Abstract Background: This blog post is going to show you how to write a reproducible article in the field of clinical chemistry using R Mardkown. The only thing that will change for journal to journal will be the reference fomating and perhaps section numbering. The source code itself will be provided so that you can … Continue reading Reproducible...
Background Let me preface this by saying I am not making a recommendation to use the Hoffman method. Neither am I advocating for reference interval mining from routine data. There are many challenges associated with this kind of effort. That's for another post I think. However, I am going to how one does the calculations … Continue reading Mining...
Background At the AACC meeting recently, there was an enthusiastic discussion of standardization of reporting for serum protein electrophoresis (SPEP) presented by a working group headed up by Dr. Chris McCudden and Dr. Ron Booth, both of the University of Ottawa. One of the discussions pertained to how monoclonal bands, especially small ones, should be … Continue reading Non-Linear...
Background Sometimes we might want to compare three or four tube types for a particular analyte on a group of patients or we might want to see if a particular analyte is stable over time in aliqioted samples. In these experiments are essentially doing the multivariable analogue of the paired t-test. In the tube-type experiment, … Continue reading Compare...
Background From time to time I have wanted to bring an online table into an R dataframe. While in principle, the data can be cut and paste into Excel, sometimes the table is very large and sometimes the columns get goofed up in the process. Fortunately, there are a number of R tools for accomplishing … Continue reading Parse...
Background At the AACC meeting last week, some of my friends were bugging me that I had not made a blog post in 10 months. Without getting into it too much, let's just say I can blame Cerner. Thanks also to a prod from a friend, here is an approach to a fairly common problem. … Continue reading Determine...
Background There are a few ways to approach the problem of a conditionally formatted table in R. You can use the ReporteRs package's FlexTable() function, the formattable package, or the condformat package. These allow you to produce a conditionally formatted tables in HTML. You can also use xtable package and essentially program what you want … Continue reading Conditional...
The Problem In two previous posts, I discussed visualizing your turnaround times (TATs). These posts are here and here. One other nice way to visualize your TAT is by means of a heatmap. In particular, we would like to look at the TAT for every hour of the week in a single figure. This manner … Continue reading Make...
The Problem As you know in Clinical Chemistry, we are not always writing a major paper but sometimes just preparing a short-report to answer a technical question that we've encounted at work. For shorter papers, journals often have more stringent rules about how many figures you can submit and even sometimes forbid multipanelled figures. In … Continue reading Make...
Background Back in 2011 I was not aware of any tool in R for Passing Bablok (PB) regression, a form of robust regression described in a series of three papers in Clinical Chemistry and Laboratory Medicine (then J Clin Chem and Biochem) available here, here and here. For reasons that are not entirely clear to … Continue reading A...
