Tag Archives: Writing research papers

Recommended: LaTeX/Mathematics

You can incorporate very nice looking mathematical formulas in R Markdown fairly easily. The system relies on LaTeX for displaying formulas and is surprisingly easy to learn. But every once in a while you want to do something a bit exotic, like placing a “hat” in your equation. I’ve typically just done a quick Google search on something like “LaTeX hat symbol” and each different search yields a different website. Recently, I stumbled up a fairly comprehensive guide to displaying mathematical formulas in LaTex. It is published as an eBook.

Note: Some of the examples require additional libraries like amsmath and I haven’t figured out yet how to take advantage of these libraries in R Markdown. Continue reading

Recommended: A Systematic Examination of the Citation of Prior Research

This was a nice study, and shows a very easy model to adapt to other research problems. The authors were concerned that many reports of randomized clinical trials (RCTs) seemed to miss out on citing previous RCTs on the same topic. So they dug out a bunch of meta-analysis and looked at the bibliographies of the individual RCTs in those trials. The meta-analysis gives you a reasonably comprehensive history of the RCTs done on a particular topic, and you would think that any RCTs in the meta-analysis should have cited any other RCT in that same meta-analysis that preceded it by at least one year. But that happened very rarely. Continue reading

Recommended: In UC’s battle with the world’s largest scientific publisher, the future of information is at stake

The University of California (UC) is in the midst of a difficult negotiation with Reed Elsevier, a major publisher of research journals. The dispute relates to the traditional model of publishing where the author writes for a journal for free and the journal sells subscriptions to individuals and libraries. A newer publication model is Open Source, where the author pays a fee to get the article published, and then the article is made available for free to any and all readers. The UC library wants a large reduction in subscription fees and is threatening to cancel the Elsevier subscription and rely solely on open source journals. The issues are complicated and this article lays out both sides carefully. Continue reading

Recommended: TinyTeX: A lightweight, cross-platform, portable, and easy-to-maintain LaTeX distribution based on TeX Live

I’ve been using a version of LaTeX (MikTeX) for a couple of years, and it’s not bad. But when I heard about Yihui Xie’s R package, tinytex, I jumped at the opportunity to try it. Dr. Xie is the author of knitr, a package that makes it easy to create well documented R programs where the code and the output are gracefully merged. He created this new package, tinytex, because he felt that the current versions of LaTex had complex installation processes and forced you to choose between a minimal installation that couldn’t do anything useful and a full installation that was bloated with features you’d never use. I can’t say too much about the package yet except that he is right in that it is very easy to install. If I find out more, I’ll let you know. Continue reading

Recommended: Good Publication Practice for Communicating Company-Sponsored Medical Research: GPP3

Very little of my research fits into the category of company-sponsored medical research, but it is important to be aware of the special concerns and the extra oversight that this research requires. This article cover a consensus standard of guidelines that make a lot of sense, in my opinion, to avoid some of the recent controversies about research abuses. It is also a pretty good guideline, for the most part, for other medical research beyond company-sponsored research. Continue reading

PMean: The unthinking approach to borderline p-values

I ran across a nice discussion of how to write the results section of a research paper, but it has one comment about the phrase “trend towards significance” that I had to disagree with. So I wrote a comment that they may or may not end up publishing (note: it did look like the published my comment, but it’s a bit tricky to find).

Here’s what I submitted. Continue reading