2010-08-17 18:31:12 8 Comments

Whenever I want to do something "map"py in R, I usually try to use a function in the `apply`

family.

However, I've never quite understood the differences between them -- how {`sapply`

, `lapply`

, etc.} apply the function to the input/grouped input, what the output will look like, or even what the input can be -- so I often just go through them all until I get what I want.

Can someone explain how to use which one when?

My current (probably incorrect/incomplete) understanding is...

`sapply(vec, f)`

: input is a vector. output is a vector/matrix, where element`i`

is`f(vec[i])`

, giving you a matrix if`f`

has a multi-element output`lapply(vec, f)`

: same as`sapply`

, but output is a list?`apply(matrix, 1/2, f)`

: input is a matrix. output is a vector, where element`i`

is f(row/col i of the matrix)`tapply(vector, grouping, f)`

: output is a matrix/array, where an element in the matrix/array is the value of`f`

at a grouping`g`

of the vector, and`g`

gets pushed to the row/col names`by(dataframe, grouping, f)`

: let`g`

be a grouping. apply`f`

to each column of the group/dataframe. pretty print the grouping and the value of`f`

at each column.`aggregate(matrix, grouping, f)`

: similar to`by`

, but instead of pretty printing the output, aggregate sticks everything into a dataframe.

Side question: I still haven't learned plyr or reshape -- would `plyr`

or `reshape`

replace all of these entirely?

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## 9 comments

## @joran 2011-08-21 22:50:17

R has many *apply functions which are ably described in the help files (e.g.

`?apply`

). There are enough of them, though, that beginning useRs may have difficulty deciding which one is appropriate for their situation or even remembering them all. They may have a general sense that "I should be using an *apply function here", but it can be tough to keep them all straight at first.Despite the fact (noted in other answers) that much of the functionality of the *apply family is covered by the extremely popular

`plyr`

package, the base functions remain useful and worth knowing.This answer is intended to act as a sort of

signpostfor new useRs to help direct them to the correct *apply function for their particular problem. Note, this isnotintended to simply regurgitate or replace the R documentation! The hope is that this answer helps you to decide which *apply function suits your situation and then it is up to you to research it further. With one exception, performance differences will not be addressed.apply-When you want to apply a function to the rows or columns of a matrix (and higher-dimensional analogues); not generally advisable for data frames as it will coerce to a matrix first.If you want row/column means or sums for a 2D matrix, be sure to investigate the highly optimized, lightning-quick

`colMeans`

,`rowMeans`

,`colSums`

,`rowSums`

.lapply-When you want to apply a function to each element of a list in turn and get a list back.This is the workhorse of many of the other *apply functions. Peel back their code and you will often find

`lapply`

underneath.sapply-When you want to apply a function to each element of a list in turn, but you want avectorback, rather than a list.If you find yourself typing

`unlist(lapply(...))`

, stop and consider`sapply`

.In more advanced uses of

`sapply`

it will attempt to coerce the result to a multi-dimensional array, if appropriate. For example, if our function returns vectors of the same length,`sapply`

will use them as columns of a matrix:If our function returns a 2 dimensional matrix,

`sapply`

will do essentially the same thing, treating each returned matrix as a single long vector:Unless we specify

`simplify = "array"`

, in which case it will use the individual matrices to build a multi-dimensional array:Each of these behaviors is of course contingent on our function returning vectors or matrices of the same length or dimension.

vapply-When you want to use`sapply`

but perhaps need to squeeze some more speed out of your code.For

`vapply`

, you basically give R an example of what sort of thing your function will return, which can save some time coercing returned values to fit in a single atomic vector.mapply-For when you have several data structures (e.g. vectors, lists) and you want to apply a function to the 1st elements of each, and then the 2nd elements of each, etc., coercing the result to a vector/array as in`sapply`

.This is multivariate in the sense that your function must accept multiple arguments.

