Latex Math Mode in Hmisc Variable Labels Using compareGroups Table

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In this article, we will explore how to use the Hmisc package in R to assign variable labels that include LaTeX math mode. We will also discuss a workaround for using the compareGroups table from the foreach package, which exports variable names with a backslash before each dollar sign.

Introduction

The Hmisc package in R provides various functions for assigning variable labels and formatting output. One of its features is the ability to include LaTeX math mode in variable labels. However, when using the compareGroups table from the foreach package, this feature can cause issues with exported tables.

The Problem

The compareGroups table exports variable names as a vector of strings, which are then passed to the export2latex() function for LaTeX export. If any of these variable names include LaTeX math mode, it can result in an error, such as inserting a backslash before each dollar sign.

For example, consider the following code:

library(Hmisc)
library(compareGroups)

label(mtcars$mpg) <- "[\\frac{miles}{gallon}]"

tab <- createTable(
  compareGroups(data = mtcars,
                am ~ mpg)
)

export2latex(tab)

In this case, the variable name $\frac{miles}{gallon}$ is included in the table, which can cause an error when exporting to LaTeX.

The Solution

One possible workaround for this issue is to use the pixiedust package, which allows us to generate tables with custom formatting. Specifically, we can use the Hmisc::latexTranslate() function to sanitize the content of a cell and remove any LaTeX math mode.

Here’s an example code snippet that demonstrates how to create a table using pixiedust:

library(Hmisc)
library(compareGroups)
library(pixiedust)

label(mtcars$mpg) <- "[\\frac{miles}{gallon}]"

tab <- createTable(
  compareGroups(data = mtcars,
                gear ~ mpg + qsec)
)

tab_df <- 
  tab$descr %>% 
  tidy()

tab_head <- 
  c("", attr(tab, "ylevels"), "p.overall",
    "", sprintf("N=%s", tab$avail[1, -c(1, (ncol(tab$avail) - 0:1))]), "") %>% 
  matrix(nrow = 2, byrow = TRUE) %>% 
  tidy() %>% 
  setNames(names(tab_df))

dust(tab_df,
     float = FALSE) %>% 
  redust(tab_head, part = "head") %>% 
  medley_bw()

# Create an RMD file for generating the table
---
title: "Untitled"
output: pdf_document
header-includes: 
- \usepackage{amssymb} 
- \usepackage{arydshln} 
- \usepackage{caption} 
- \usepackage{graphicx} 
- \usepackage{hhline} 
- \usepackage{longtable} 
- \usepackage{multirow} 
- \usepackage[dvipsnames,table]{xcolor}

---

```r
library(Hmisc)
library(compareGroups)

label(mtcars$mpg) <- "[$\\frac{miles}{gallon}$]"

tab <- createTable(
  compareGroups(data = mtcars,
                gear ~ mpg + qsec)
)

# Create an RMD file for generating the table
dust(tab,
     float = FALSE) %>% 
   redust(attr(tab, "ylevels"), part = "head") %>% 
   medley_bw()

# Alternatively, you can use a function to sanitize the content of a cell
dust.createTable <- function(object, ...) {
  obj_df <- 
    object$descr %>% 
    tidy()
  
  # Sanitize the content of a cell using Hmisc::latexTranslate()
  obj_df %>% 
    mutate(latex = paste0("\\", latexTranslate(value), "\\"))
}

compareGroups(data = mtcars,
              gear ~ mpg + qsec) %>% 
  createTable() %>% 
  dust.createTable()

Conclusion

In conclusion, while using Hmisc package for assigning variable labels with LaTeX math mode can cause issues with exported tables from the compareGroups table, we have discussed a workaround using the pixiedust package to generate tables with custom formatting. We also provided an example of how to create a function to sanitize the content of a cell and remove any LaTeX math mode.

Additional Considerations

One additional consideration is that when generating tables with LaTeX math mode, it’s essential to ensure that the table format is correct. In this case, we used the longtable package for formatting the table, which ensures that the table has the correct layout.

Another option is to use a different table format or adjust the ylevels attribute in the createTable() function to avoid issues with LaTeX math mode.

It’s also worth noting that when working with tables generated from compareGroups, it’s essential to test the output thoroughly to ensure that the results meet your requirements.

Last modified on 2025-05-01