Background As part of our lab accreditation requirements, we have to provide measurement uncertianty estimates for all tests at all hospital sites. As you might imagine, with thousands of testcodes in Sunquest LIS, getting all the coefficients of variation (CVs) represents a daunting task for the quality technologist to accomplish. ...
Background R dogma is that for loops are bad because they are slow but this is not the case in C++. I had never programmed a line of C++ as of last week but my beloved firstborn started university last week and is enrolled in a C++ intro course, so ...
MSACL Conference There are two RStats Data Science courses happening in Salzburg Austria on September 22–24, 2019 at the 6th annual MSACL Clinical Mass Spectrometry Conference. These courses are held twice annually, once in Europe and once in Palm Springs. Introductory Course The introductory course will be taught by Dan Holmes, MD ...
Background I like writing my academic papers in RMarkdown because it allows reproducible research. The cleanest way to submit a manuscript made in RMarkdown is using the LaTeX code that it generates using the YAML switch keep_tex = true. A minimalist YAML header would look like so: [crayon-5d640e2...
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 ... [Read more...]
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 ... [Read more...]
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, ... [Read more...]
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 ... [Read more...]
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 ... [Read more...]
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 ... [Read more...]
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 ... [Read more...]
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 ... [Read more...]
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 ... [Read more...]
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 ... [Read more...]
The Problem As Clinical Pathologists we work hard to create laboratory developed tests (LDTs) using liquid chromatography and tandem mass spectrometry (LC-MS/MS) that are robust, repeatable, accurate and have a wider dynamic range than commercial immunoassays. In our experience, properly developed LC-MS/MS assays are much less expensive and ...
Recently, while working on quantifying the inpatient workload volume of routine tests as a function of the day of the week, I needed to be able to count the number of Mondays, Tuesdays, etc in a time–interval so I could calculate the average volume for each weekday in a ... [Read more...]
Background I was honoured by a site visit by Drs. Yeo-Min Yun and Junghan Song of the Korean Society for Clinical Chemistry a few weeks ago. As both professors are on the organizing committee of the Cherry Blossom Symposium for Lab Automation in Seoul in Spring 2016, their primary motivation for ...
Regression Methods In this post we will be discussing how to perform Passing Bablok and Deming regression in R. Those who work in Clinical Chemistry know that these two approaches are required by the journals in the field. The idiosyncratic affection for these two forms of regression appears to be ...
Removing NA’s from a Data Frame in R The Problem Suppose you are doing a method comparison for which some results are above or below the linear range of your assay(s). Generally, these will appear in your spreadsheet (gasp!) program as ( y) or, in the case of our ...
The Problem We want to have a closer look at the time–dependence of turn around times (TATs). In particular, we would like to see if there is a significant trend in TAT over time (improvement or deterioration) and we would like the data to inform us of slowdowns and ...