Map-A wrapper to`mapply`

with`SIMPLIFY = FALSE`

, so it is guaranteed to return a list.rapply-For when you want to apply a function to each element of anested liststructure, recursively.To give you some idea of how uncommon

`rapply`

is, I forgot about it when first posting this answer! Obviously, I'm sure many people use it, but YMMV.`rapply`

is best illustrated with a user-defined function to apply:tapply-For when you want to apply a function tosubsetsof a vector and the subsets are defined by some other vector, usually a factor.The black sheep of the *apply family, of sorts. The help file's use of the phrase "ragged array" can be a bit confusing, but it is actually quite simple.

A vector:

A factor (of the same length!) defining groups:

Add up the values in

`x`

within each subgroup defined by`y`

:More complex examples can be handled where the subgroups are defined by the unique combinations of a list of several factors.

`tapply`

is similar in spirit to the split-apply-combine functions that are common in R (`aggregate`

,`by`

,`ave`

,`ddply`

, etc.) Hence its black sheep status.## @42- 2011-09-14 03:42:55

Believe you will find that

`by`

is pure split-lapply and`aggregate`

is`tapply`

at their cores. I think black sheep make excellent fabric.## @grautur 2011-09-14 18:54:28

Fantastic response! This should be part of the official R documentation :). One tiny suggestion: perhaps add some bullets on using

`aggregate`

and`by`

as well? (I finally understand them after your description!, but they're pretty common, so it might be useful to separate out and have some specific examples for those two functions.)## @joran 2011-09-14 23:03:22

@grautur I was actively pruning things from this answer to avoid it being (a) too long and (b) a re-write of the documentation. I decided that while

`aggregate`

,`by`

, etc. are based on *apply functions, the way you approach using them is different enough from a users perspective that they ought to be summarized in a separate answer. I may attempt that if I have time, or maybe someone else will beat me to it and earn my upvote.## @isomorphismes 2011-10-10 06:01:53

Yeah ... what is a ragged array, anyway?

## @baptiste 2012-02-16 05:53:24

also,

`?Map`

as a relative of`mapply`

## @aL3xa 2012-10-14 13:05:20

Small correction

`but you want a vector back, rather than a list`

.`is.vector(list())`

gives`TRUE`

. IMO, what`sapply`

does issimplificationof the results to`data.frame`

-like structure or`array`

-like structure, hence the formal argument`SIMPLIFY`

(`TRUE`

by default). But yeah... awesome answer indeed!!! You should start project on kickstarter.com to (re)write R manual the proper way! =)## @Ari B. Friedman 2013-10-05 21:12:08

`rapply`

example here: stackoverflow.com/a/15581766/636656## @landroni 2014-01-19 10:51:36

I'm curious, how does this answer change wrt the new

`dplyr`

package?## @joran 2014-01-20 03:48:15

@landroni Not at all. I'm covering base R functions. A similarly complete answer would be great for package based solutions (plyr, data.table, doBy and not dplyr).

## @Ari B. Friedman 2014-04-18 21:54:32

Great answer. Quibble with the

`vapply`

description--it's less about speed than type safety Also if anyone is looking for *apply-ing over groupings of data, see this answer.## @jsanders 2014-06-11 14:23:49

Thanks for this wonderful answer! It seems notable that your answer doesn't mention data frames at all. In learning R, it has struck me that as far as the *apply functions are concerned, data frames are largely a second class citizen, and other approaches like data.table or plyr seem more natural.

## @thelatemail 2014-08-20 06:08:15

@jsanders - I wouldn't agree with that at all.

`data.frame`

s are an absolutely central part of R and as a`list`

object are frequently manipulated using`lapply`

particularly. They also act as containers for grouping vectors/factors of many types together in a traditional rectangular dataset. While`data.table`

and`plyr`

might add a certain type of syntax that some might find more comfortable, they are extending and acting on`data.frame`

s respectively.## @jsanders 2014-08-20 18:19:26

@thelatemail: Whoops, my comment sounds like I meant something I didn't. What I meant was just that, despite how fundamental

`data.frame`

s are, this comprehensive answer about`*apply`

doesn't talk about them at all, which says a lot about how well they work for`data.frame`

s (not very well). Interesting point about`lapply`

though, I'll have to get more comfortable with that.## @skan 2015-03-03 19:17:55

It would be great if you also add aggregate and by on your answer.

