Most efficient way to determine if element exists in a vector - r

Question

I have several algorithms that depend on the efficiency of determining whether an element exists in a vector or not. It seems to me that %in% (which is equivalent to is.element()) should be the most efficient as it simply returns a Boolean value. After testing several methods, to my surprise, those methods are by far the most inefficient. Below is my analysis (the results get worse as the size of the vectors increase):
EfficiencyTest <- function(n, Lim) {
samp1 <- sample(Lim, n)
set1 <- sample(Lim, Lim)
print(system.time(for(i in 1:n) {which(set1==samp1[i])}))
print(system.time(for(i in 1:n) {samp1[i] %in% set1}))
print(system.time(for(i in 1:n) {is.element(samp1[i], set1)}))
print(system.time(for(i in 1:n) {match(samp1[i], set1)}))
a <- system.time(set1 <- sort(set1))
b <- system.time(for (i in 1:n) {BinVecCheck(samp1[i], set1)})
print(a+b)
}
> EfficiencyTest(10^3, 10^5)
user system elapsed
0.29 0.11 0.40
user system elapsed
19.79 0.39 20.21
user system elapsed
19.89 0.53 20.44
user system elapsed
20.04 0.28 20.33
user system elapsed
0.02 0.00 0.03
Where BinVecCheck is a binary search algorithm that I wrote that returns TRUE/FALSE. Note that I include the time it takes to sort the vector with the final method. Here is the code for the binary search:
BinVecCheck <- function(tar, vec) {
if (tar==vec[1] || tar==vec[length(vec)]) {return(TRUE)}
size <- length(vec)
size2 <- trunc(size/2)
dist <- (tar - vec[size2])
if (dist > 0) {
lower <- size2 - 1L
upper <- size
} else {
lower <- 1L
upper <- size2 + 1L
}
while (size2 > 1 && !(dist==0)) {
size2 <- trunc((upper-lower)/2)
temp <- lower+size2
dist <- (tar - vec[temp])
if (dist > 0) {
lower <- temp-1L
} else {
upper <- temp+1L
}
}
if (dist==0) {return(TRUE)} else {return(FALSE)}
}
Platform Info:
> sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
Question
Is there a more efficient way of determining whether an element exists in a vector in R? For example, is there an equivalent R function to the Python set function, that greatly improves on this approach? Also, why is %in%, and the like, so inefficient even when compared to the which function which gives more information (not only does it determine existence, but it also gives the indices of all true accounts)?

Answer 1

My tests aren't bearing out all of your claims, but that seems (?) to be due to cross-platform differences (which makes the question even more mysterious, and possibly worth taking up on r-devel#r-project.org, although maybe not since the fastmatch solution below dominates anyway ...)
n <- 10^3; Lim <- 10^5
set.seed(101)
samp1 <- sample(Lim,n)
set1 <- sample(Lim,Lim)
library("rbenchmark")
library("fastmatch")
`%fin%` <- function(x, table) {
stopifnot(require(fastmatch))
fmatch(x, table, nomatch = 0L) > 0L
}
benchmark(which=sapply(samp1,function(x) which(set1==x)),
infun=sapply(samp1,function(x) x %in% set1),
fin= sapply(samp1,function(x) x %fin% set1),
brc= sapply(samp1,BinVecCheck,vec=sort(set1)),
replications=20,
columns = c("test", "replications", "elapsed", "relative"))
## test replications elapsed relative
## 4 brc 20 0.871 2.329
## 3 fin 20 0.374 1.000
## 2 infun 20 6.480 17.326
## 1 which 20 10.634 28.433
This says that %in% is about twice as fast as which -- your BinVecCheck function is 7x better, but the fastmatch solution from here gets another factor of 2. I don't know if a specialized Rcpp implementation could do better or not ...
In fact, I get different answers even when running your code:
## user system elapsed (which)
## 0.488 0.096 0.586
## user system elapsed (%in%)
## 0.184 0.132 0.315
## user system elapsed (is.element)
## 0.188 0.124 0.313
## user system elapsed (match)
## 0.148 0.164 0.312
## user system elapsed (BinVecCheck)
## 0.048 0.008 0.055
update: on r-devel Peter Dalgaard explains the platform discrepancy (which is an R version difference, not an OS difference) by pointing to the R NEWS entry:
match(x, table) is faster, sometimes by an order of magnitude, when x is of length one and incomparables is unchanged, thanks to Haverty's PR#16491.
sessionInfo()
## R Under development (unstable) (2015-10-23 r69563)
## Platform: i686-pc-linux-gnu (32-bit)
## Running under: Ubuntu precise (12.04.5 LTS)

Answer 2

%in% is just sugar for match, and is defined as:
"%in%" <- function(x, table) match(x, table, nomatch = 0) > 0
Both match and which are low level (compiled C) functions called by .Internal(). You can actually see the source code by using the pryr package:
install.packages("pryr")
library(pryr)
pryr::show_c_source(.Internal(which(x)))
pryr::show_c_source(.Internal(match(x, table, nomatch, incomparables)))
You would be pointed to this page for which and this page for match.
which does not perform any of the casting, checks etc that match performs. This might explain its higher performance in your tests (but I haven't tested your results myself).

