combiter

combiter: Combinatorics Iterators for R

Overview

This package provides iterators for combinations, permutations, subsets, and cartesian product, with which one can go through the elements without creating a huge set of all possible values.

Since v1.0.2, the iterator objects of the package inherit the iter class from iterators package. As a result, the objects are also compatible with foreach library.

Installation and Import

Install from CRAN:

install.packages("combiter")

Install development version:

devtools::install_github("kota7/combiter")

Import:

library(combiter)

Basic Iterators

This package provides four iterator classes for integer vectors: icomb, iperm, isubset, and icartes.

icomb(n, k) goes through all combinations of k integers out of 1 to n.
iperm(n, k) goes through all permutations of size k consisting of integers 1 to n of size k.
isubset(n) goes through all subsets of integers 1 to n.
icartes(c(n1, n2, ...)), available for v1.0.2+, goes through cartesian products of 1 to n1, 1 to n2 ….

The iterators do not store all possible values inside the object. Instead, they compute the next or previous element on spot. This implementation would be more memory efficient with a large n, since the number of possible cases grows exponentially or even faster for these Combinatorics operations.

Examples

x <- icomb(5, 3)
ct <- 0
while (hasNext(x))
{
  ct <- ct + 1
  i <- nextElem(x)
  cat(sprintf("%3d : %s\n", ct, paste0(i, collapse = " ")))
}

##   1 : 1 2 3
##   2 : 1 2 4
##   3 : 1 2 5
##   4 : 1 3 4
##   5 : 1 3 5
##   6 : 1 4 5
##   7 : 2 3 4
##   8 : 2 3 5
##   9 : 2 4 5
##  10 : 3 4 5

x <- iperm(4, 2)
ct <- 0
while (hasNext(x))
{
  ct <- ct + 1
  i <- nextElem(x)
  cat(sprintf("%3d : %s\n", ct, paste0(i, collapse = " ")))
}

##   1 : 1 2
##   2 : 1 3
##   3 : 1 4
##   4 : 2 1
##   5 : 2 3
##   6 : 2 4
##   7 : 3 1
##   8 : 3 2
##   9 : 3 4
##  10 : 4 1
##  11 : 4 2
##  12 : 4 3

x <- isubset(3)
ct <- 0
while (hasNext(x))
{
  ct <- ct + 1
  i <- nextElem(x)
  cat(sprintf("%3d : %s\n", ct, paste0(i, collapse = " ")))
}

##   1 : 
##   2 : 1
##   3 : 2
##   4 : 3
##   5 : 1 2
##   6 : 1 3
##   7 : 2 3
##   8 : 1 2 3

x <- icartes(c(3, 4))
ct <- 0
while (hasNext(x))
{
  ct <- ct + 1
  i <- nextElem(x)
  cat(sprintf("%3d : %s\n", ct, paste0(i, collapse = " ")))
}

##   1 : 1 1
##   2 : 1 2
##   3 : 1 3
##   4 : 1 4
##   5 : 2 1
##   6 : 2 2
##   7 : 2 3
##   8 : 2 4
##   9 : 3 1
##  10 : 3 2
##  11 : 3 3
##  12 : 3 4

Iterate through Values (v1.0.2+)

Each iterator shown above has its value counterpart. For example, ipermv, the value version of iperm, iterates through all permutations of k elements from n values.

x <- ipermv(c("A", "G", "C"), 2)
ct <- 0
while (hasNext(x))
{
  ct <- ct + 1
  i <- nextElem(x)
  cat(sprintf("%3d : %s\n", ct, paste0(i, collapse = " ")))
}

##   1 : A G
##   2 : A C
##   3 : G A
##   4 : G C
##   5 : C A
##   6 : C G

icombv, isubsetv, and icartesv are also defined analogously.

Use with `foreach` (v1.0.2+)

Since v1.0.2, the iterator objects can be used with foreach function from foreach.

library(foreach)
foreach(i = icomb(3, 2)) %do% sum(i)

## [[1]]
## [1] 3
## 
## [[2]]
## [1] 4
## 
## [[3]]
## [1] 5