# Code-Pointwise Comparing#

This tutorial is based on the paper on stringi that was published in the Journal of Statistical Software; see [2]. To learn more about R, check out Marek’s open-access (free!) textbook Deep R Programming [3].

There are many settings where we are faced with testing whether two strings (or parts thereof) consist of exactly the same Unicode code points, in exactly the same order. These include, for instance, matching a nucleotide sequence in a DNA profile and querying for system resources based on file names or UUIDs. Such tasks, due to their simplicity, can be performed very efficiently.

## Testing for Equality of Strings#

To quickly test whether the corresponding strings in two character vectors are identical (in a code-pointwise manner), we can use the %s===% operator or, equivalently, the stri_cmp_eq() function. Moreover, %s!==% and stri_cmp_neq() implement the not-equal-to relation.

"actg" %s===% c("ACTG", "actg", "act", "actga", NA)
## [1] FALSE  TRUE FALSE FALSE    NA


Due to recycling, the first string was compared against the five strings in the 2nd operand. There is only one exact match.

## Searching for Fixed Strings#

For detecting if a string contains a given fixed substring (code-pointwisely), the fast KMP [7] algorithm, with worst time complexity of O(n+p) (where n is the length of the string and p is the length of the pattern), has been implemented in stringi (with numerous tweaks for even faster matching).

The table below lists the string search functions available in stringi. Below we explain their behaviour in the context of fixed pattern matching. Notably, their description is quite detailed because – as we shall soon find out – the corresponding operations are available for the two other search engines: based on regular expressions and the ICU Collator, see Regular Expressions and Collation.

Name(s)

Meaning

stri_count()

count pattern matches

stri_detect()

detect pattern matches

stri_endswith()

[all but regex] detect pattern matches at end of string

stri_extract_all(), stri_extract_first(), stri_extract_last()

extract pattern matches

stri_locate_all(), stri_locate_first(), stri_locate_last()

locate pattern matches

stri_match_all(), stri_match_first(), stri_match_last()

[regex only] extract matches to regex capture groups

stri_replace_all(), stri_replace_first(), stri_replace_last()

substitute pattern matches with some replacement strings

stri_split()

split up a string at pattern matches

stri_startswith()

[all but regex] detect pattern matches at start of string

stri_subset(), ‘stri_subset<-‘()

return or replace strings that contain pattern matches

## Counting Matches#

The stri_count_fixed() function counts the number of times a fixed pattern occurs in a given string.

stri_count_fixed("abcabcdefabcabcabdc", "abc")  # search pattern is "abc"
## [1] 4


Equivalently, we can call the more generic (see below) function stri_count() with the fixed=pattern argument:

stri_count("abcabcdefabcabcabdc", fixed="abc")
## [1] 4


Note that, unlike in the base R grep() function (and the like), the pattern (“needle”) is given by the second argument (here: “abc”). This makes our function more pipe-operator-friendly, because “haystack” can be forwarded as follows:

c("abcabcdefabcabcabdc", "cba", NA) |> stri_count_fixed("abc")
## [1]  4  0 NA


## Search Engine Options#

The pattern matching engine may be tuned up by passing further arguments to the search functions (via “...”; they are redirected as-is to stri_opts_fixed()). The table below gives the list of available options.

Option

Purpose

case_insensitive

logical; whether to enable the simple case-insensitive matching (defaults to FALSE)

overlap

logical; whether to enable the detection of overlapping matches (defaults to FALSE); available in stri_extract_all_fixed(), stri_locate_all_fixed(), and stri_count_fixed()

First, we may switch on the simplistic[1] case-insensitive matching.

stri_count_fixed("ACTGACGacgggACg", "acg", case_insensitive=TRUE)
## [1] 3


Second, we can indicate our interest in detecting overlapping pattern matches or whether searching should continue at the end of each match (the latter being the default behaviour):

stri_count_fixed("acatgacaca", "aca")  # overlap=FALSE (default)
## [1] 2
stri_count_fixed("acatgacaca", "aca", overlap=TRUE)
## [1] 3


## Detecting and Subsetting Patterns#

A somewhat simplified version of the above search task asks whether a pattern occurs in a string at all. Such an operation can be performed with a call to stri_detect_fixed().

x <- c("abc", "abcd", "def", "xyzabc", "uabdc", "dab", NA, "abc")
stri_detect_fixed(x, "abc")
## [1]  TRUE  TRUE FALSE  TRUE FALSE FALSE    NA  TRUE


We can also indicate that a no-match is rather of our interest by passing negate=TRUE. What is more, there is an option to stop searching once a given number of matches has been found in the haystack vector (as a whole), which can speed up the processing of larger data sets:

stri_detect_fixed(x, "abc", negate=TRUE, max_count=2)
## [1] FALSE FALSE  TRUE FALSE  TRUE    NA    NA    NA


This can be useful in scenarios such as “find the first 2 matching resource IDs”.

There are also functions that verify whether a string starts or ends[2] with a pattern match:

stri_startswith_fixed(x, "abc")  # from=1 - match at start
## [1]  TRUE  TRUE FALSE FALSE FALSE FALSE    NA  TRUE
stri_endswith_fixed(x, "abc")    # to=-1 - match at end
## [1]  TRUE FALSE FALSE  TRUE FALSE FALSE    NA  TRUE


Pattern detection is often performed in conjunction with character vector subsetting. This is why we have a specialised (and hence slightly faster) function that returns only the strings that match a given pattern.

stri_subset_fixed(x, "abc", omit_na=TRUE)
## [1] "abc"    "abcd"   "xyzabc" "abc"


The above is equivalent to x[which(stri_detect_fixed(x, "abc"))] (note the argument responsible for the removal of missing values), but avoids writing x twice. It is particularly convenient when x is generated programmatically on the fly, using some complicated expression. Also, it works well with the forward pipe operator, as we can write “x |> stri_subset_fixed("abc", omit_na=TRUE)”.

