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grep: Pattern Matching and Replacement

grep	R Documentation

Pattern Matching and Replacement

Description

grep, grepl, regexpr, gregexpr, regexec and gregexec search for matches to argument pattern within each element of a character vector: they differ in the format of and amount of detail in the results.

sub and gsub perform replacement of the first and all matches respectively.

Usage

grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = FALSE,
     fixed = FALSE, useBytes = FALSE, invert = FALSE)

grepl(pattern, x, ignore.case = FALSE, perl = FALSE,
      fixed = FALSE, useBytes = FALSE)

sub(pattern, replacement, x, ignore.case = FALSE, perl = FALSE,
    fixed = FALSE, useBytes = FALSE)

gsub(pattern, replacement, x, ignore.case = FALSE, perl = FALSE,
     fixed = FALSE, useBytes = FALSE)

regexpr(pattern, text, ignore.case = FALSE, perl = FALSE,
        fixed = FALSE, useBytes = FALSE)

gregexpr(pattern, text, ignore.case = FALSE, perl = FALSE,
         fixed = FALSE, useBytes = FALSE)

regexec(pattern, text, ignore.case = FALSE, perl = FALSE,
        fixed = FALSE, useBytes = FALSE)

gregexec(pattern, text, ignore.case = FALSE, perl = FALSE,
        fixed = FALSE, useBytes = FALSE)

Arguments

`pattern`	character string containing a regular expression (or character string for `fixed = TRUE`) to be matched in the given character vector. Coerced by `as.character` to a character string if possible. If a character vector of length 2 or more is supplied, the first element is used with a warning. Missing values are allowed except for `regexpr`, `gregexpr` and `regexec`.
`x, text`	a character vector where matches are sought, or an object which can be coerced by `as.character` to a character vector. Long vectors are supported.
`ignore.case`	if `FALSE`, the pattern matching is case sensitive and if `TRUE`, case is ignored during matching.
`perl`	logical. Should Perl-compatible regexps be used?
`value`	if `FALSE`, a vector containing the (`integer`) indices of the matches determined by `grep` is returned, and if `TRUE`, a vector containing the matching elements themselves is returned.
`fixed`	logical. If `TRUE`, `pattern` is a string to be matched as is. Overrides all conflicting arguments.
`useBytes`	logical. If `TRUE` the matching is done byte-by-byte rather than character-by-character. See ‘Details’.
`invert`	logical. If `TRUE` return indices or values for elements that do not match.
`replacement`	a replacement for matched pattern in `sub` and `gsub`. Coerced to character if possible. For `fixed = FALSE` this can include backreferences `"\1"` to `"\9"` to parenthesized subexpressions of `pattern`. For `perl = TRUE` only, it can also contain `"\U"` or `"\L"` to convert the rest of the replacement to upper or lower case and `"\E"` to end case conversion. If a character vector of length 2 or more is supplied, the first element is used with a warning. If `NA`, all elements in the result corresponding to matches will be set to `NA`.

Details

Arguments which should be character strings or character vectors are coerced to character if possible.

Each of these functions operates in one of three modes:

fixed = TRUE: use exact matching.
perl = TRUE: use Perl-style regular expressions.
fixed = FALSE, perl = FALSE: use POSIX 1003.2 extended regular expressions (the default).

See the help pages on regular expression for details of the different types of regular expressions.

The two *sub functions differ only in that sub replaces only the first occurrence of a pattern whereas gsub replaces all occurrences. If replacement contains backreferences which are not defined in pattern the result is undefined (but most often the backreference is taken to be "").

For regexpr, gregexpr, regexec and gregexec it is an error for pattern to be NA, otherwise NA is permitted and gives an NA match.

Both grep and grepl take missing values in x as not matching a non-missing pattern.

The main effect of useBytes = TRUE is to avoid errors/warnings about invalid inputs and spurious matches in multibyte locales, but for regexpr it changes the interpretation of the output. It inhibits the conversion of inputs with marked encodings, and is forced if any input is found which is marked as "bytes" (see Encoding).

Caseless matching does not make much sense for bytes in a multibyte locale, and you should expect it only to work for ASCII characters if useBytes = TRUE.

regexpr and gregexpr with perl = TRUE allow Python-style named captures, but not for long vector inputs.

Invalid inputs in the current locale are warned about up to 5 times.

