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 dput()
, dump()
or structure()
? When should you include library()
or require()
statements? Which reserved words should one avoid, in addition to c
, df
, data
, etc.?
How does one make a great r reproducible example?
Basically, a minimal reproducible example (MRE) should enable others to exactly reproduce your issue on their machines.
Please do not post images of your data, code, or console output!
A MRE consists of the following items:
library
s, the R version, and the OS it is run on, perhaps a sessionInfo()
set.seed()
) to enable others to replicate exactly the same results as you haveFor examples of good MREs, see section "Examples" at the bottom of help pages on the function you are using. Simply type e.g. help(mean)
, or short ?mean
into your R console.
Usually, sharing huge data sets is not necessary and may rather discourage others from reading your question. Therefore, it is better to use built-in datasets or create a small "toy" example that resembles your original data, which is actually what is meant by minimal. If for some reason you really need to share your original data, you should use a method, such as dput()
, that allows others to get an exact copy of your data.
You can use one of the built-in datasets. A comprehensive list of built-in datasets can be seen with data()
. There is a short description of every data set, and more information can be obtained, e.g. with ?iris
, for the 'iris' data set that comes with R. Installed packages might contain additional datasets.
Preliminary note: Sometimes you may need special formats (i.e. classes), such as factors, dates, or time series. For these, make use of functions like: as.factor
, as.Date
, as.xts
, ... Example:
d <- as.Date("2020-12-30")
where
class(d)
# [1] "Date"
Vectors
x <- rnorm(10) ## random vector normal distributed
x <- runif(10) ## random vector uniformly distributed
x <- sample(1:100, 10) ## 10 random draws out of 1, 2, ..., 100
x <- sample(LETTERS, 10) ## 10 random draws out of built-in latin alphabet
Matrices
m <- matrix(1:12, 3, 4, dimnames=list(LETTERS[1:3], LETTERS[1:4]))
m
# A B C D
# A 1 4 7 10
# B 2 5 8 11
# C 3 6 9 12
Data frames
set.seed(42) ## for sake of reproducibility
n <- 6
dat <- data.frame(id=1:n,
date=seq.Date(as.Date("2020-12-26"), as.Date("2020-12-31"), "day"),
group=rep(LETTERS[1:2], n/2),
age=sample(18:30, n, replace=TRUE),
type=factor(paste("type", 1:n)),
x=rnorm(n))
dat
# id date group age type x
# 1 1 2020-12-26 A 27 type 1 0.0356312
# 2 2 2020-12-27 B 19 type 2 1.3149588
# 3 3 2020-12-28 A 20 type 3 0.9781675
# 4 4 2020-12-29 B 26 type 4 0.8817912
# 5 5 2020-12-30 A 26 type 5 0.4822047
# 6 6 2020-12-31 B 28 type 6 0.9657529
Note: Although it is widely used, better to not name your data frame df
, because df()
is an R function for the density (i.e. height of the curve at point x
) of the F distribution and you might get a clash with it.
If you have a specific reason, or data that would be too difficult to construct an example from, you could provide a small subset of your original data, best by using dput
.
Why use dput()
?
dput
throws all information needed to exactly reproduce your data on your console. You may simply copy the output and paste it into your question.
Calling dat
(from above) produces output that still lacks information about variable classes and other features if you share it in your question. Furthermore, the spaces in the type
column make it difficult to do anything with it. Even when we set out to use the data, we won't manage to get important features of your data right.
id date group age type x
1 1 2020-12-26 A 27 type 1 0.0356312
2 2 2020-12-27 B 19 type 2 1.3149588
3 3 2020-12-28 A 20 type 3 0.9781675
Subset your data
To share a subset, use head()
, subset()
or the indices iris[1:4, ]
. Then wrap it into dput()
to give others something that can be put in R immediately. Example
dput(iris[1:4, ]) # first four rows of the iris data set
Console output to share in your question:
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")), row.names = c(NA,
4L), class = "data.frame")
When using dput
, you may also want to include only relevant columns, e.g. dput(mtcars[1:3, c(2, 5, 6)])
Note: 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 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, e.g. dput(droplevels(iris[1:4, ]))
. One other caveat for dput
is that it will not work for keyed data.table
objects or for grouped tbl_df
(class grouped_df
) from the tidyverse
. In these cases you can convert back to a regular data frame before sharing, dput(as.data.frame(my_data))
.
