Blog Archives

Is the pain worth it?: Can Rcpp speed up Passing Bablok Regression?

September 9, 2019
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Is the pain worth it?: Can Rcpp speed up Passing Bablok Regression?

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 I thought I would try … Continue reading Is...

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Break up with Excel: Intro and Advanced R Data Science Courses at MSACL.org Salzburg Austria, September 21–23, 2019

August 30, 2019
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Break up with Excel: Intro and Advanced R Data Science Courses at MSACL.org Salzburg Austria, September 21–23, 2019

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 of the University … Continue reading Break...

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RMarkdown Template that Manages Academic Affiliations – docx or PDF output

August 26, 2019
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RMarkdown Template that Manages Academic Affiliations – docx or PDF output

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: Introduction However, when you want mutliple authors … Continue reading RMarkdown...

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Reproducible Research: Write your Clinical Chemistry paper using R Markdown

February 4, 2018
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Reproducible Research: Write your Clinical Chemistry paper using R Markdown

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...

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Mining Your Routine Data for Reference Intervals: Hoffman, Bhattacharya and Maximum Likelihood

September 5, 2017
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Mining Your Routine Data for Reference Intervals: Hoffman, Bhattacharya and Maximum Likelihood

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...

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Non-Linear Regression: Application to Monoclonal Peak Integration in Serum Protein Electrophoresis

August 28, 2017
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Non-Linear Regression: Application to Monoclonal Peak Integration in Serum Protein Electrophoresis

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...

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Compare Tube Types with R – Repeated Measures ANOVA

August 21, 2017
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Compare Tube Types with R – Repeated Measures ANOVA

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...

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Parse an Online Table into an R Dataframe – Westgard’s Biological Variation Database

August 14, 2017
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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...

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Determine the CV of a Calculated Lab Reportable – Bioavailable Testosterone

August 7, 2017
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Determine the CV of a Calculated Lab Reportable – Bioavailable Testosterone

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...

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Conditional Formatting of a Table in R

November 7, 2016
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Conditional Formatting of a Table in R

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...

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