Caseless matching with perl = TRUE for non-ASCII characters depends on the PCRE library being compiled with ‘Unicode property support’, which PCRE2 is by default.

Value

grep(value = FALSE) returns a vector of the indices of the elements of x that yielded a match (or not, for invert = TRUE). This will be an integer vector unless the input is a long vector, when it will be a double vector.

grep(value = TRUE) returns a character vector containing the selected elements of x (after coercion, preserving names but no other attributes).

grepl returns a logical vector (match or not for each element of x).

sub and gsub return a character vector of the same length and with the same attributes as x (after possible coercion to character). Elements of character vectors x which are not substituted will be returned unchanged (including any declared encoding). If useBytes = FALSE a non-ASCII substituted result will often be in UTF-8 with a marked encoding (e.g., if there is a UTF-8 input, and in a multibyte locale unless fixed = TRUE). Such strings can be re-encoded by enc2native.

regexpr returns an integer vector of the same length as text giving the starting position of the first match or -1 if there is none, with attribute "match.length", an integer vector giving the length of the matched text (or -1 for no match). The match positions and lengths are in characters unless useBytes = TRUE is used, when they are in bytes (as they are for ASCII-only matching: in either case an attribute useBytes with value TRUE is set on the result). If named capture is used there are further attributes "capture.start", "capture.length" and "capture.names".

gregexpr returns a list of the same length as text each element of which is of the same form as the return value for regexpr, except that the starting positions of every (disjoint) match are given.

regexec returns a list of the same length as text each element of which is either -1 if there is no match, or a sequence of integers with the starting positions of the match and all substrings corresponding to parenthesized subexpressions of pattern, with attribute "match.length" a vector giving the lengths of the matches (or -1 for no match). The interpretation of positions and length and the attributes follows regexpr.

gregexec returns the same as regexec, except that to accommodate multiple matches per element of text, the integer sequences for each match are made into columns of a matrix, with one matrix per element of text with matches.

Where matching failed because of resource limits (especially for perl = TRUE) this is regarded as a non-match, usually with a warning.

Warning

The POSIX 1003.2 mode of gsub and gregexpr does not work correctly with repeated word-boundaries (e.g., pattern = "\b"). Use perl = TRUE for such matches (but that may not work as expected with non-ASCII inputs, as the meaning of ‘word’ is system-dependent).

Performance considerations

If you are doing a lot of regular expression matching, including on very long strings, you will want to consider the options used. Generally perl = TRUE will be faster than the default regular expression engine, and fixed = TRUE faster still (especially when each pattern is matched only a few times).

If you are working in a single-byte locale and have marked UTF-8 strings that are representable in that locale, convert them first as just one UTF-8 string will force all the matching to be done in Unicode, which attracts a penalty of around 3x for the default POSIX 1003.2 mode.

If you can make use of useBytes = TRUE, the strings will not be checked before matching, and the actual matching will be faster. Often byte-based matching suffices in a UTF-8 locale since byte patterns of one character never match part of another. Character ranges may produce unexpected results.

PCRE-based matching by default used to put additional effort into ‘studying’ the compiled pattern when x/text has length 10 or more. That study may use the PCRE JIT compiler on platforms where it is available (see pcre_config). As from PCRE2 (PCRE version >= 10.00 as reported by extSoftVersion), there is no study phase, but the patterns are optimized automatically when possible, and PCRE JIT is used when enabled. The details are controlled by options PCRE_study and PCRE_use_JIT. (Some timing comparisons can be seen by running file ‘tests/PCRE.R’ in the R sources (and perhaps installed).) People working with PCRE and very long strings can adjust the maximum size of the JIT stack by setting environment variable R_PCRE_JIT_STACK_MAXSIZE before JIT is used to a value between 1 and 1000 in MB: the default is 64. When JIT is not used with PCRE version < 10.30 (that is with PCRE1 and old versions of PCRE2), it might also be wise to set the option PCRE_limit_recursion.

Note

Aspects will be platform-dependent as well as local-dependent: for example the implementation of character classes (except [:digit:] and [:xdigit:]). One can expect results to be consistent for ASCII inputs and when working in UTF-8 mode (when most platforms will use Unicode character tables, although those are updated frequently and subject to some degree of interpretation – is a circled capital letter alphabetic or a symbol?). However, results in 8-bit encodings can differ considerably between platforms, modes and from the UTF-8 versions.

