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Portfolio R for Medical Diagnostics students

The Portfolio Assignment

As the R part is only 1 EC for Medical Diagnostics students, the R part is considerably shorter. It consists only of the Base R part and an Excel import of lab data. Tidyverse will be omitted.

Thus it consists of the following parts:

• R Basics
• R Basics Exercises
• R Basics Solutions
• R Basics Extra Exercises
• R Basics Extra Solutions

And for loading data from an Excel file:

• R data import

For the import, just focus on the part about readxl.

Your Workflow: Step-by-Step

Follow these steps to complete your portfolio effectively:

• Take a lab notebook from a previous theme/module that contains a (linear) calibration curve (or calibration line). Note: it must be your own lab notebook!
• Ensure that you share this lab notebook with your instructor (collaborate).
• Export you lab notebook as pdf file.
• Include your pdf file in your portfolio.
• Transfer the data from the lab notebook into an Excel file (xlsx file).
• Load this data into R as a data frame using the readxl function.
• Calculate the minimum, median, and maximum of your data points. Do this for both X and Y.
• Plot your calibration curve using base R.
• Add a linear model to your plot.
• Ensure your plot has a good title and proper axis labels including quantities and units.
• Put everything in a neat RMarkdown document.
• Create a proper YAML front matter at the top of an R Markdown (.Rmd) file. See below for an example.
• Knit your RMarkdown file to HTML.
• Create a zip file of your R portfolio including the Excel file with the data, the pdf file of your lab notebook, the RMarkdown file of your analysis and the knitted HTML document.
• Upload this zip file to Brightspace.

Example YAML:

---
title: "Calories Food"
author: "Jane Doe"
date: "2025-04-10"
output: 
  prettydoc::html_pretty:
    theme: cayman
    highlight: github
---

Note that the YAML front matter code block should start and end with 3 dashes.

The prettydoc package is required. You can install it using:

install.packages("prettydoc")

And you can load it using:

library(prettydoc)

Good luck! 🍀

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