## @TMOTTM 2015-08-04 22:01:21

When

`lapply`

passes an item of the list it is operating on to`FUN`

, what type is that element when it arrives at FUN? Is it a one-membered sublist of`X`

, or is it passed as its "elementary" type? So if I'm lapplying on a list of data.frames, are the elements passed to FUN, of type data.frames or sublists of length 1?## @gented 2015-10-25 23:59:29

@joran Just a footnote: the dimension of an object is not what you think it is (or at least what your answer shows). A vector with

`N`

(independent) entries is`N`

dimensional (not one-dimensional at all), as well as an`N x M`

matrix is in general`NM`

dimensional (not two-dimensional), and so on and so forth. The dimension of an object is the number of independent variables one needs to fully specify it. Other than that, awesome explanation!## @joran 2015-10-26 00:01:08

@GennaroTedesco If we were talking math, I'd agree with you, but that is how the R programming language uses the "dimension" concept with it's data objects.

## @r2evans 2018-04-05 19:10:51

I'd add that the differentiation between

`sapply`

and`lapply`

is not just the optionally-simplified return value, but also in the preservation of names. You can mimic`sapply`

's name-keeping with`setNames(lapply(vec,func), names(vec))`

, which is a degradation from`simplify2array`

. I think the utility of name-preservation is critical in many areas and nice-to-have in almost all; very rarely do I feel discarding the`list`

names is intentionally desired.## @vonjd 2017-06-16 16:03:27

I recently discovered the rather useful

`sweep`

function and add it here for the sake of completeness:sweepThe basic idea is to

sweepthrough an array row- or column-wise and return a modified array. An example will make this clear (source: datacamp):Let's say you have a matrix and want to standardize it column-wise:

NB: for this simple example the same result can of course be achieved more easily by

`apply(dataPoints, 2, scale)`

## @Frank 2017-06-16 16:55:03

Is this related to grouping?

## @vonjd 2017-06-16 17:03:57

@Frank: Well, to be honest with you the title of this post is rather misleading: when you read the question itself it is about "the apply family".

`sweep`

is a higher-order function like all the others mentioned here, e.g.`apply`

,`sapply`

,`lapply`

So the same question could be asked about the accepted answer with over 1,000 upvotes and the examples given therein. Just have a look at the example given for`apply`

there.## @Frank 2017-06-16 18:08:14

Oh right, good point.

## @Moody_Mudskipper 2018-03-24 15:04:09

sweep has a misleading name, misleading defaults, and misleading parameter name :). It's easier for me to understand it this way : 1) STATS is vector or single value that will be repeated to form a matrix of the same size as first input, 2) FUN will be applied on 1st input and this new matrix. Maybe better illustrated by :

`sweep(matrix(1:6,nrow=2),2,7:9,list)`

. It's usually more efficient than`apply`

because where`apply`

loops,`sweep`

is able to use vectorised functions.## @Assad Ebrahim 2014-04-25 00:20:19

First start with Joran's excellent answer -- doubtful anything can better that.

Then the following mnemonics may help to remember the distinctions between each. Whilst some are obvious, others may be less so --- for these you'll find justification in Joran's discussions.

Mnemonics`lapply`

is alistapply which acts on a list or vector and returns a list.`sapply`

is asimple`lapply`

(function defaults to returning a vector or matrix when possible)`vapply`

is averified apply(allows the return object type to be prespecified)`rapply`

is arecursiveapply for nested lists, i.e. lists within lists`tapply`

is ataggedapply where the tags identify the subsets`apply`

isgeneric: applies a function to a matrix's rows or columns (or, more generally, to dimensions of an array)Building the Right BackgroundIf using the

`apply`

family still feels a bit alien to you, then it might be that you're missing a key point of view.These two articles can help. They provide the necessary background to motivate the

functional programming techniquesthat are being provided by the`apply`

family of functions.Users of Lisp will recognise the paradigm immediately. If you're not familiar with Lisp, once you get your head around FP, you'll have gained a powerful point of view for use in R -- and

