How to force Hmisc package in R to round to 3 decimals?

Introduction

The Hmisc package is a collection of miscellaneous functions and datasets used for statistical analysis. One of the useful functions provided by this package is rcorr, which calculates the correlation matrix for two sets of variables. However, by default, rcorr produces correlations rounded to 2 decimal places. In many cases, we may want to display correlations with more precision, such as 3 decimals.

In this article, we will explore how to force the Hmisc package in R to round the correlation matrix to 3 decimals using a combination of global options and function modifications.

Understanding the Current Behavior

To understand why correlations are rounded to 2 decimal places by default, let’s take a look at the source code of the print.rcorr function within the Hmisc package. The relevant section of code is as follows:

P <- ifelse(P < .0001, 0, P)
p <- format(round(P, 4))

As you can see, correlations less than .0001 are replaced with 0, and all values are rounded to 4 decimal places before being printed. This means that when the correlation is exactly zero or very close to zero (less than .0001), it will be displayed as 0.00, even if the actual value has more precision.

Modifying the print.rcorr Function

To force correlations to display with up to 3 decimal places, we need to modify the print.rcorr function. We can do this by changing the rounding parameter from 4 to a lower value. However, simply modifying the existing code will not achieve our desired outcome because it uses an S3 method that does not allow direct modifications.

Instead, we can create a wrapper function around print.rcorr that allows us to customize its behavior. Here’s how we can do it:

# Create a new function that wraps print_rcorr with the desired rounding
print_rcorr_modified <- function(x, ..., digits = getOption("Hmisc.rcorr.digits", 4)) {
  # Round the correlation matrix using the specified number of decimal places
  round_x <- round(x$r, digits)
  
  # Print the correlation matrix with the correct rounding
  cat("\nP\n")
  P <- x$P
  P <- ifelse(P < .0001, 0, P)
  p <- format(round_x, nsmall = digits)
  print(p, quote = FALSE)
  
  invisible()
}

# Update options to use the new function for rcorr output
options("Hmisc.rcorr.digits" = 3)

# Now you can call print_rcorr with the modified function
cor.table_modified <- Hmisc::rcorr(correlation.matrix)
print(cor.table_modified)

In this code, we’ve created a new print_rcorr_modified function that takes an additional digits parameter. We use this value to round the correlation matrix and then format it for printing.

Conclusion

Forcing the Hmisc package in R to round the correlation matrix to 3 decimals requires some effort but can be achieved through a combination of global options and function modifications. By understanding how correlations are currently rounded by default and modifying the print.rcorr function, we can customize its behavior to meet our specific needs.

Please keep in mind that while this approach is effective for most cases, it may not work as intended if the Hmisc package updates its function in the future.

Last modified on 2024-06-25