Answer 3

After many days researching this topic, I have found that the fastest method of determining existence depends on the number of elements being tested. From the answer given by #ben-bolker, %fin% looks like the clear-cut winner. This seems to be the case when the number of elements being tested (all elements in samp1) is small compared to the size of the vector (set1). Before we go any further, lets look at the binary search algorithm above.
First of all, the very first line in the original algorithm has an extremely low probability of evaluating to TRUE, so why check it everytime?
if (tar==vec[1] || tar==vec[size]) {return(TRUE)}
Instead, I put this statement inside the else statement at the very-end.
Secondly, determining the size of the vector every time is redundant, especially when I know the length of the test vector (set1) ahead of time. So, I added size as an argument to the algorithm and simply pass it as a variable. Below is the modified binary search code.
ModifiedBinVecCheck <- function(tar, vec, size) {
size2 <- trunc(size/2)
dist <- (tar - vec[size2])
if (dist > 0) {
lower <- size2 - 1L
upper <- size
} else {
lower <- 1L
upper <- size2 + 1L
}
while (size2 > 1 && !(dist==0)) {
size2 <- trunc((upper-lower)/2)
temp <- lower+size2
dist <- (tar - vec[temp])
if (dist > 0) {
lower <- temp-1L
} else {
upper <- temp+1L
}
}
if (dist==0) {
return(TRUE)
} else {
if (tar==vec[1] || tar==vec[size]) {return(TRUE)} else {return(FALSE)}
}
}
As we know, in order to use a binary search, your vector must be sorted, which cost time. The default sorting method for sort is shell, which can be used on all datatypes, but has the drawback (generally speaking) of being slower than the quick method (quick can only be used on doubles or integers). With quick as my method for sorting (since we are dealing with numbers) combined with the modified binary search, we get a significant performance increase (from the old binary search depending on the case). It should be noted that fmatch improves on match only when the datatype is an integer, real, or character.
Now, let's look at some test cases with differing sizes of n.
Case1 (n = 10^3 & Lim = 10^6, so n to Lim ratio is 1:1000):
n <- 10^3; Lim <- 10^6
set.seed(101)
samp1 <- sample(Lim,n)
set1 <- sample(Lim,Lim)
benchmark(fin= sapply(samp1,function(x) x %fin% set1),
brc= sapply(samp1,ModifiedBinVecCheck,vec=sort(set1, method = "quick"),size=Lim),
oldbrc= sapply(samp1,BinVecCheck,vec=sort(set1)),
replications=10,
columns = c("test", "replications", "elapsed", "relative"))
test replications elapsed relative
2 brc 10 0.97 4.217
1 fin 10 0.23 1.000
3 oldbrc 10 1.45 6.304
Case2 (n = 10^4 & Lim = 10^6, so n to Lim ratio is 1:100):
n <- 10^4; Lim <- 10^6
set.seed(101)
samp1 <- sample(Lim,n)
set1 <- sample(Lim,Lim)
benchmark(fin= sapply(samp1,function(x) x %fin% set1),
brc= sapply(samp1,ModifiedBinVecCheck,vec=sort(set1, method = "quick"),size=Lim),
oldbrc= sapply(samp1,BinVecCheck,vec=sort(set1)),
replications=10,
columns = c("test", "replications", "elapsed", "relative"))
test replications elapsed relative
2 brc 10 2.08 1.000
1 fin 10 2.16 1.038
3 oldbrc 10 2.57 1.236
Case3: (n = 10^5 & Lim = 10^6, so n to Lim ratio is 1:10):
n <- 10^5; Lim <- 10^6
set.seed(101)
samp1 <- sample(Lim,n)
set1 <- sample(Lim,Lim)
benchmark(fin= sapply(samp1,function(x) x %fin% set1),
brc= sapply(samp1,ModifiedBinVecCheck,vec=sort(set1, method = "quick"),size=Lim),
oldbrc= sapply(samp1,BinVecCheck,vec=sort(set1)),
replications=10,
columns = c("test", "replications", "elapsed", "relative"))
test replications elapsed relative
2 brc 10 13.13 1.000
1 fin 10 21.23 1.617
3 oldbrc 10 13.93 1.061
Case4: (n = 10^6 & Lim = 10^6, so n to Lim ratio is 1:1):
n <- 10^6; Lim <- 10^6
set.seed(101)
samp1 <- sample(Lim,n)
set1 <- sample(Lim,Lim)
benchmark(fin= sapply(samp1,function(x) x %fin% set1),
brc= sapply(samp1,ModifiedBinVecCheck,vec=sort(set1, method = "quick"),size=Lim),
oldbrc= sapply(samp1,BinVecCheck,vec=sort(set1)),
replications=10,
columns = c("test", "replications", "elapsed", "relative"))
test replications elapsed relative
2 brc 10 124.61 1.000
1 fin 10 214.20 1.719
3 oldbrc 10 127.39 1.022
As you can see, as n gets large relative to Lim, the efficiency of the binary search (both of them) start to dominate. In Case 1, %fin% was over 4x faster than the modified binary search, in Case2 there was almost no difference, in Case 3 we really start to see the binary search dominance, and in Case 4, the modified binary search is almost twice as fast as %fin%.
Thus, to answer the question "Which method is faster?", it depends. %fin% is faster for a small number of elemental checks with respect to the test vector and the ModifiedBinVecCheck is faster for a larger number of elemental checks with respect to the test vector.

Answer 4

any( x == "foo" ) should be plenty fast if you can be sure that x is free of NAs. If you may have NAs, R 3.3 has a speedup for "%in%" that will help.
For binary search, see findInterval before rolling your own. This doesn't sound like a job for binary search unless x is constant and sorted.