[R] avoid a loop

[Joshua Wiley]

And to wrap it up and help you choose, here are four functions based
on these emails (the first one is my own slight variant):

library(ecodist)
a <- sample(1:1000, 10^4, replace = TRUE)
b <- sample(letters[1:6], 10^4, replace = TRUE)

foo1 <- function() {
  x <- table(a, b)
  return(x %*% t(x))
}

foo2 <- function() {
  x <- crosstab(a, b, rep(1, length(a)))
  return(x %*% t(x))
}

foo3 <- function() {
  sapply(1:1000, function(y) {
    sapply(1:1000, function(x) {
      length(intersect(b[a==y], b[a==x]))
    })
  })
}

foo4 <- function() {crossprod(t(as.matrix(table(a, b))))}

> system.time(x1 <- foo1())
   user  system elapsed
  0.028   0.008   0.038
> system.time(x2 <- foo2())
   user  system elapsed
  0.076   0.008   0.087
## I got tired of waiting
> system.time(x3 <- foo3())
  <menu-bar> <signals> <break>
Timing stopped at: 104.951 1.336 110.909
> system.time(x4 <- foo4())
   user  system elapsed
  0.024   0.020   0.043

> all.equal(x1, x2, check.attributes = FALSE)
[1] TRUE
> all.equal(x1, x4, check.attributes = FALSE)
[1] TRUE

This suggests the speeds are:

foo1 < foo4 < foo2 < foo3

Cheers,

Josh

On Thu, Nov 4, 2010 at 12:42 PM, cory n <corynissen at gmail.com> wrote:
> Let's suppose I have userids and associated attributes...  columns a and b
>
> a <- c(1,1,1,2,2,3,3,3,3)
> b <- c("a","b","c","a","d","a", "b", "e", "f")
>
> so a unique list of a would be
>
> id <- unique(a)
>
> I want a matrix like this...
>
>     [,1] [,2] [,3]
> [1,]    3    1    2
> [2,]    1    2    1
> [3,]    2    1    4
>
> Where element i,j is the number of items in b that id[i] and id[j] share...
>
> So for example, in element [1,3] of the result matrix, I want to see
> 2.  That is, id's 1 and 3 share two common elements in b, namely "a"
> and "b".
>
> This is hard to articulate, so sorry for the terrible description
> here.  The way I have solved it is to do a double loop, looping over
> every member of the id column and comparing it to every other member
> of id to see how many elements of b they share.  This takes forever.
>
> Thanks
>
> cn
>
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> and provide commented, minimal, self-contained, reproducible code.
>



-- 
Joshua Wiley
Ph.D. Student, Health Psychology
University of California, Los Angeles
http://www.joshuawiley.com/