YAPOEH! (Yet another post on error handling)

[This article was first published on R | Adi Sarid - Personal Blog, and kindly contributed to R-bloggers]. (You can report issue about the content on this page here)
Want to share your content on R-bloggers? click here if you have a blog, or here if you don't.

Error catching can be hard to catch at times (no pun intended). If you’re not used to error handling, this short post might help you do it elegantly.

There are many posts about error handling in R (and in fact the examples in the purrr package documentation are not bad either). In this sense, this post is not original.

However, I do demonstrate two approaches: both the base-R approach (tryCatch) and the purrr approach (safely and possibly). The post contains a concise summary of the two methods, with a very simple example.

In this post I’m assuming you’re familiar with the basic concepts of functional programming.

A simple example for a function with errors

Let’s analyze a very simple function which divides number by 2. The function should return an error if its input is not an actual number, otherwise it will return number/2. This function looks like this:

divide2 <- function(number){
  
  # make sure the input is numeric (otherwise yield an error)
  if (!is.numeric(number)) {
    stop(paste(number, "is not a number!"))
  }
  
  # everything is fine, return the result
  number/2
}

divide2(10)
## [1] 5
divide2(pi)
## [1] 1.570796

But trying a string will yield an error:

divide2("foobar")
Error in divide2("foobar") : foobar is not a number!

Where is the problem?

What happens if we have a dataframe (or a list, or any other object for that matter) and we want to try to divide numbers within that object? Invalid values might crash our attempt completely.

For example, this loops through two values (10 and \(\pi\)) and yields their division by 2.

library(purrr)
map(list(10, pi), divide2)
## [[1]]
## [1] 5
## 
## [[2]]
## [1] 1.570796

But the next version fails completely, because it tries to loop through “foobar” which cannot be divided.

map(list("foobar", 10, pi), divide2)
Error in .f(.x[[i]], ...) : foobar is not a number!

No matter where we place the invalid value “foobar”, it will fail our code completely, and we get nothing.

The solution: a safely/possibly wrapper

Fortunately, there are very simple wrappers which can help us handle the errors elegantly. These are the two functions from the purrr package: safely and possibly.

We’ll first demonstrate the simpler version, possibly. It allows us to replace errors with a chosen value. Since we expect a number, let’s replace errors with NA_real_ (which is like saying an unknown value which is a real number).

possibly_divide2 <- possibly(divide2, otherwise = NA_real_, quiet = TRUE)

The quiet = TRUE argument is just so errors will not be printed during the loop. Now we are ready to try our error safe variation.

possibly_out <- map(list("foobar", 10, pi), possibly_divide2)
possibly_out
## [[1]]
## [1] NA
## 
## [[2]]
## [1] 5
## 
## [[3]]
## [1] 1.570796

We can also use unlist to turn the output into a simple vector, i.e. unlist(possibly_out) will yield the vector NA, 5, 1.5707963.

The safely variation has some more strength into it, since it also provides the error messages. The output is slightly more complex though.

safely_divide2 <- safely(.f = divide2, otherwise = NA_real_, quiet = T)
safely_out <- map(list("foobar", 10, pi), safely_divide2)
safely_out
## [[1]]
## [[1]]$result
## [1] NA
## 
## [[1]]$error
## 
## 
## 
## [[2]]
## [[2]]$result
## [1] 5
## 
## [[2]]$error
## NULL
## 
## 
## [[3]]
## [[3]]$result
## [1] 1.570796
## 
## [[3]]$error
## NULL

Following the approach suggested in the documentation of safely (in the examples section), we can use transpose() and simplify_all() to arrange the output.

simply_safe <- safely_out %>% 
  transpose() %>% 
  simplify_all()

simply_safe$result  # for the output values
## [1]       NA 5.000000 1.570796
simply_safe$error  # for the error messages
## [[1]]
## 
## 
## [[2]]
## NULL
## 
## [[3]]
## NULL

For comparison’s sake, how would you tryCatch it?