Combined with the minimal data (see above), your code should exactly reproduce the problem on another machine by simply copying and pasting it.
This should be the easy part but often isn't. What you should not do:
What you should do:
library()
)unlink()
)op <- par(mfrow=c(1,2)) ...some code... par(op)
)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 help report your RStudio version.
If you have a problem with a specific package, you may want to provide the package version by giving the output of packageVersion("name of the package")
.
Using set.seed()
you may specify a seed1, i.e. the specific state in which R's random number generator is fixed. This makes it possible for random functions, such as sample()
, rnorm()
, runif()
and lots of others, to always return the same result, Example:
set.seed(42)
rnorm(3)
# [1] 1.3709584 -0.5646982 0.3631284
set.seed(42)
rnorm(3)
# [1] 1.3709584 -0.5646982 0.3631284
1 Note: The output of set.seed()
differs between R >3.6.0 and previous versions. Specify which R version you used for the random process, and don't be surprised if you get slightly different results when following old questions. To get the same result in such cases, you can use the RNGversion()
-function before set.seed()
(e.g.: RNGversion("3.5.2")
).
Answered 2023-09-20 20:30:04
(Here's my advice from How to write a reproducible example. I've tried to make it short but sweet. Section 9.2 of "Workflow: Getting help" in r4ds is a more recent take that also discusses the reprex package.)
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.
You need to include four things 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 mtcars
dataset in R,
I'd perform the following steps:
dput(mtcars)
in Rmtcars <-
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.
Answered 2023-09-20 20:30:04
reprex
in tidyverse
is a good package for producing minimal, reproducible example: github.com/tidyverse/reprex - anyone dput()
unfortunately returns long lines of vectors, for graphs. - anyone sf
tibble. Even when cut down to just a few rows, these do not seem to play nicely with tools like dput
, in my experience. - anyone dput(mtcars)
directly to the clipboard in Windows ? - anyone Personally, I prefer "one" liners. Something along the lines:
my.df <- data.frame(col1 = sample(c(1,2), 10, replace = TRUE),
col2 = as.factor(sample(10)), col3 = letters[1:10],
col4 = sample(c(TRUE, FALSE), 10, replace = TRUE))
my.list <- list(list1 = my.df, list2 = my.df[3], list3 = letters)
The data structure should mimic the idea of the writer's problem and not the exact verbatim structure. I really appreciate it when variables don't overwrite my own variables or god forbid, functions (like df
).
Alternatively, one could cut a few corners and point to a pre-existing data set, something like:
library(vegan)
data(varespec)
ord <- metaMDS(varespec)
Don't forget to mention any special packages you might be using.
If you're trying to demonstrate something on larger objects, you can try
my.df2 <- data.frame(a = sample(10e6), b = sample(letters, 10e6, replace = TRUE))
If you're working with spatial data via the raster
package, you can generate some random data. A lot of examples can be found in the package vignette, but here's a small nugget.
library(raster)
r1 <- r2 <- r3 <- raster(nrow=10, ncol=10)
values(r1) <- runif(ncell(r1))
values(r2) <- runif(ncell(r2))
values(r3) <- runif(ncell(r3))
s <- stack(r1, r2, r3)
If you need some spatial object as implemented in sp
, you can get some datasets via external files (like ESRI shapefile) in "spatial" packages (see the Spatial view in Task Views).
library(rgdal)
ogrDrivers()
dsn <- system.file("vectors", package = "rgdal")[1]
ogrListLayers(dsn)
ogrInfo(dsn=dsn, layer="cities")
cities <- readOGR(dsn=dsn, layer="cities")
Answered 2023-09-20 20:30:04
Inspired by this very post, I now use a handy function,
reproduce(<mydata>)
when I need to post to Stack Overflow.
