Monthly Archives: March 2018

PMean: Starting a heron-i2b2-analytics repository

I am working on a CTSA grant to develop repeatable downstream pipelines that directly access i2b2 and CDM. In order to promote this work and encourage others to participate, I was given a repository site on github, kumc-bmi/heron-i2b2-analytics. Right now, it is just a shell, but here’s what I want to do with it, short term and long term. Continue reading

PMean: Recommended format for homework assignments

I’m teaching a couple of classes, Introduction to R and Introduction to SAS, and I’m finding that students will turn in homework a variety of different ways. I’m fine with this up to a point, but I think that I should encourage a simple uniform approach, because out in the real world, your boss or your clients will not appreciate a haphazard and disorganized approach. Here’s a suggested format for homework assignments that will (hopefully) get you in the practice of turning into things in an organized fashion. 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: Next stop, BMC Medical Informatics and Decision Making

I’m working part-time on a research grant and I want to publish some of the work I’ve done on this grant. The title of the paper tentatively is “Validating elastic net generated electronic health record breast cancer phenotypes against hospital tumor registries: a case control study.” My co-authors are Dan Connolly and Russ Waitman. I want to summarize the history of the effort so far and why I am considering the BMC Medical Informatics and Decision Making as the next place to submit the article. Continue reading

Recommended: Textbook Examples Applied Survival Analysis

I’m teaching an online workshop for The Analysis Factor on survival analysis. It’s not announced yet, and I have a LOT of work to do before it is ready. One thing that will save me time is that I am taking many of my examples from the excellent textbook, Applied Survival Analysis Second Edition. One nice perk of this book is that the helpful folks at UCLA have taken every textbook example, and written up code (with comments!) to reproduce the book’s results. With the exception of a few advanced methods in later chapters, where only one or two software packages have the right capability, the code is written in parallel in R, SAS, SPSS, and Stata. They also have links to the raw data at the publishers website, and datasets stored in SAS format and SPSS format. How nice! Browse around and you’ll find software code for all the examples in other popular statistics textbooks as well.

Warning! The R examples look like they are from the first edition, not the second edition. A small nitpick for an otherwise very nice resource. Continue reading

PMean: They want a short biography from me

I should have titled this page “I’m a Star!” because the School of Medicine’s Marketing and Communications Office is asking me questions to prepare a short biography to highlight the research I’m doing. Actually, that office is talking to over a hundred researchers in the School of Medicine, so I’m not really a star after all. But here are the questions that they started with. I’ll reply by email and they may get more information by email or a face-to-face interview. Makeup! Continue reading