How to remove warning messages in R Markdown document?

R Markdown is a powerful tool for creating reproducible reports and presentations in R. However when working with R code, it is common to encounter warning messages that can disrupt the flow of the document. These warning messages can be confusing to the reader and may hinder the overall quality of the document. In this article, we will discuss how to remove warning messages in R Markdown documents.

• R Markdown: A tool for creating reproducible reports and presentations in R Programming Language.
• Warning messages: Notifications generated by R that indicate a potential issue with the code.
• Knitr: A package used in R Markdown to compile and execute R code within the document.
• SuppressWarnings() function: A function in R used to temporarily suppress warnings in R code.
• opts_chunk function: A code chunk to turn off warning messages and messages for all code chunks in the document.

Using SupressWarnings()

Install and load the knitr package by running the following code. Wrap the code that generates the warning messages in the suppressWarnings() function, like this. Knit the R Markdown document as usual to generate the final output. The warning messages will not appear in the final output.

R

install.packages("knitr")
library(knitr)

suppressWarnings({
 # Code that generates warning messages
})

Using non-numeric Values in a Numeric Operation

The expression is mean(x), where x <- c(1, 2, 3, “a”). Since the mean function only works with numeric or logical values, the expression generates a warning message that the argument is not numeric or logical and returns NA. Hence this code generates the following warning message:

R

x <- c(1, 2, 3, "a")
mean(x)

Output:

Warning message:
In mean.default(x) : argument is not numeric or logical: returning NA

To suppress this warning message, we can wrap the code in the suppressWarnings() function:

R

suppressWarnings({
  x <- c(1, 2, 3, "a")
  mean(x)
})

Output:

[1] NA

NA or NaN values (Warning)

Since the logarithm of a negative number is undefined, the expression generates a warning message that NaNs (Not a Number) are produced and returns NaN.

R

log(-1)

Output:

Warning message:
In log(-1) : NaNs produced

To suppress this warning message, we can wrap the code in the suppressWarnings() function.

R

suppressWarnings({
  log(-1)
})

Output:

[1] NaN

By suppressing the warning, the output of the expression can be obtained without the distraction of the warning message. This is particularly useful when the warning message is expected and not relevant to the purpose of the report or presentation.

Argument Recycling (Warning)

R

x <- c(1,2,3)
y <- c(4,5)
z <- x + y

Output:

## Warning in x + y: longer object length is not a multiple of shorter object
## length

To suppress this warning, we can wrap the expression in suppressWarnings().

R

suppressWarnings({
  x <- c(1,2,3)
  y <- c(4,5)
  z <- x + y
})
z

Output

## [1] 5 7 7

Converting a character to a numeric value

R

a <- "abc"
b <- as.numeric(a)

Output

## Warning: NAs introduced by coercion

this warning is generated because R cannot convert a character string to a numeric value. To remove the warning, you can either convert the character string to a valid numeric value or use suppressWarnings() to suppress the warning message.

R

a <- "abc"
b <- suppressWarnings(as.numeric(a))
b

Output

## [1] NA

Note: In this case, the value of b will be NA, since R cannot convert the string “abc” to a numeric value.

Using opts_chunk

opts_chunk function to set global options for all code chunks in the document. The opts_chunk function is provided by the knitr package, which is used to process R code and generate output in R Markdown documents. To turn off warning messages and messages for all code chunks in the document, you can use the following code chunk after the YAML metadata at the top of the document.

knitr::opts_chunk$set(warning = FALSE, message = FALSE)

OR

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, warning = FALSE, message = FALSE)
```

This code chunk uses the $set method of the opts_chunk function to set the global options for all code chunks in the document. The warning option is set to FALSE to turn off warning messages, and the message option is also set to FALSE to turn off messages. By default, the value of these options is TRUE.

However, it is generally recommended to use suppressWarnings() instead of disabling all warning messages, as disabling warnings may hide important information that could indicate a problem with the code.

Conclusion

In conclusion, warning messages can sometimes be distracting or unnecessary in R Markdown documents. We discussed three methods to remove warning messages in R Markdown documents: using suppressWarnings() function, setting the warnings option to FALSE in YAML metadata, and using the knitr::opts_chunk$set() function to set global options for all code chunks in the document.

While suppressWarnings() and warnings option in YAML metadata can be used for individual code chunks, the knitr::opts_chunk$set() function is useful if you want to turn off warning messages and messages for all code chunks in the document. By applying these methods, you can control which warning messages are displayed and improve the readability of your R Markdown documents.