Suppressing Warnings with Pipe Operator

The suppressWarnings() function in R is often used to suppress warnings emitted by functions. However, when using the pipe operator (%>%) to apply this function, it seems to ignore the suppression and continue printing warnings as usual.

In this article, we will explore why this behavior occurs and provide several solutions to work around this limitation.

Why suppressWarnings() doesn’t work with pipe operator

To understand what’s going on here, let’s delve into how R handles functions and pipes. The pipe operator (%>%) is a shorthand for the following code:

library(magrittr)

f %>% g(a, b)

is equivalent to

library(magrittr)

function() {
  f()
  g(a, b)
}

In this case, f() and g() are functions that take a and b as arguments. When we use the pipe operator, R calls f() first and then passes its output to g().

When it comes to suppressWarnings(), this function modifies the behavior of R when warnings occur but does not directly modify the output of the function being piped.

In the following code snippet:

library(magrittr)

c("1", "2", "ABC") %>% as.numeric()

as.numeric() is a function that attempts to convert its input into a numeric value. When as.numeric() encounters non-numeric values like "ABC", it throws warnings.

# Warning message:
# In function_list[[k]](value) : NAs introduced by coercion

This warning occurs because R is unable to coerce the string "ABC" into a numeric value.

Now, when we use suppressWarnings() with pipe operator:

c("1", "2", "ABC") %>% suppressWarnings(as.numeric())

suppressWarnings() attempts to silence warnings. However, since it doesn’t directly modify the output of as.numeric(), but rather its warning behavior, it effectively silences the warning.

However, when we apply suppressWarnings() after as.numeric():

c("1", "2", "ABC") %>% as.numeric() %>% suppressWarnings()

suppressWarnings() comes too late. The warning has already been emitted by as.numeric(), and there’s no way to silence it at this point.

The reason for this behavior is that warnings are not part of the objects being piped but rather a side effect of certain operations, such as coercion or division by zero. They are cast when they occur and cannot be passed from one function to another.

Workarounds

While suppressWarnings() doesn’t work with pipe operator directly, there are several other approaches you can take to silence warnings in your R code:

Using %T>%

One solution is to use the %T>% version of pipes, which allows you to modify options. Here’s an example:

library(magrittr)

c("1", "2", "ABC") %T>% {options(warn=-1)} %>% as.numeric()

In this case, we set warn=-1, which tells R to suppress warnings entirely.

Using purrr::quietly

Another solution is to use the quietly() function from the purrr package. This function wraps its argument in a way that prevents it from emitting warnings:

library(purrr)

c("1", "2", "ABC") %>% quietly(as.numeric())

You can also chain multiple operations together using map_dbl() and then extract the result with extract2():

library(purrr)

c("1", "2", "ABC") %>% map(quietly(as.numeric)) %>% map_dbl("result")

In this case, we use quietly() to prevent warnings from occurring while still passing the numeric values through. Finally, we extract the result with map_dbl().

Custom Pipe

There is a solution using custom pipes provided by @Benjamin:

c("1", "2", "ABC") %W>% as.numeric

This way, you can simply write code without worrying about warnings.

Conclusion

While suppressWarnings() doesn’t work with pipe operator directly in R, there are several other approaches that allow you to silence warnings and continue working with your data. The main takeaway here is that R handles functions and pipes differently than other languages, resulting in this behavior.

In conclusion, when dealing with functions like as.numeric() or any function that emits warnings, be sure to consider these alternative solutions before deciding on using suppressWarnings().

Last modified on 2024-02-16