How to Suppress Output Warnings in R Markdown

When working in r programming sometimes it is necessary to suppress potential output warnings. This is particularly true when working with r markdown since it will run in a web browser. In this case, you are going to need to place an r code chunk after the yaml header in the final document there are several chunk options for carrying out this task.

Description

Within r markdown you will usually suppress messages using a code chunk What the following format.

“`{r setup, include=FALSE}
knitr::opts_chunk$set(warning = FALSE, message = FALSE)
“`
This will turn off the warnings coming from your r markdown file. You can also use the options function which has the format of options(warn = x) where x is minus one turns off warnings and x is minus zero turns them back on. In both cases, the warnings will be suppressed on output for your r markdown document. While the above code chunk will suppress messages in r markdown, the options function works in R Studio as well. This would give your program cross-platform usability. Suppressing these messages prevents them from showing up when the user is using your program in either format. This is a standing programming procedure for making a program user-friendly so you want to use it whether you are using r markup or our studio. Ultimately for a user, your program needs to run right, and these types of code help make it possible.

Explanation

There are many factors that can cause output warnings, but you want to deal with them when programming for others. Even if you are writing a program for yourself you may want to deal with them just because they can become annoying. Regardless of the platform that you are using you want to be able to avoid having unwanted messages coming up because users will become uncomfortable with your program if they see lots of warning messages.

Ideally, you are going to want something that is not platform-specific, so that your program can be moved to other platforms without having any problems. Suppressing warnings can be an essential part of preventing problems when your program is being run by a user rather than yourself. Warnings do not stop the program from running, they just let you know that there is a problem that you should address. Being able to suppress these warnings when they just get in the way is an important part of user-friendly programing.

Examples

Here are some examples of code that is used to suppress messages. There are four segments of code that illustrate the functionality of the options function. These illustrations include the pmax and options functions.

> pmax(1:7)
[1] 1 2 3 4 5 6 7

This first example illustrates using the pmax function in a manner that produces the same results but it does not produce warnings. It is not always this easy to avoid producing warnings.

> pmax(1:4, 1:7)
[1] 1 2 3 4 5 6 7
Warning message:
In pmax(1:4, 1:7) : an argument will be fractionally recycled

This example uses a variation on the pmax function in a manner that produces a warning message. Note that this version has an extra parameter that does not actually get used.

> options(warn = -1)
> pmax(1:4, 1:7)
[1] 1 2 3 4 5 6 7

This example includes the options function using the minus one value to suppress the warning message on this version of the pmax function. Note, that there are no warnings in this example.

> options(warn = -0)
> pmax(1:4, 1:7)
[1] 1 2 3 4 5 6 7
Warning message:
In pmax(1:4, 1:7) : an argument will be fractionally recycled

In this case, we use the options function to restore the warnings. As a result, when we run this version of the pmax function we get our warning message again.

Application

One reason for suppressing messages during runtime is to prevent package loading messages from coming up while the program is being used. This is particularly important if someone other than the programmer is using the program. However even if you are using it, having such messages come up can be a nuisance, as a result, you will want to suppress them. Furthermore, any warning messages that come up as a result of missing values should also be suppressed as a way of being user-friendly.

Suppressing warnings is probably a good idea for the programmer when someone else is going to be using your program. Even if as the programmer you are the end user, you will want to suppress warnings to prevent them from becoming a nuisance. If you only have a couple of regular warnings that come up, they may not bother you. If you have many coming up all the time, and even if it is not something that you can eliminate, suppressing them will still be a good idea.

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