`apply`

will make a lot more sense.## @John Paul 2016-05-16 03:59:13

Despite all the great answers here, there are 2 more base functions that deserve to be mentioned, the useful

`outer`

function and the obscure`eapply`

functionouter`outer`

is a very useful function hidden as a more mundane one. If you read the help for`outer`

its description says:which makes it seem like this is only useful for linear algebra type things. However, it can be used much like

`mapply`

to apply a function to two vectors of inputs. The difference is that`mapply`

will apply the function to the first two elements and then the second two etc, whereas`outer`

will apply the function to every combination of one element from the first vector and one from the second. For example:I have personally used this when I have a vector of values and a vector of conditions and wish to see which values meet which conditions.

eapply`eapply`

is like`lapply`

except that rather than applying a function to every element in a list, it applies a function to every element in an environment. For example if you want to find a list of user defined functions in the global environment:Frankly I don't use this very much but if you are building a lot of packages or create a lot of environments it may come in handy.

## @jangorecki 2015-12-08 22:42:43

There are lots of great answers which discuss differences in the use cases for each function. None of the answer discuss the differences in performance. That is reasonable cause various functions expects various input and produces various output, yet most of them have a general common objective to evaluate by series/groups. My answer is going to focus on performance. Due to above the input creation from the vectors is included in the timing, also the

`apply`

function is not measured.I have tested two different functions

`sum`

and`length`

at once. Volume tested is 50M on input and 50K on output. I have also included two currently popular packages which were not widely used at the time when question was asked,`data.table`

and`dplyr`

. Both are definitely worth to look if you are aiming for good performance.## @Dimitri Petrenko 2016-06-08 09:35:21

Is it normal that dplyr is lower than the applt functions ?

## @jangorecki 2016-06-08 11:48:54

@DimitriPetrenko I don't think so, not sure why it is here. It is best to test against your own data, as there are many factors that comes into play.

## @SabDeM 2015-08-28 02:28:10

Since I realized that (the very excellent) answers of this post lack of

`by`

and`aggregate`

explanations. Here is my contribution.## BY

The

`by`

function, as stated in the documentation can be though, as a "wrapper" for`tapply`

. The power of`by`

arises when we want to compute a task that`tapply`

can't handle. One example is this code:If we print these two objects,

`ct`

and`cb`

, we "essentially" have the same results and the only differences are in how they are shown and the different`class`

attributes, respectively`by`

for`cb`

and`array`

for`ct`

.As I've said, the power of

`by`

arises when we can't use`tapply`

; the following code is one example:R says that arguments must have the same lengths, say "we want to calculate the

`summary`

of all variable in`iris`

along the factor`Species`

": but R just can't do that because it does not know how to handle.With the

`by`

function R dispatch a specific method for`data frame`

class and then let the`summary`

function works even if the length of the first argument (and the type too) are different.it works indeed and the result is very surprising. It is an object of class

`by`

that along`Species`

(say, for each of them) computes the`summary`

of each variable.Note that if the first argument is a

`data frame`

, the dispatched function must have a method for that class of objects. For example is we use this code with the`mean`

function we will have this code that has no sense at all:## AGGREGATE

`aggregate`

can be seen as another a different way of use`tapply`

if we use it in such a way.The two immediate differences are that the second argument of

`aggregate`

mustbe a list while`tapply`

can(not mandatory) be a list and that the output of`aggregate`

is a data frame while the one of`tapply`

is an`array`

.The power of

`aggregate`

is that it can handle easily subsets of the data with`subset`

argument and that it has methods for`ts`

objects and`formula`

as well.These elements make

`aggregate`

easier to work with that`tapply`

in some situations. Here are some examples (available in documentation):We can achieve the same with

`tapply`

but the syntax is slightly harder and the output (in some circumstances) less readable:There are other times when we can't use

`by`

or`tapply`

and we have to use`aggregate`

.We cannot obtain the previous result with

`tapply`

in one call but we have to calculate the mean along`Month`

for each elements and then combine them (also note that we have to call the`na.rm = TRUE`

, because the`formula`

methods of the`aggregate`

function has by default the`na.action = na.omit`

):while with

`by`

we just can't achieve that in fact the following function call returns an error (but most likely it is related to the supplied function,`mean`

):Other times the results are the same and the differences are just in the class (and then how it is shown/printed and not only -- example, how to subset it) object:

The previous code achieve the same goal and results, at some points what tool to use is just a matter of personal tastes and needs; the previous two objects have very different needs in terms of subsetting.

