Understanding R Markdown Code Execution in Script vs Knit Mode
As a technical blogger, I’ve encountered numerous questions regarding the execution of R Markdown code in script mode versus knit mode. In this article, we will delve into the world of R Markdown and explore the differences between running R code in a script versus knitting it to HTML.
What is R Markdown?
R Markdown is a markup language that combines the power of R with the convenience of Markdown. It allows users to write documents using a syntax similar to Markdown, but with the ability to include R code directly into the document. This enables users to create interactive documents that can be easily shared and collaborated on.
Script Mode vs Knit Mode
When running R Markdown in script mode, the code is executed by the R interpreter directly. This means that any errors or warnings generated during execution are displayed in real-time, allowing for immediate feedback and debugging.
On the other hand, when knitting R Markdown to HTML using the rmarkdown package, the code is compiled into HTML before being rendered. In this mode, any errors or warnings generated during compilation are typically ignored or masked, and instead, the document is rendered with a " compilation error" message.
The Problem
In the given Stack Overflow post, the user encountered an issue where R Markdown code executed successfully in script mode but failed to compile when knitted. Specifically, the line predObj <- crawl::crwPredict(object.crwFit = crawl_models_list[[d$segmentid[1]]], predTime = d$MidTime, speedEst=TRUE, flat=TRUE) generated an error message indicating that there was an unexpected symbol.
The Solution
To resolve this issue, the user removed a part of the code from the ddply function call. Specifically, they removed the line d= bhv_df[bhv_df$segmentid == bhv_df$segmentid[1],. By doing so, they were able to compile the document successfully.
However, as we will see below, this solution may not be entirely correct, and there are other potential reasons why the code may fail to compile in knit mode.
Why Does Code Execution Matter?
When running R Markdown in script mode versus knit mode, it’s essential to understand that code execution is handled differently. In script mode, errors are displayed immediately, allowing for real-time debugging and feedback. On the other hand, when knitting to HTML, compilation occurs before rendering, and any errors generated during compilation may be ignored or masked.
The Importance of Code Validation
In order to avoid issues like the one in the Stack Overflow post, it’s crucial to validate code execution before compiling to HTML. This can involve running individual R scripts or using tools like rmarkdown::render() to validate compilation before knitting the document.
How to Validate Code Execution
To ensure that your R Markdown code executes correctly, follow these steps:
- Run your R script directly using the R interpreter.
- Check for any errors or warnings generated during execution.
- Validate that your code produces the expected output.
- Use tools like
rmarkdown::render()to validate compilation before knitting the document.
Best Practices for Writing R Markdown
To avoid issues like the one in the Stack Overflow post, follow these best practices when writing R Markdown:
- Keep your code concise and readable.
- Validate code execution using tools like
rmarkdown::render(). - Test your code thoroughly before compiling to HTML.
- Use proper Markdown syntax for formatting and rendering.
Conclusion
In this article, we explored the differences between running R code in script mode versus knit mode. We also discussed the importance of code validation and provided best practices for writing effective R Markdown documents. By following these guidelines and taking steps to validate your code execution, you can ensure that your R Markdown documents compile successfully and provide high-quality output.
Additional Resources
Last modified on 2023-11-12