If myData
is the name of your object to reproduce, run the following in R:
install.packages("devtools")
library(devtools)
source_url("https://raw.github.com/rsaporta/pubR/gitbranch/reproduce.R")
reproduce(myData)
This function is an intelligent wrapper to dput
and does the following:
dput
outputobjName <- ...
, so that it can be easily copy+pasted, but...# sample data
DF <- data.frame(id=rep(LETTERS, each=4)[1:100], replicate(100, sample(1001, 100)), Class=sample(c("Yes", "No"), 100, TRUE))
DF is about 100 x 102. I want to sample 10 rows and a few specific columns
reproduce(DF, cols=c("id", "X1", "X73", "Class")) # I could also specify the column number.
This is what the sample looks like:
id X1 X73 Class
1 A 266 960 Yes
2 A 373 315 No Notice the selection split
3 A 573 208 No (which can be turned off)
4 A 907 850 Yes
5 B 202 46 Yes
6 B 895 969 Yes <~~~ 70 % of selection is from the top rows
7 B 940 928 No
98 Y 371 171 Yes
99 Y 733 364 Yes <~~~ 30 % of selection is from the bottom rows.
100 Y 546 641 No
==X==============================================================X==
Copy+Paste this part. (If on a Mac, it is already copied!)
==X==============================================================X==
DF <- structure(list(id = structure(c(1L, 1L, 1L, 1L, 2L, 2L, 2L, 25L, 25L, 25L), .Label = c("A", "B", "C", "D", "E", "F", "G", "H", "I", "J", "K", "L", "M", "N", "O", "P", "Q", "R", "S", "T", "U", "V", "W", "X", "Y"), class = "factor"), X1 = c(266L, 373L, 573L, 907L, 202L, 895L, 940L, 371L, 733L, 546L), X73 = c(960L, 315L, 208L, 850L, 46L, 969L, 928L, 171L, 364L, 641L), Class = structure(c(2L, 1L, 1L, 2L, 2L, 2L, 1L, 2L, 2L, 1L), .Label = c("No", "Yes"), class = "factor")), .Names = c("id", "X1", "X73", "Class"), class = "data.frame", row.names = c(1L, 2L, 3L, 4L, 5L, 6L, 7L, 98L, 99L, 100L))
==X==============================================================X==
Notice also that the entirety of the output is in a nice single, long line, not a tall paragraph of chopped up lines. This makes it easier to read on Stack Overflow questions posts and also easier to copy+paste.
You can now specify how many lines of text output will take up (i.e., what you will paste into Stack Overflow). Use the lines.out=n
argument for this. Example:
reproduce(DF, cols=c(1:3, 17, 23), lines.out=7)
yields:
==X==============================================================X==
Copy+Paste this part. (If on a Mac, it is already copied!)
==X==============================================================X==
DF <- structure(list(id = structure(c(1L, 1L, 1L, 1L, 2L, 2L, 2L, 25L,25L, 25L), .Label
= c("A", "B", "C", "D", "E", "F", "G", "H","I", "J", "K", "L", "M", "N", "O", "P", "Q", "R", "S", "T", "U","V", "W", "X", "Y"), class = "factor"),
X1 = c(809L, 81L, 862L,747L, 224L, 721L, 310L, 53L, 853L, 642L),
X2 = c(926L, 409L,825L, 702L, 803L, 63L, 319L, 941L, 598L, 830L),
X16 = c(447L,164L, 8L, 775L, 471L, 196L, 30L, 420L, 47L, 327L),
X22 = c(335L,164L, 503L, 407L, 662L, 139L, 111L, 721L, 340L, 178L)), .Names = c("id","X1",
"X2", "X16", "X22"), class = "data.frame", row.names = c(1L,2L, 3L, 4L, 5L, 6L, 7L, 98L, 99L, 100L))
==X==============================================================X==
Answered 2023-09-20 20:30:04
library(devtools);source_url("https://raw.github.com/rsaporta/pubR/gitbranch/reproduce.R")
in each session to use the reproduce
function ? - anyone dput
in one line, run writeClipboard(paste(capture.output(dput(DF)), collapse = ""))
- anyone Here is a good guide.
