Efficient way to Calculate the squared distances for a set ofvectors to a fixed vector

R will subtract the vector columnwise from the matrix (so the vectors need
be the columns).

x <- matrix(0, nrow = 10L, ncol = 5L)
y <- 1:5
x - y

? ? ?[,1] [,2] [,3] [,4] [,5]
?[1,] ? -1 ? -1 ? -1 ? -1 ? -1
?[2,] ? -2 ? -2 ? -2 ? -2 ? -2
?[3,] ? -3 ? -3 ? -3 ? -3 ? -3
?[4,] ? -4 ? -4 ? -4 ? -4 ? -4
?[5,] ? -5 ? -5 ? -5 ? -5 ? -5
?[6,] ? -1 ? -1 ? -1 ? -1 ? -1
?[7,] ? -2 ? -2 ? -2 ? -2 ? -2
?[8,] ? -3 ? -3 ? -3 ? -3 ? -3
?[9,] ? -4 ? -4 ? -4 ? -4 ? -4
[10,] ? -5 ? -5 ? -5 ? -5 ? -5

-----Urspr?ngliche Nachricht-----
Von: Tsjerk Wassenaar [mailto:tsjerkw at gmail.com]
Gesendet: Mittwoch, 24. August 2011 09:02
An: Enrico Schumann
Cc: Wei Wu; r-help at r-project.org
Betreff: Re: [R] Efficient way to Calculate the squared
distances for a set ofvectors to a fixed vector

Hi Wei Wu,

What about:

x <- matrix(rnorm(20000*5),ncol=5)
y <- rnorm(5)
distances <- rowSums((x-y)**2)

Cheers,

Tsjerk

On Wed, Aug 24, 2011 at 8:43 AM, Enrico Schumann
<enricoschumann at yahoo.de> wrote:

You could do something like this:

# data
nrows <- 20000L
ncols <- 5L
myVec <- array(rnorm(nrows * ncols), dim = c(nrows, ncols)) y <-
rnorm(ncols)

temp <- t(myVec) - y
result <- colSums(temp * temp)

# check
all.equal(as.numeric(crossprod(myVec[1L, ] - y)), result[1L]) #...

(And don't use a data.frame, but a matrix.)

regards,
Enrico

-----Urspr?ngliche Nachricht-----
Von: r-help-bounces at r-project.org
[mailto:r-help-bounces at r-project.org] Im Auftrag von Wei Wu
Gesendet: Mittwoch, 24. August 2011 07:18
An: r-help at r-project.org
Betreff: [R] Efficient way to Calculate the squared

distances for a

set ofvectors to a fixed vector

I am pretty new to R. So this may be an easy question for

most of you.

I would like to calculate the squared distances of a large

set (let's

say 20000) of vectors (let's say dimension of 5) to a fixed vector.

Say I have a data frame MY_VECTORS with 20000 rows and 5

columns, and

one 5x1 vector y. I would like to efficiently calculate

the squared

distances?between each of the 20000 vectors in MY_VECTORS and y.

The squared distance between two vectors x and y can be calculated:
distance <- crossprod(x-y)

Without looping, what is?the efficient code to achieve this?

Thanks.

--
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials University of
Groningen The Netherlands