Understanding the Issue with Inline Code in R Markdown and LaTeX

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As a technical blogger, it’s not uncommon to encounter unexpected errors when working with various programming languages, formatting tools, and libraries. In this article, we’ll delve into the world of inline code, R Markdown, and LaTeX to understand why they’re throwing an “unexpected symbol” error.

Background: R Markdown and LaTeX

R Markdown is a document format that allows users to create reports, presentations, and other documents with Markdown formatting. It’s widely used in data science, statistics, and programming communities for creating reproducible documents. LaTeX is a typesetting system that provides a set of markup commands for producing high-quality documents.

When combined with R Markdown, inline code can be formatted using Markdown syntax or LaTeX commands. The r package (R Markdown) integrates LaTeX with R, allowing users to create documents with mathematical equations and other advanced formatting options.

Understanding the Error

The error message “unexpected symbol” typically occurs when the interpreter encounters a character that doesn’t match any expected token. In this case, it seems like the issue is related to the way inline code is formatted in R Markdown.

To reproduce the error, let’s examine the provided code:

output: pdf_document: latex_engine: xelatex toc: true toc_depth: 2 number_sections: true df_print: kable fig_width: 7 fig_height: 6 fig_caption: true geometry: margin=1in header-includes:

- \usepackage[utf8]{inputenc}
\usepackage{booktabs}
\usepackage{fontspec}
\setmainfont{Avenir Light} # GFS Didot
\setsansfont{Raleway}

knitr::opts_chunk$set(echo = TRUE)

# Load Libraries
library(rio) # multiple format file import
library(dplyr)
library(tidyverse)
library(kableExtra) 
library(pander)
library(viridis)
library(ggplot2)

install_formats()

# Load Datasets
transcodeData &lt;- rio::import("Data/transcoding_mesurment.tsv", format = "tsv")
youtubeData &lt;- rio::import("Data/youtube_videos.tsv", format = "tsv")

# View DF Heads
options(knitr.kable.NA = "**") 

pander(head(transcodeData), caption= "Video Transcode Specifications\n")
# View structure
# str(transcodeData)
dim &lt;- dim(transcodeData)
dim[2]

noVideos &lt;- length(unique(transcodeData[,"id"]))

The problematic code snippet is:

dim &lt;- dim(transcodeData)
dim[2]
noVideos &lt;- length(unique(transcodeData[,"id"]))

Notice the use of < and > characters, which are not typical in R Markdown or LaTeX.

The Role of Knitr

Knitr is a package that integrates R with document formatting. It provides functions for creating documents, importing data, and managing output formats.

In this example, we’re using knitr’s opts_chunk function to set the echoing behavior:

knitr::opts_chunk$set(echo = TRUE)

This line enables code echoing in the document.

However, it seems like there’s a misconfiguration somewhere. Knitr uses LaTeX commands for formatting, and sometimes these commands can interfere with Markdown syntax or other packages.

A Closer Look at Knitr Configuration

Let’s take a closer look at knitr’s configuration options:

# Load Libraries
library(rio) # multiple format file import
library(dplyr)
library(tidyverse)
library(kableExtra) 
library(pander)
library(viridis)
library(ggplot2)

install_formats()

knitr::opts_chunk$set(echo = TRUE,  # Enable code echoing
                     latex_engine = "xelatex") # Specify LaTeX engine

Notice the latex_engine option. This specifies the LaTeX engine to use for rendering documents.

The Issue with `dim[2]`

Now that we’ve examined knitr’s configuration options, let’s take a closer look at the problematic line:

dim &lt;- dim(transcodeData)
dim[2]

The issue here is not just with the < and > characters but also with the syntax. In R Markdown, you would use dim() to get the dimensions of a data frame, like this:

dim(transcodeData)

Notice the difference? The first line uses parentheses (()) instead of angle brackets (< and >).

Fixing the Issue

To fix the issue, we need to identify where the problem is occurring. Based on our analysis, it seems like the problem lies with knitr’s configuration options.

Let’s try modifying the knitr configuration to see if that resolves the issue:

knitr::opts_chunk$set(echo = TRUE,
                     latex_engine = "xelatex",
                     pandoc_version = "2.15.0")

Notice the addition of pandoc_version. This specifies the version of Pandoc to use for rendering documents.

Conclusion

In this article, we explored the issue with inline code in R Markdown and LaTeX, specifically focusing on knitr configuration options. We analyzed the provided code snippet and identified the problematic lines that were causing the “unexpected symbol” error.

By understanding the role of knitr and its configuration options, we can take steps to resolve issues like this one. Remember to always check your configuration options carefully, especially when working with packages like knitr or Pandoc.

Additional Tips and Best Practices

Always use parentheses (()) instead of angle brackets (< and >), unless specifically instructed otherwise.
Make sure to check your knitr configuration options regularly to ensure they are correct and up-to-date.
Use knitr::opts_chunk$set(echo = TRUE) to enable code echoing in documents.

By following these tips and best practices, you can avoid common issues like the one we encountered here and create high-quality documents with ease.

Last modified on 2025-02-23