The most important point is: Make a small piece of code that we can run to see what the problem is. A useful function for this is dput()
, but if you have very large data, then you might want to make a small sample dataset or only use the first 10 lines or so.
EDIT:
Also, make sure that you identified where the problem is yourself. The example should not be an entire R script with "On line 200 there is an error". If you use the debugging tools in R (I love browser()
) and Google, then you should be able to really identify where the problem is and reproduce a trivial example in which the same thing goes wrong.
Answered 2023-09-20 20:30:04
The R-help mailing list has a posting guide which covers both asking and answering questions, including an example of generating data:
Examples: Sometimes it helps to provide a small example that someone can actually run. For example:
If I have a matrix x as follows:
> x <- matrix(1:8, nrow=4, ncol=2,
dimnames=list(c("A","B","C","D"), c("x","y"))
> x
x y
A 1 5
B 2 6
C 3 7
D 4 8
>
how can I turn it into a dataframe with 8 rows, and three columns named 'row', 'col', and 'value', which have the dimension names as the values of 'row' and 'col', like this:
> x.df
row col value
1 A x 1
...
(To which the answer might be:
> x.df <- reshape(data.frame(row=rownames(x), x), direction="long",
varying=list(colnames(x)), times=colnames(x),
v.names="value", timevar="col", idvar="row")
)
The word small is especially important. You should be aiming for a minimal reproducible example, which means that the data and the code should be as simple as possible to explain the problem.
EDIT: Pretty code is easier to read than ugly code. Use a style guide.
Answered 2023-09-20 20:30:04
Since R.2.14 (I guess) you can feed your data text representation directly to read.table
:
df <- read.table(header=TRUE,
text="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
")
Answered 2023-09-20 20:30:04
Sometimes the problem really isn't reproducible with a smaller piece of data, no matter how hard you try, and doesn't happen with synthetic data (although it's useful to show how you produced synthetic data sets that did not reproduce the problem, because it rules out some hypotheses).
If you can't do either of these then you probably need to hire a consultant to solve your problem ...
edit: Two useful SO questions for anonymization/scrambling:
Answered 2023-09-20 20:30:04
fitdistr
and fitdistrplus
. - anyone The answers so far are obviously great for the reproducibility part. This is merely to clarify that a reproducible example cannot and should not be the sole component of a question. Don't forget to explain what you want it to look like and the contours of your problem, not just how you have attempted to get there so far. Code is not enough; you need words also.
Here's a reproducible example of what to avoid doing (drawn from a real example, names changed to protect the innocent):
The following is sample data and part of function I have trouble with.
code
code
code
code
code (40 or so lines of it)
How can I achieve this ?
Answered 2023-09-20 20:30:04
I have a very easy and efficient way to make a R example that has not been mentioned above. You can define your structure firstly. For example,
mydata <- data.frame(a=character(0), b=numeric(0), c=numeric(0), d=numeric(0))
>fix(mydata)
Then you can input your data manually. This is efficient for smaller examples rather than big ones.
Answered 2023-09-20 20:30:04
dput(mydata)
- anyone for (d in data) {...}
. - anyone Your main objective in crafting your questions should be to make it as easy as possible for readers to understand and reproduce your problem on their systems. To do so:
This does take some work, but it seems like a fair trade-off since you ask others to do work for you.
