Dividing columns by colSums in R

Question

I am trying to scale the values in a matrix so that each column adds up to one. I have tried:

m = matrix(c(1:9),nrow=3, ncol=3, byrow=T)      [,1] [,2] [,3] [1,]    1    2    3 [2,]    4    5    6 [3,]    7    8    9  colSums(m) 12 15 18  m = m/colSums(m)           [,1]      [,2] [,3] [1,] 0.08333333 0.1666667 0.25 [2,] 0.26666667 0.3333333 0.40 [3,] 0.38888889 0.4444444 0.50  colSums(m) [1] 0.7388889 0.9444444 1.1500000 

so obviously this doesn't work. I then tried this:

m = m/matrix(rep(colSums(m),3), nrow=3, ncol=3, byrow=T)           [,1]      [,2]      [,3] [1,] 0.08333333 0.1333333 0.1666667 [2,] 0.33333333 0.3333333 0.3333333 [3,] 0.58333333 0.5333333 0.5000000   m = colSums(m) [1] 1 1 1 

so this works, but it feels like I'm missing something here. This can't be how it is routinely done. I'm certain I am being stupid here. Any help you can give would be appreciated Cheers, Davy

Answer 1

See ?sweep, eg:

> sweep(m,2,colSums(m),`/`)            [,1]      [,2]      [,3] [1,] 0.08333333 0.1333333 0.1666667 [2,] 0.33333333 0.3333333 0.3333333 [3,] 0.58333333 0.5333333 0.5000000 

or you can transpose the matrix and then colSums(m) gets recycled correctly. Don't forget to transpose afterwards again, like this :

> t(t(m)/colSums(m))            [,1]      [,2]      [,3] [1,] 0.08333333 0.1333333 0.1666667 [2,] 0.33333333 0.3333333 0.3333333 [3,] 0.58333333 0.5333333 0.5000000 

Or you use the function prop.table() to do basically the same:

> prop.table(m,2)            [,1]      [,2]      [,3] [1,] 0.08333333 0.1333333 0.1666667 [2,] 0.33333333 0.3333333 0.3333333 [3,] 0.58333333 0.5333333 0.5000000 

The time differences are rather small. the sweep() function and the t() trick are the most flexible solutions, prop.table() is only for this particular case