can find the code here on github:

Snippet usage  

This works nicely with the new snippet I created. In RStudio > Preferences > code > Edit Snippets... copy the lines below, and save the updated snippets file.

snippet stup
## ${1:title}
## Karl Cottenie
`r paste("##", Sys.Date())`
# Add as much code here that you want to execute each time your script file is loaded.  
# Startup ends here 

Now if you type "stup" at the beginning of a file, it will paste the above code, you can add the title of your script file, and when you press your tab key the cursor will jump to the library command, and you can for instance add tidyverse, or ggplot, or whatever you normally use. The snippet will automatically add the date, of course you can/should change the author :-)

Problems with my code, other options?  

Just let me know, because there are probably edge cases I did not think about, and more elegant solutions that I will not find on my own.