Generating Meaningful Turaround Time Plots for Clinical Laboratory Medicine

 

The Problem

It is standard practice in Clinical Laboratory Medicine to monitor turn around times (TATs) for high volume tests like potassium (K), Troponin (Tn) and Hemoglobin (Hb). The term TAT is typically understood to mean “the time elapsed from when the doctor orders the test to the time the result is available in the Laboratory Information System (LIS)”. This of course does not take into account the lag between the result availability and the time when the physician logs in to view it and respond, but let’s just say that we are not there yet.

Traditionally, some dedicated soul would take .csv extracts from the LIS and do laborious things in Excel to generate the median TAT for the month for each test and each lab location for which they were responsible. Not only is it impossible to automate such a process, it is entirely manual and produces fairly uninformative output since (at least at our site) only medians were generated.

What really frustrates physicians is not where the median goes each month, it is the behaviour of, say, the 90th percentile of TAT or the outliers. These are the ones they remember.

R allows us to produce a much more informative figure in an automatable fashion. I provide here an example of a TAT figure for Hb with some statistical metric included.

Look at the Data

Let’s start by reading in our data and looking at how it is structured.

In this simplified anonymized data set we can see that we have 4497 observations with all of the necessary time points to calculate the turnaround times of the preanalytical and analytical processes. For the sake of this example, let’s focus on the order-to-file time.

We are going to need to handle the dates, for which there is only one package worth discussing, namely lubridate.

Basic Data Preparation

The first thing we need to do is to convert the order, collect, receive and result times to lubridate objects (i.e. time and date objects) so that we can do some algebra on them. We can see from the structure of myData that the order, collect, receive and result time points are in the format “YYYY-MM-DD HH:MM”. Therefore we can use the lubridate function ymd_hm() to perform the conversion.

Applying str() again to myData, you will see that the dates and times are now POSIXct, that is, they are now dates and times. This allows use to calculate the order-to-file TAT, we can do with the difftime() function exporting the result in minutes. We will also append the order-to-file (otf) TAT to the dataframe and do some quick sanity-checking.

Sanity Check

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This looks reasonable, so we can proceed with a TAT scatterplot.

Scatterplot

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Beautifying

This is kind-of problematic because we really want to focus on results in the 0-200 minute range. There are some wild-outliers as occurs in real life because of instrument down-time, add-ons, etc. We can leave this matter for the present. Notice that I have displayed every day on the x-axis because this will allow us to investigate any problems we see. So we will adjust the ylim and we will also make the plot points semitransparent by using hexidecimal colour codes followed by a fractional transparency expressed in hexidecimal. Black is “#000000” and “20” is hexidecimal for 32 which is 32/256 or 12.5% opacity.

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We’ll accept the fact that we know that there are a number of outliers. We could easily have a plot that displayed them or a tabular summary of them.

Now we will need to prepare the vector of daily medians, 10th and 90th percentiles to plot. We will loop through each day of the month and then calculate the statistics for that day.

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But this is not all that easy to look at. First, it’s kind-of ugly and second, if we find a problem date, we can’t read it from the figure. So let’s start by fixing the x-axis labels:

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To paint the central 80% as a band, we will need to use the polygon() function. I am going to write a function to which and x-vector and two y-vectors is supplied which then fills the area between then with a supplied color. Naturally, the three vectors must have the same length.

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Final Product

Now we should just finish it off with a legend.

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And that is a little more informative. There are many features you could add from this point – like smoothing, statistical analysis, outlier report. You could also loop over different tests, examine both the preanalytical and analytical processes at different locations, and produce a pdf report using MarkDown for all the institutions you look after.

-Dan

 

“The LORD detests dishonest scales, but accurate weights find favor with him.”
Proverbs 11:1

 

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