## @Onyambu 2017-12-24 20:23:13

As I've said, the power of by arises when we can't use tapply; the following code is one example: THIS ARE THE WORDS YOU HAVE USED ABOVE. And you have given an example of computing the summary. Well lets say that the summary statistics can be computed only that it will need cleaning: eg

`data.frame(tapply(unlist(iris[,-5]),list(rep(iris[,5],ncol(iris[-5])),col(iris[-5])),summary))`

this is a use of tapply`. With the right splitting there is nothing you cant do with`

tapply`. The only thing is it returns a matrix. Please be careful by saying we cant use`

tapply`## @user3603486 2014-11-06 00:00:25

It is maybe worth mentioning

`ave`

.`ave`

is`tapply`

's friendly cousin. It returns results in a form that you can plug straight back into your data frame.There is nothing in the base package that works like

`ave`

for whole data frames (as`by`

is like`tapply`

for data frames). But you can fudge it:## @isomorphismes 2011-10-09 05:29:32

From slide 21 of http://www.slideshare.net/hadley/plyr-one-data-analytic-strategy:

(Hopefully it's clear that

`apply`

corresponds to @Hadley's`aaply`

and`aggregate`

corresponds to @Hadley's`ddply`

etc. Slide 20 of the same slideshare will clarify if you don't get it from this image.)(on the left is input, on the top is output)

## @JHowIX 2016-09-16 18:16:25

is there a typo in the slide? The top left cell should be aaply

## @JoFrhwld 2010-08-17 19:20:09

On the side note, here is how the various

`plyr`

functions correspond to the base`*apply`

functions (from the intro to plyr document from the plyr webpage http://had.co.nz/plyr/)One of the goals of

`plyr`

is to provide consistent naming conventions for each of the functions, encoding the input and output data types in the function name. It also provides consistency in output, in that output from`dlply()`

is easily passable to`ldply()`

to produce useful output, etc.Conceptually, learning

`plyr`

is no more difficult than understanding the base`*apply`

functions.`plyr`

and`reshape`

functions have replaced almost all of these functions in my every day use. But, also from the Intro to Plyr document:## @JD Long 2010-08-17 19:23:29

When I started learning R from scratch I found plyr MUCH easier to learn than the

`*apply()`

family of functions. For me,`ddply()`

was very intuitive as I was familiar with SQL aggregation functions.`ddply()`

became my hammer for solving many problems, some of which could have been better solved with other commands.## @JoFrhwld 2010-08-17 19:36:22

I guess I figured that the concept behind

`plyr`

functions is similar to`*apply`

functions, so if you can do one, you can do the other, but`plyr`

functions are easier to remember. But I totally agree on the`ddply()`

hammer!## @grautur 2010-08-17 22:28:44

Got it, I'll have to finally pick up plyr soon! Its prefix naming alone is gold...

## @John Robertson 2012-06-22 19:01:29

+1 For adding the note about tapply and sweep. Great to know both what plyr can and can't do.

## @marbel 2014-01-02 23:04:26

The plyr package has the

`join()`

function that performs tasks similar to merge. Perhaps it's more to the point to mention it in the context of plyr.## @jsanders 2014-06-11 14:26:06

@JdLong - this isn't a great forum for it, but I'd love to know what types of problems you've come across that you shouldn't have attempted to solve with plyr.

## @JD Long 2014-07-01 14:28:05

@jsanders some of my problems could have been much faster without ddply... but that was 4 years ago. I'm not sure that still applies. ddply is a dataframe approach. As I've been coding more I've gotten more comfortable with different data structures and am less tightly bound to dataframes. Although I still like them very much.