longest common substring in R finding non-contiguous matches between the two strings

Question

I have a question regarding finding the longest common substring in R. While searching through a few posts on StackOverflow, I got to know about the qualV package. However,

Answer 1

Here are three possible solutions.

library(stringi)
library(stringdist)

a <- "hello"
b <- "hel123l5678o"

## get all forward substrings of 'b'
sb <- stri_sub(b, 1, 1:nchar(b))
## extract them from 'a' if they exist
sstr <- na.omit(stri_extract_all_coll(a, sb, simplify=TRUE))
## match the longest one
sstr[which.max(nchar(sstr))]
# [1] "hel"

There are also adist() and agrep() in base R, and the stringdist package has a few functions that run the LCS method. Here's a look at stringsidt. It returns the number of unpaired characters.

stringdist(a, b, method="lcs")
# [1] 7

Filter("!", mapply(
    stringdist, 
    stri_sub(b, 1, 1:nchar(b)),
    stri_sub(a, 1, 1:nchar(b)),
    MoreArgs = list(method = "lcs")
))
#  h  he hel 
#  0   0   0 

Now that I've explored this a bit more, I think adist() might be the way to go. If we set counts=TRUE we get a sequence of Matches, Insertions, etc. So if you give that to stri_locate() we can use that matrix to get the matches from a to b.

ta <- drop(attr(adist(a, b, counts=TRUE), "trafos")))
# [1] "MMMIIIMIIIIM"

So the M values denote straight across matches. We can go and get the substrings with stri_sub()

stri_sub(b, stri_locate_all_regex(ta, "M+")[[1]])
# [1] "hel" "l"   "o" 

Sorry I haven't explained that very well as I'm not well versed in string distance algorithms.