The function tryCatch is a base-R approach for error handling. The concept is similar but the syntax is different. Here is an example of how to build a safe divide2 function with tryCatch:

try_divide2 <- function(number){
  tryCatch(expr = {
    divide2(number)
  }, 
  error = function(e){
    NA_real_
  }
  )
}

map(list("foobar", pi, 10), try_divide2)
## [[1]]
## [1] NA
## 
## [[2]]
## [1] 1.570796
## 
## [[3]]
## [1] 5

As said - same output, different syntax. Choose your approach. As an appetizer, the same works with base-R functional programming as well. For example, with lapply it will look like this:

lapply(list("foobar", pi, 10), try_divide2)
## [[1]]
## [1] NA
## 
## [[2]]
## [1] 1.570796
## 
## [[3]]
## [1] 5

Bonus: a benchmark

Before going off on your merry, error handled way, I also provide a short comparison between safely, possibly, and tryCatch.

Let’s assume a data set with 20% errors. For simplicity, we’ll use a modified log instead of our divide2 (similar to the example provided in purrr’s documentation). It makes sense to fail log in an all numeric vector (yield an error if there is a negative value). Since a negative log is NaN (not an error but rather a warning) I’m creating an error_prone_log function.

library(tibble)
library(dplyr)
library(microbenchmark)
library(ggplot2)

error_prone_log <- function(x){
  if (x < 0){
    stop("Negative x")
  }
  
  log(x)
}

safe_log <- safely(error_prone_log, otherwise = NaN, quiet = T)
possible_log <- possibly(error_prone_log, otherwise = NaN, quiet = T)
tryCatch_log <- function(x){
  tryCatch(expr = error_prone_log(x),
           error = function(e){
             NaN
             })
}

set.seed(42)
test_values <- sample(
  c(runif(n = 80, min = 0, max = 100),
    runif(n = 20, min = -100, max = 0)),
  size = 100, replace = FALSE)

bench_results <- microbenchmark(map(test_values, safe_log),
                                map(test_values, possible_log),
                                map(test_values, tryCatch_log), 
                                times = 1000)

gt::gt(summary(bench_results)) %>% 
  gt::fmt_number(columns = 2:7, decimals = 2)
expr min lq mean median uq max neval
map(test_values, safe_log) 2.89 3.28 3.50 3.34 3.42 11.94 1000
map(test_values, possible_log) 2.62 3.14 3.35 3.21 3.28 7.62 1000
map(test_values, tryCatch_log) 1.96 2.29 2.52 2.33 2.38 77.12 1000
autoplot(bench_results) + 
  ggtitle("Comparison of safely, possibly, and tryCatch") + 
  coord_flip(ylim = c(1.5, 15))

As can be seen from the benchmark’s results, there is no doubt about it: tryCatch is the fastest. The purrr functions safely and possibly take longer to run. In my opinion though they are slightly more convenient in terms of syntax.

In addition, the safely variation allows us to retrieve the error messages conveniently for later examination. Again, this capability comes with a price when compared to tryCatch, but it is roughly the same run time when compared to possibly.

Conclusion

When you have a long looping process which is prone to errors, for example a pricey web API call or a really large data set, you should aim to catch and handle errors gracefully instead of hoping for the best.

If you really need to be efficient, it’s probably worth while to tryCatch, and if your looking more for ease of use and code readability you should use possibly. In case you need to examine the error messages more thoroughly, use safely.

Good luck hunting down the errors!

To leave a comment for the author, please follow the link and comment on their blog: R | Adi Sarid - Personal Blog.

R-bloggers.com offers daily e-mail updates about R news and tutorials about learning R and many other topics. Click here if you're looking to post or find an R/data-science job.
Want to share your content on R-bloggers? click here if you have a blog, or here if you don't.

Never miss an update!
Subscribe to R-bloggers to receive
e-mails with the latest R posts.
(You will not see this message again.)

Click here to close (This popup will not appear again)