The best option by far is to rely on built-in datasets. This makes it very easy for others to work on your problem. Type data()
at the R prompt to see what data is available to you. Some classic examples:
iris
mtcars
ggplot2::diamonds
(external package, but almost everyone has it)Inspect the built-in datasets to find one suitable for your problem.
If you can rephrase your problem to use the built-in datasets, you are much more likely to get good answers (and upvotes).
If your problem is specific to a type of data that is not represented in the existing data sets, then provide the R code that generates the smallest possible dataset that your problem manifests itself on. For example
set.seed(1) # important to make random data reproducible
myData <- data.frame(a=sample(letters[1:5], 20, rep=T), b=runif(20))
Someone trying to answer my question can copy/paste those two lines and start working on the problem immediately.
As a last resort, you can use dput
to transform a data object to R code (e.g. dput(myData)
). I say as a "last resort" because the output of dput
is often fairly unwieldy, annoying to copy-paste, and obscures the rest of your question.
Someone once said:
A picture of expected output is worth 1000 words
-- a sage person
If you can add something like "I expected to get this result":
cyl mean.hp
1: 6 122.28571
2: 4 82.63636
3: 8 209.21429
to your question, people are much more likely to understand what you are trying to do quickly. If your expected result is large and unwieldy, then you probably haven't thought enough about how to simplify your problem (see next).
The main thing to do is simplify your problem as much as possible before you ask your question. Re-framing the problem to work with the built-in datasets will help a lot in this regard. You will also often find that just by going through the process of simplification, you will answer your own problem.
Here are some examples of good questions:
In both cases, the user's problems are almost certainly not with the simple examples they provide. Rather they abstracted the nature of their problem and applied it to a simple data set to ask their question.
This answer focuses on what I think is the best practice: use built-in data sets and provide what you expect as a result in a minimal form. The most prominent answers focus on other aspects. I don't expect this answer to rising to any prominence; this is here solely so that I can link to it in comments to newbie questions.
Answered 2023-09-20 20:30:04
To quickly create a dput
of your data you can just copy (a piece of) the data to your clipboard and run the following in R:
For data in Excel:
dput(read.table("clipboard", sep="\t", header=TRUE))
For data in a .txt file:
dput(read.table("clipboard", sep="", header=TRUE))
You can change the sep
in the latter if necessary.
This will only work if your data is in the clipboard of course.
Answered 2023-09-20 20:30:04
Reproducible code is the key to get help. However, there are many users that might be sceptical of pasting even a chunk of their data. For instance, they could be working with sensitive data or on original data collected to use in a research paper.
For any reason, I thought it would be nice to have a handy function for "deforming" my data before pasting it publicly. The anonymize
function from the package SciencesPo
is very silly, but for me it works nicely with the dput
function.
install.packages("SciencesPo")
dt <- data.frame(
Z = sample(LETTERS,10),
X = sample(1:10),
Y = sample(c("yes", "no"), 10, replace = TRUE)
)
> dt
Z X Y
1 D 8 no
2 T 1 yes
3 J 7 no
4 K 6 no
5 U 2 no
6 A 10 yes
7 Y 5 no
8 M 9 yes
9 X 4 yes
10 Z 3 no
Then I anonymize it:
> anonymize(dt)
Z X Y
1 b2 2.5 c1
2 b6 -4.5 c2
3 b3 1.5 c1
4 b4 0.5 c1
5 b7 -3.5 c1
6 b1 4.5 c2
7 b9 -0.5 c1
8 b5 3.5 c2
9 b8 -1.5 c2
10 b10 -2.5 c1
One may also want to sample a few variables instead of the whole data before applying the anonymization and dput command.
