When discussing performance with colleagues, teaching, sending a bug report or searching for guidance on mailing lists and here on Stack Overflow, a reproducible example is often asked and always helpful.
What are your tips for creating an excellent example? How do you paste data structures from r in a text format? What other information should you include?
Are there other tricks in addition to using
structure()? When should you include
require() statements? Which reserved words should one avoid, in addition to
How does one make a great r reproducible example?
A minimal reproducible example consists of the following items:
- a minimal dataset, necessary to reproduce the error
- the minimal runnable code necessary to reproduce the error, which can be run on the given dataset.
- the necessary information on the used packages, R version, and system it is run on.
- in the case of random processes, a seed (set by
set.seed()) for reproducibility
Looking at the examples in the help files of the used functions is often helpful. In general, all the code given there fulfills the requirements of a minimal reproducible example: data is provided, minimal code is provided, and everything is runnable.
Producing a minimal dataset
For most cases, this can be easily done by just providing a vector/data frame with some values. Or you can use one of the built-in datasets, which are provided with most packages.
A comprehensive list of built-in datasets can be seen with
library(help = "datasets"). There is a short description to every dataset and more information can be obtained for example with
?mtcars where ‘mtcars’ is one of the datasets in the list. Other packages might contain additional datasets.
Making a vector is easy. Sometimes it is necessary to add some randomness to it, and there are a whole number of functions to make that.
sample() can randomize a vector, or give a random vector with only a few values.
letters is a useful vector containing the alphabet. This can be used for making factors.
A few examples :
- random values :
x <- rnorm(10)for normal distribution,
x <- runif(10)for uniform distribution, …
- a permutation of some values :
x <- sample(1:10)for vector 1:10 in random order.
- a random factor :
x <- sample(letters[1:4], 20, replace = TRUE)
For matrices, one can use
matrix(), eg :
matrix(1:10, ncol = 2)
Making data frames can be done using
data.frame(). One should pay attention to name the entries in the data frame, and to not make it overly complicated.
An example :
set.seed(1) Data <- data.frame( X = sample(1:10), Y = sample(c("yes", "no"), 10, replace = TRUE) )
For some questions, specific formats can be needed. For these, one can use any of the provided
as.someType functions :
as.xts, … These in combination with the vector and/or data frame tricks.
Copy your data
If you have some data that would be too difficult to construct using these tips, then you can always make a subset of your original data, using eg
subset() or the indices. Then use eg.
dput() to give us something that can be put in R immediately :
> dput(head(iris,4)) structure(list(Sepal.Length = c(5.1, 4.9, 4.7, 4.6), Sepal.Width = c(3.5, 3, 3.2, 3.1), Petal.Length = c(1.4, 1.4, 1.3, 1.5), Petal.Width = c(0.2, 0.2, 0.2, 0.2), Species = structure(c(1L, 1L, 1L, 1L), .Label = c("setosa", "versicolor", "virginica"), class = "factor")), .Names = c("Sepal.Length", "Sepal.Width", "Petal.Length", "Petal.Width", "Species"), row.names = c(NA, 4L), class = "data.frame")
If your data frame has a factor with many levels, the
dput output can be unwieldy because it will still list all the possible factor levels even if they aren’t present in the the subset of your data. To solve this issue, you can use the
droplevels() function. Notice below how species is a factor with only one level:
> dput(droplevels(head(iris, 4))) structure(list(Sepal.Length = c(5.1, 4.9, 4.7, 4.6), Sepal.Width = c(3.5, 3, 3.2, 3.1), Petal.Length = c(1.4, 1.4, 1.3, 1.5), Petal.Width = c(0.2, 0.2, 0.2, 0.2), Species = structure(c(1L, 1L, 1L, 1L), .Label = "setosa", class = "factor")), .Names = c("Sepal.Length", "Sepal.Width", "Petal.Length", "Petal.Width", "Species"), row.names = c(NA, 4L), class = "data.frame")
One other caveat for
dput is that it will not work for keyed
data.table objects or for grouped
dplyr. In these cases you can convert back to a regular data frame before sharing,
Worst case scenario, you can give a text representation that can be read in using the
text parameter of
zz <- "Sepal.Length Sepal.Width Petal.Length Petal.Width Species 1 5.1 3.5 1.4 0.2 setosa 2 4.9 3.0 1.4 0.2 setosa 3 4.7 3.2 1.3 0.2 setosa 4 4.6 3.1 1.5 0.2 setosa 5 5.0 3.6 1.4 0.2 setosa 6 5.4 3.9 1.7 0.4 setosa" Data <- read.table(text=zz, header = TRUE)
Producing minimal code
This should be the easy part but often isn’t. What you should not do, is:
- add all kind of data conversions. Make sure the provided data is already in the correct format (unless that is the problem of course)
- copy-paste a whole function/chunk of code that gives an error. First, try to locate which lines exactly result in the error. More often than not you’ll find out what the problem is yourself.
What you should do, is:
- add which packages should be used if you use any (using
- if you open connections or create files, add some code to close them or delete the files (using
- if you change options, make sure the code contains a statement to revert them back to the original ones. (eg
op <- par(mfrow=c(1,2)) ...some code... par(op))
- test run your code in a new, empty R session to make sure the code is runnable. People should be able to just copy-paste your data and your code in the console and get exactly the same as you have.
Give extra information
In most cases, just the R version and the operating system will suffice. When conflicts arise with packages, giving the output of
sessionInfo() can really help. When talking about connections to other applications (be it through ODBC or anything else), one should also provide version numbers for those, and if possible also the necessary information on the setup.
If you are running R in R Studio using
rstudioapi::versionInfo() can be helpful to report your RStudio version.
If you have a problem with a specific package you may want to provide the version of the package by giving the output of
packageVersion("name of the package").
How to write a reproducible example.
You are most likely to get good help with your R problem if you provide a reproducible example. A reproducible example allows someone else to recreate your problem by just copying and pasting R code.
There are four things you need to include to make your example reproducible: required packages, data, code, and a description of your R environment.
- Packages should be loaded at the top of the script, so it’s easy to see which ones the example needs.
- The easiest way to include data in an email or Stack Overflow question is to use
dput()to generate the R code to recreate it. For example, to recreate the
mtcarsdataset in R, I’d perform the following steps:
- Copy the output
- In my reproducible script, type
mtcars <-then paste.
- Spend a little bit of time ensuring that your code is easy for others to read:
- make sure you’ve used spaces and your variable names are concise, but informative
- use comments to indicate where your problem lies
- do your best to remove everything that is not related to the problem.
The shorter your code is, the easier it is to understand.
- Include the output of
sessionInfo()in a comment in your code. This summarises your R environment and makes it easy to check if you’re using an out-of-date package.
You can check you have actually made a reproducible example by starting up a fresh R session and pasting your script in.
Before putting all of your code in an email, consider putting it on Gist github . It will give your code nice syntax highlighting, and you don’t have to worry about anything getting mangled by the email system.