What is a better way to write this nested for loop in R?

Question

I am writing a for loop to calculate a numerator which is part of a larger formula. I used a for loop but it is taking a lot of time to compute. What would be a better way to do this.

city is a dataframe with the following columns: pop, not.white, pct.not.white

  n <- nrow(city)

  numerator = 0

  for(i in 1:n) {

    ti <- city$pop[i]
    pi<- city$pct.not.white[i]

    for(j in 1:n) {

      tj <- city$pop[j]
      pj <- city$pct.not.white[j]

      numerator = numerator + (ti * tj) * abs(pi -pj)

    }

  }

Zheyuan Li · Accepted Answer · 2018-10-28T07:35:36.680

Use the following toy data for result validation.

set.seed(0)
city <- data.frame(pop = runif(101), pct.not.white = runif(101))

The most obvious "vectorization":

# n <- nrow(city)
titj <- tcrossprod(city$pop)
pipj <- outer(city$pct.not.white, city$pct.not.white, "-")
numerator <- sum(titj * abs(pipj))

Will probably have memory problem if n > 5000.

A clever workaround (exploiting symmetry; more memory efficient "vectorization"):

## see https://stackoverflow.com/a/52086291/4891738 for function: tri_ind
n <- nrow(city)
ij <- tri_ind(n, lower = TRUE, diag = FALSE)
titj <- city$pop[ij$i] * city$pop[ij$j]
pipj <- abs(city$pct.not.white[ij$i] - city$pct.not.white[ij$j])
numerator <- 2 * crossprod(titj, pipj)[1]

The ultimate solution is to write C / C++ loop, which I will not showcase.

What is a better way to write this nested for loop in R?

1 Answers1