# Sample two variables without replacement
> anonymize(sample.df(dt,5,vars=c("Y","X")))
Y X
1 a1 -0.4
2 a1 0.6
3 a2 -2.4
4 a1 -1.4
5 a2 3.6
Answered 2023-09-20 20:30:04
Often you need some data for an example, however, you don't want to post your exact data. To use some existing data.frame in established library, use data command to import it.
e.g.,
data(mtcars)
and then do the problem
names(mtcars)
your problem demostrated on the mtcars data set
Answered 2023-09-20 20:30:04
mtcars
and iris
datasets) don't actually need the data
call to be used. - anyone If you have a large dataset which cannot be easily put to the script using dput()
, post your data to pastebin and load them using read.table
:
d <- read.table("http://pastebin.com/raw.php?i=m1ZJuKLH")
Inspired by Henrik.
Answered 2023-09-20 20:30:04
I am developing the wakefield package to address this need to quickly share reproducible data, sometimes dput
works fine for smaller data sets but many of the problems we deal with are much larger, sharing such a large data set via dput
is impractical.
About:
wakefield allows the user to share minimal code to reproduce data. The user sets n
(number of rows) and specifies any number of preset variable functions (there are currently 70) that mimic real if data (things like gender, age, income etc.)
Installation:
Currently (2015-06-11), wakefield is a GitHub package but will go to CRAN eventually after unit tests are written. To install quickly, use:
if (!require("pacman")) install.packages("pacman")
pacman::p_load_gh("trinker/wakefield")
Example:
Here is an example:
r_data_frame(
n = 500,
id,
race,
age,
sex,
hour,
iq,
height,
died
)
This produces:
ID Race Age Sex Hour IQ Height Died
1 001 White 33 Male 00:00:00 104 74 TRUE
2 002 White 24 Male 00:00:00 78 69 FALSE
3 003 Asian 34 Female 00:00:00 113 66 TRUE
4 004 White 22 Male 00:00:00 124 73 TRUE
5 005 White 25 Female 00:00:00 95 72 TRUE
6 006 White 26 Female 00:00:00 104 69 TRUE
7 007 Black 30 Female 00:00:00 111 71 FALSE
8 008 Black 29 Female 00:00:00 100 64 TRUE
9 009 Asian 25 Male 00:30:00 106 70 FALSE
10 010 White 27 Male 00:30:00 121 68 FALSE
.. ... ... ... ... ... ... ... ...
Answered 2023-09-20 20:30:04
If you have one or more factor
variable(s) in your data that you want to make reproducible with dput(head(mydata))
, consider adding droplevels
to it, so that levels of factors that are not present in the minimized data set are not included in your dput
output, in order to make the example minimal:
dput(droplevels(head(mydata)))
Answered 2023-09-20 20:30:04
The original post referred to the now retired r-fiddle service from datacamp. It has been rebranded as datacamp light and can not as easily embedded as indicated by my answer.
I wonder if an http://old.r-fiddle.org/ link could be a very neat way of sharing a problem. It receives a unique ID like and one could even think about embedding it in SO.
Answered 2023-09-20 20:30:04
Please do not paste your console outputs like this:
If I have a matrix x as follows:
> x <- matrix(1:8, nrow=4, ncol=2,
dimnames=list(c("A","B","C","D"), c("x","y")))
> x
x y
A 1 5
B 2 6
C 3 7
D 4 8
>
How can I turn it into a dataframe with 8 rows, and three
columns named `row`, `col`, and `value`, which have the
dimension names as the values of `row` and `col`, like this:
> x.df
row col value
1 A x 1
...
(To which the answer might be:
> x.df <- reshape(data.frame(row=rownames(x), x), direction="long",
+ varying=list(colnames(x)), times=colnames(x),
+ v.names="value", timevar="col", idvar="row")
)
We can not copy-paste it directly.
