Apply a function to every row of a matrix or a data frame

Question

Suppose I have a n by 2 matrix and a function that takes a 2-vector as one of its arguments  I would like to apply the function to each row of the matrix and get a n-vector  How to do this in R   For example  I would like to compute the density of a 2D standard Normal distribution on three points   bivariate density x   c 0  0   mu   c 0  0   sigma   c 1  1   rho   0       exp -1  2  1-rho 2    x 1  2 sigma 1  2 x 2  2 sigma 2  2-2 rho x 1  x 2   sigma 1  sigma 2       1  2 pi sigma 1  sigma 2  sqrt 1-rho 2      out  lt - rbind c 1  2   c 3  4   c 5  6     How to apply the function to each row of out   How to pass values for the other arguments besides the points to the function in the way you specify

User · Answer

In case you want to apply common functions such as sum or mean, you should use rowSums or rowMeans since they're faster than apply(data, 1, sum) approach. Otherwise, stick with apply(data, 1, fun). You can pass additional arguments after FUN argument (as Dirk already suggested):

set.seed(1)
m <- matrix(round(runif(20, 1, 5)), ncol=4)
diag(m) <- NA
m
     [,1] [,2] [,3] [,4]
[1,]   NA    5    2    3
[2,]    2   NA    2    4
[3,]    3    4   NA    5
[4,]    5    4    3   NA
[5,]    2    1    4    4

Then you can do something like this:

apply(m, 1, quantile, probs=c(.25,.5, .75), na.rm=TRUE)
    [,1] [,2] [,3] [,4] [,5]
25%  2.5    2  3.5  3.5 1.75
50%  3.0    2  4.0  4.0 3.00
75%  4.0    3  4.5  4.5 4.00

User · Answer

Apply does the job well  but is quite slow   Using sapply and vapply could be useful  dplyr s rowwise could also be useful Let s see an example of how to do row wise product of any data frame   a   data frame t iris 1 10 1 3    vapply a  prod  0  sapply a  prod    Note that assigning to variable before using vapply sapply  apply is good practice as it reduces time a lot  Let s see microbenchmark results  a   data frame t iris 1 10 1 3    b   iris 1 10 1 3  microbenchmark  microbenchmark      apply b  1   prod       vapply a  prod  0       sapply a  prod         apply iris 1 10 1 3   1   prod       vapply data frame t iris 1 10 1 3     prod  0       sapply data frame t iris 1 10 1 3     prod        b   gt    rowwise     gt           summarise p   prod Sepal Length Sepal Width Petal Length       Have a careful look at how t   is being used

User · Answer

First step would be making the function object  then applying it  If you want a matrix object that has the same number of rows  you can predefine it and use the object   form as illustrated  otherwise the returned value will be simplified to a vector    bvnormdens  lt - function x c 0 0  mu c 0 0   sigma c 1 1   rho 0        exp -1  2  1-rho 2    x 1  2 sigma 1  2                             x 2  2 sigma 2  2-                            2 rho x 1  x 2   sigma 1  sigma 2             1  2 pi sigma 1  sigma 2  sqrt 1-rho 2           out rbind c 1 2  c 3 4  c 5 6      bvout lt -matrix NA  ncol 1  nrow 3   bvout    lt -apply out  1  bvnormdens   bvout                1   1   1 306423e-02  2   5 931153e-07  3   9 033134e-15   If you wanted to use other than your default parameters then the call should include named arguments after the function   bvout    lt -apply out  1  FUN bvnormdens  mu c -1 1   rho 0 6    apply   can also be used on higher dimensional arrays and the MARGIN argument can be a vector as well as a single integer

User · Answer

Another approach if you want to use a varying portion of the dataset instead of a single value is to use rollapply data  width  FUN         Using a vector of widths allows you to apply a function on a varying window of the dataset   I ve used this to build an adaptive filtering routine  though it isn t very efficient

User · Answer

You simply use the apply   function   R gt  M  lt - matrix 1 6  nrow 3  byrow TRUE  R gt  M        1    2   1      1    2  2      3    4  3      5    6 R gt  apply M  1  function x  2 x 1  x 2    1   4 10 16 R gt     This takes a matrix and applies a  silly  function to each row  You pass extra arguments to the function as fourth  fifth      arguments to apply

User · Answer

Here is a short example of applying a function to each row of a matrix   Here  the function applied normalizes every row to 1    Note  The result from the apply   had to be transposed using t   to get the same layout as the input matrix A   A  lt - matrix c    0  1  1  2    0  0  1  3    0  0  1  3    nrow   3  byrow   TRUE   t apply A  1  function x  x   sum x       Result          1    2    3    4   1      0 0 25 0 25 0 50  2      0 0 00 0 25 0 75  3      0 0 00 0 25 0 75

[r] Apply a function to every row of a matrix or a data frame

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