Week 6 - How to create better scripts

CHU0397 | National Taiwan Normal University

🎯 Goals

• Advanced scripts: How to use Markdown documents to share better scripts?

📊 Better and reproducible scripts with R Markdown

From raw script to functional: R Markdown

1. Create the file 📄
Go to New File > R Markdown. This moves you from raw code to a “living” document.

2. Configure (YAML) ⚙️
The header between --- controls your title, author, and output format (HTML/PDF).

3. Text + Code chunks 📝
Write text normally; insert Code Chunks ({r}) for analysis.

4. Run your codes ▶️
Use the green Play Button to test individual steps.

5. The final “Knit” 🧶
Click Knit to stitch everything into a polished report automatically!

::: {.column width = “45%”} ::: {.r-stack}

:::

:::

😱 Common problem

When you try to knit your R Markdown document into a PDF file, you may encounter this message:

sh: pdflatex: command not found

Error: LaTeX failed to compile Untitled.tex. See The R package tinytex - Helper Functions to Manage TinyTeX, and Compile LaTeX Documents - Yihui Xie | 谢益辉 for debugging tips. See Untitled.log for more info.
In addition: Warning message:
In system2(..., stdout = if (use_file_stdout()) f1 else FALSE, stderr = f2) :
error in running command
Execution halted

The solution

You need to install a package before creating the PDF document.

Here are the steps:

1. Run this line of code in the console block:

tinytex::install_tinytex()

It can take some time, up to 5 minutes.

2. Click one more time on “Knit to PDF”

It’s supposed to work. If it still doesn’t work, please contact me!

📊 R Markdown cheatsheet

You can find more about how to write R Markdown documents on this website:

Link to the cheatsheet

📝 In-class exercise!

Task list:

• Create a new Markdown document, and call it ScriptWeek5_Markdown.
• Use the script from last week, but adapt it to the Markdown format. Be creative!

📝 Assignment for next week

• Please comment each line of code from the script we wrote on Week 5.
• Finish transposing the raw script into a Markdown document, and knit to a PDF file.
• Upload the two documents on Moodle!