How to Call a R Script within R Markdown

In this article, we will discuss how to call R scripts from within an R Markdown document. This is a common requirement for many users who use R Markdown as their primary tool for creating documents that combine text and code.

Understanding the Basics of R Markdown

Before diving into the details of calling R scripts in R Markdown, it’s essential to understand the basics of R Markdown. R Markdown is a document format that allows you to write documents with R code embedded within them. The knitr package is used to render R code chunks in R Markdown documents.

What is a Code Chunk?

In R Markdown, a code chunk is a block of R code that is wrapped in triple backticks (```). Code chunks can be used to execute R code, display output, and include text. There are several types of code chunks available in R Markdown, including:

r: Used to display output from R code.
**`{}``: Used to create a code chunk that is not evaluated by default.
{r your_code_chunk, eval = TRUE, echo = FALSE}: Used to evaluate R code and display output in the document.

How to Call an R Script within R Markdown

Calling an R script from within an R Markdown document involves using a combination of knitr functions and file paths. In this section, we will discuss how to call two R scripts (A.R and B.R) from within an R Markdown document.

Step 1: Set the Working Directory

Before calling any R scripts, it’s essential to set the working directory. The working directory is the location where R looks for files and directories. In this case, we want to set the working directory to C:/Users/SQ/Documents/.

To set the working directory in R Markdown, you can use the following code:

# Set the working directory to C:/Users/SQ/Documents/
setwd("C:/Users/SQ/Documents/")

Step 2: Call an R Script using knitr::source()

Once the working directory is set, we can call an R script using the knitr::source() function. This function takes a file path as an argument and executes the code in that file.

To call an R script using knitr::source(), you can use the following code:

# Call A.R using knitr::source()
knitr::source(file.path("A.R"), local = TRUE)

Step 3: Call an R Script Using read_chunk()

In addition to calling an R script using knitr::source(), you can also call it using the read_chunk() function. This function takes a file path as an argument and executes the code in that file.

To call an R script using read_chunk(), you can use the following code:

# Call B.R using read_chunk()
read_chunk(file.path("B.R"))

Tips and Best Practices

Here are some tips and best practices to keep in mind when calling R scripts from within an R Markdown document:

**Use knitr::source() instead of knitr::knit_global():knitr::knit_global() is not necessary when using the knitr::source() function.
Set the working directory before calling an R script: Setting the working directory before calling an R script ensures that the file paths are correct.
Use file.path() to construct file paths: The file.path() function helps ensure that file paths are correct and consistent.

Conclusion

In this article, we discussed how to call R scripts from within an R Markdown document. We covered topics such as setting the working directory, calling an R script using knitr::source(), and calling an R script using read_chunk(). We also provided tips and best practices for successful code chunk creation in R Markdown documents.

Common Issues and Solutions

Here are some common issues that you may encounter when calling R scripts from within an R Markdown document, along with their solutions:

knitr::source() not found: Make sure that the knitr package is installed and loaded in your R Markdown document.
File path errors: Ensure that file paths are correct and consistent. Use file.path() to construct file paths.
Output not displayed correctly: Check that output is being displayed correctly by verifying that it is written to the console or displayed in a chunk.

Troubleshooting Code Chunk Issues

Here are some common issues that you may encounter when creating code chunks, along with their solutions:

r environment not defined: Make sure that the r environment is defined in your R Markdown document.
Chunk output not displayed correctly: Check that output is being displayed correctly by verifying that it is written to the console or displayed in a chunk.
Code execution errors: Check that code is executed correctly by verifying that output is correct and error messages are displayed.

Common Code Chunk Types

Here are some common types of code chunks available in R Markdown:

r: Used to display output from R code.
{}: Used to create a code chunk that is not evaluated by default.
{r your_code_chunk, eval = TRUE, echo = FALSE}: Used to evaluate R code and display output in the document.

Additional Resources

Here are some additional resources that you can use to learn more about calling R scripts from within an R Markdown document:

R Markdown documentation: The official R Markdown documentation provides comprehensive information on creating code chunks, setting working directories, and more.
Knitr documentation: The Knitr documentation provides detailed information on using the knitr package to create R Markdown documents with code chunks.

Last modified on 2025-03-06