There is also a replacement version of this function:

stri_subset_fixed(x, "abc") <- c("*****", "***")  # modifies x in-place
print(x)  # x has changed
## [1] "*****" "***"   "def"   "*****" "uabdc" "dab"   NA      "***"


## Locating and Extracting Patterns#

The functions from the stri_locate() family aim to pinpoint the positions of pattern matches. First, we may be interested in getting to know the location of the first or the last pattern occurrence:

x <- c("aga", "actg", NA, "AGagaGAgaga")
stri_locate_first_fixed(x, "aga")
##      start end
## [1,]     1   3
## [2,]    NA  NA
## [3,]    NA  NA
## [4,]     3   5
stri_locate_last_fixed(x, "aga", get_length=TRUE)
##      start length
## [1,]     1      3
## [2,]    -1     -1
## [3,]    NA     NA
## [4,]     9      3


In both examples, we obtain a two-column matrix with the number of rows determined by the recycling rule (here: the length of x). In the former case, we get a “from–to” matrix (get_length=FALSE; the default) where missing values correspond to either missing inputs or no-matches. The latter gives a “from–length”-type matrix, where negative lengths correspond to the not-founds.

Second, we may be yearning for the locations of all the matching substrings. As the number of possible answers may vary from string to string, the result is a list of index matrices.

stri_locate_all_fixed(x, "aga", overlap=TRUE, case_insensitive=TRUE)
## [[1]]
##      start end
## [1,]     1   3
##
## [[2]]
##      start end
## [1,]    NA  NA
##
## [[3]]
##      start end
## [1,]    NA  NA
##
## [[4]]
##      start end
## [1,]     1   3
## [2,]     3   5
## [3,]     5   7
## [4,]     7   9
## [5,]     9  11


Note again that a no-match is indicated by a single-row matrix with two missing values (or with negative length if get_length=TRUE). This behaviour can be changed by setting the omit_no_match argument to TRUE.

Let us recall that “from–to” and “from–length” matrices of the above kind constitute particularly fine inputs to stri_sub() and stri_sub_all(). However, if merely the extraction of the matching substrings is needed, it will be more convenient to rely on the functions from the stri_extract() family:

stri_extract_first_fixed(x, "aga", case_insensitive=TRUE)
## [1] "aga" NA    NA    "AGa"
stri_extract_all_fixed(x, "aga",
overlap=TRUE, case_insensitive=TRUE, omit_no_match=TRUE)
## [[1]]
## [1] "aga"
##
## [[2]]
## character(0)
##
## [[3]]
## [1] NA
##
## [[4]]
## [1] "AGa" "aga" "aGA" "Aga" "aga"


## Replacing Pattern Occurrences#

In order to replace each match with a corresponding replacement string, we can refer to stri_replace_all():

x <- c("aga", "actg", NA, "ggAGAGAgaGAca", "agagagaga")
stri_replace_all_fixed(x, "aga", "~", case_insensitive=TRUE)
## [1] "~"         "actg"      NA          "gg~G~GAca" "~g~ga"


Note that the inputs that are not part of any match are left unchanged. The input object is left unchanged because it is not a replacement function per se.

The operation is vectorised with respect to all the three arguments (haystack, needle, replacement string), with the usual recycling behaviour if necessary. If a different arguments’ vectorisation scheme is required, we can set the vectorise_all argument of stri_replace_all() to FALSE. Compare the following:

stri_replace_all_fixed("The quick brown fox jumped over the lazy dog.",
c("quick", "brown",      "fox", "lazy",    "dog"),
c("slow",  "yellow-ish", "hen", "spamity", "llama"))
## [1] "The slow brown fox jumped over the lazy dog."
## [2] "The quick yellow-ish fox jumped over the lazy dog."
## [3] "The quick brown hen jumped over the lazy dog."
## [4] "The quick brown fox jumped over the spamity dog."
## [5] "The quick brown fox jumped over the lazy llama."
stri_replace_all_fixed("The quick brown fox jumped over the lazy dog.",
c("quick", "brown",      "fox", "lazy", "dog"),
c("slow",  "yellow-ish", "hen", "spamity", "llama"),
vectorise_all=FALSE)
## [1] "The slow yellow-ish hen jumped over the spamity llama."


Here, for every string in the haystack, we observe the vectorisation independently over the needles and replacement strings. Each occurrence of the 1st needle is superseded by the 1st replacement string, then the search is repeated for the 2nd needle so as to replace it with the 2nd corresponding replacement string, and so forth.

Moreover, stri_replace_first() and stri_replace_last() can identify and replace the first and the last match, respectively.

## Splitting#

To split each element in the haystack into substrings, where the needles define the delimiters that separate the inputs into tokens, we call stri_split():

x <- c("a,b,c,d", "e", "", NA, "f,g,,,h,i,,j,")
stri_split_fixed(x, ",", omit_empty=TRUE)
## [[1]]
## [1] "a" "b" "c" "d"
##
## [[2]]
## [1] "e"
##
## [[3]]
## character(0)
##
## [[4]]
## [1] NA
##
## [[5]]
## [1] "f" "g" "h" "i" "j"


The result is a list of character vectors, as each string in the haystack might be split into a possibly different number of tokens.

There is also an option to limit the number of tokens (parameter n).