Richard Sprague

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Testing my blood glucose

Richard Sprague / 2017-11-27


If you’re diabetic, blood glucose testing is something you live with daily, but it’s good for the rest of us to test from time to time as well. That’s what I did this morning using a Contour Next EZ blood glucose monitor, which at $10 (or free with a doctor’s prescription and a purchase of 100 strips) is the cheapest device I know.

Serious testers will want something that does continuous monitoring and connects to your computer for easy download, but I just wanted something simple and cheap. If you can get a doctor to prescribe it, I’ve heard the Dexcom CGM device is the way to go, but this is a simple and cheap way to get started and I just want to demonstrate briefly how easy it is to generate a glucose level graph in R.

To make it interesting, I tested myself immediately after waking up and then drank a glass of sugar water. After waiting another half hour, I tested again, then again at two more intervals after that. I tracked my blood glucose levels and then wrote the following R script.

First, load the prerequisite libraries. It’s super-easy if you use Tidyverse. In this simple example I won’t use any of the Tidyverse features other than graphics, so all of this extra loading is unnecessary, but I think it’s a good idea to get used to treating Tidyverse as an extension of your normal R environment. It doesn’t take much to load it, so why not? Just ignore all the “Loading” and “conflicts” messages.

library(tidyverse)
## Loading tidyverse: ggplot2
## Loading tidyverse: tibble
## Loading tidyverse: tidyr
## Loading tidyverse: readr
## Loading tidyverse: purrr
## Loading tidyverse: dplyr
## Conflicts with tidy packages ----------------------------------------------
## filter(): dplyr, stats
## lag():    dplyr, stats

Next I’ll set up my data. These are actual numbers taken from the glucose monitor. As you can see, I’m creating a simple data frame in R code. If this were a full example, I’d have the data in Excel or as a CSV file and then load it using read_excel(), but I don’t want to deal with that now, so I’ll construct the data frame by hand:

glucose <- c(85,141,75,74)
times <- c(0,30,30+45,30+45+20)
measures <- data.frame(glucose=glucose,time=times)
measures
##   glucose time
## 1      85    0
## 2     141   30
## 3      75   75
## 4      74   95

To plot it, I can simply run the ggplot function below, which will generate the default plot style or “theme”. But to make it look a little more cool, I can use the ggthemes library, which gives you a choice of themes, everything from “fivethirtyeight” to “tufte” and “wsj”. Here I’ll make my final result look like one of those charts you see in The Economist newsmagazine.

library(ggthemes)
theme_set(theme_economist())

ggplot(data=measures,aes(x=time,y=glucose)) + geom_line() +
  ggtitle("My Glucose Levels") + 
  xlab("Time (min after waking)") +
  ylab("Glucose (mg/dL)") +
  annotate("text",x=10, y = 68,  label = "Drink Sugar Water", color = "red") +
  annotate("segment", x = 00, xend = 0, y = 70, yend = 80, colour = "red", size=1, arrow=arrow())

That’s it. Although this was a very simple – some would say trivial – example of graphing in R, I hope it’s helpful for absolute beginners who want to know how to get started.