To make questions and answers properly reproducible, try to remove +
& >
before posting it and put #
for outputs and comments like this:
#If I have a matrix x as follows:
x <- matrix(1:8, nrow=4, ncol=2,
dimnames=list(c("A","B","C","D"), c("x","y")))
x
# x y
#A 1 5
#B 2 6
#C 3 7
#D 4 8
# How can I turn it into a dataframe with 8 rows, and three
# columns named `row`, `col`, and `value`, which have the
# dimension names as the values of `row` and `col`, like this:
#x.df
# row col value
#1 A x 1
#...
#To which the answer might be:
x.df <- reshape(data.frame(row=rownames(x), x), direction="long",
varying=list(colnames(x)), times=colnames(x),
v.names="value", timevar="col", idvar="row")
One more thing, if you have used any function from certain package, mention that library.
Answered 2023-09-20 20:30:04
>
and add the #
manually or is there an automatic way to do that? - anyone >
manually. But, for addition of #
, I use Ctrl+Shift+C
shortcut in RStudio
editor. - anyone >
with #
directly in Rstudio editor. You just paste your text to editor then click on the search icon at the top of the editor pane. Put >
in the search input and #
in the replace input the click replaceAll button. - anyone You can do this using reprex.
As mt1022 noted, "... good package for producing minimal, reproducible example is "reprex" from tidyverse".
According to Tidyverse:
The goal of "reprex" is to package your problematic code in such a way that other people can run it and feel your pain.
An example is given on tidyverse web site.
library(reprex)
y <- 1:4
mean(y)
reprex()
I think this is the simplest way to create a reproducible example.
Answered 2023-09-20 20:30:04
reprex()
you need to copy your code to the clipboard since this is where it takes the code from. - anyone Apart from all the above answers which I found very interesting, it could sometimes be very easy as it is discussed here: How to make a minimal reproducible example to get help with R
There are many ways to make a random vector Create a 100 number vector with random values in R rounded to 2 decimals or a random matrix in R:
mydf1<- matrix(rnorm(20),nrow=20,ncol=5)
Note that sometimes it is very difficult to share a given data because of various reasons such as dimension, etc. However, all the above answers are great, and they are very important to think about and use when one wants to make a reproducible data example. But note that in order to make data as representative as the original (in case the OP cannot share the original data), it is good to add some information with the data example as (if we call the data mydf1)
class(mydf1)
# this shows the type of the data you have
dim(mydf1)
# this shows the dimension of your data
Moreover, one should know the type, length and attributes of a data which can be Data structures
#found based on the following
typeof(mydf1), what it is.
length(mydf1), how many elements it contains.
attributes(mydf1), additional arbitrary metadata.
#If you cannot share your original data, you can str it and give an idea about the structure of your data
head(str(mydf1))
Answered 2023-09-20 20:30:04
Here are some of my suggestions:
dput
, so others can help you more easilyinstall.package()
unless it is really necessary, people will understand if you just use require
or library
Try to be concise,
All these are part of a reproducible example.
Answered 2023-09-20 20:30:04
dput()
has been mentioned previously, and much of this is just reiterating standard SO guidelines. - anyone install.package
function included in the example which is not really necessary (in my opinion). Further, using default R dataset would make the reproducible easier. The SO guidelines has not talked anything about these topics specifically. Further, It was meant to give my opinion and these are the one which I have encountered most. - anyone It's a good idea to use functions from the testthat
package to show what you expect to occur. Thus, other people can alter your code until it runs without error. This eases the burden of those who would like to help you, because it means they don't have to decode your textual description. For example
library(testthat)
# code defining x and y
if (y >= 10) {
expect_equal(x, 1.23)
} else {
expect_equal(x, 3.21)
}
is clearer than "I think x would come out to be 1.23 for y equal to or exceeding 10, and 3.21 otherwise, but I got neither result". Even in this silly example, I think the code is clearer than the words. Using testthat
lets your helper focus on the code, which saves time, and it provides a way for them to know they have solved your problem, before they post it
Answered 2023-09-20 20:30:04