Source

The C code for POSIX-style regular expression matching has changed over the years. As from R 2.10.0 (Oct 2009) the TRE library of Ville Laurikari (https://github.com/laurikari/tre) is used. The POSIX standard does give some room for interpretation, especially in the handling of invalid regular expressions and the collation of character ranges, so the results will have changed slightly over the years.

For Perl-style matching PCRE2 or PCRE (https://www.pcre.org) is used: again the results may depend (slightly) on the version of PCRE in use.

References

Becker, R. A., Chambers, J. M. and Wilks, A. R. (1988) The New S Language. Wadsworth & Brooks/Cole (grep)

Examples

grep("[a-z]", letters)

txt <- c("arm","foot","lefroo", "bafoobar")
if(length(i <- grep("foo", txt)))
   cat("'foo' appears at least once in\n\t", txt, "\n")
i # 2 and 4
txt[i]

## Double all 'a' or 'b's;  "\" must be escaped, i.e., 'doubled'
gsub("([ab])", "\\1_\\1_", "abc and ABC")

txt <- c("The", "licenses", "for", "most", "software", "are",
  "designed", "to", "take", "away", "your", "freedom",
  "to", "share", "and", "change", "it.",
  "", "By", "contrast,", "the", "GNU", "General", "Public", "License",
  "is", "intended", "to", "guarantee", "your", "freedom", "to",
  "share", "and", "change", "free", "software", "--",
  "to", "make", "sure", "the", "software", "is",
  "free", "for", "all", "its", "users")
( i <- grep("[gu]", txt) ) # indices
stopifnot( txt[i] == grep("[gu]", txt, value = TRUE) )

## Note that for some implementations character ranges are
## locale-dependent (but not currently).  Then [b-e] in locales such as
## en_US may include B as the collation order is aAbBcCdDe ...
(ot <- sub("[b-e]",".", txt))
txt[ot != gsub("[b-e]",".", txt)]#- gsub does "global" substitution
## In caseless matching, ranges include both cases:
a <- grep("[b-e]", txt, value = TRUE)
b <- grep("[b-e]", txt, ignore.case = TRUE, value = TRUE)
setdiff(b, a)

txt[gsub("g","#", txt) !=
    gsub("g","#", txt, ignore.case = TRUE)] # the "G" words

regexpr("en", txt)

gregexpr("e", txt)

## Using grepl() for filtering
## Find functions with argument names matching "warn":
findArgs <- function(env, pattern) {
  nms <- ls(envir = as.environment(env))
  nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around "checking hack"
  aa <- sapply(nms, function(.) { o <- get(.)
               if(is.function(o)) names(formals(o)) })
  iw <- sapply(aa, function(a) any(grepl(pattern, a, ignore.case=TRUE)))
  aa[iw]
}
findArgs("package:base", "warn")

## trim trailing white space
str <- "Now is the time      "
sub(" +$", "", str)  ## spaces only
## what is considered 'white space' depends on the locale.
sub("[[:space:]]+$", "", str) ## white space, POSIX-style
## what PCRE considered white space changed in version 8.34: see ?regex
sub("\\s+$", "", str, perl = TRUE) ## PCRE-style white space

## capitalizing
txt <- "a test of capitalizing"
gsub("(\\w)(\\w*)", "\\U\\1\\L\\2", txt, perl=TRUE)
gsub("\\b(\\w)",    "\\U\\1",       txt, perl=TRUE)

txt2 <- "useRs may fly into JFK or laGuardia"
gsub("(\\w)(\\w*)(\\w)", "\\U\\1\\E\\2\\U\\3", txt2, perl=TRUE)
 sub("(\\w)(\\w*)(\\w)", "\\U\\1\\E\\2\\U\\3", txt2, perl=TRUE)

## named capture
notables <- c("  Ben Franklin and Jefferson Davis",
              "\tMillard Fillmore")
# name groups 'first' and 'last'
name.rex <- "(?<first>[[:upper:]][[:lower:]]+) (?<last>[[:upper:]][[:lower:]]+)"
(parsed <- regexpr(name.rex, notables, perl = TRUE))
gregexpr(name.rex, notables, perl = TRUE)[[2]]
parse.one <- function(res, result) {
  m <- do.call(rbind, lapply(seq_along(res), function(i) {
    if(result[i] == -1) return("")
    st <- attr(result, "capture.start")[i, ]
    substring(res[i], st, st + attr(result, "capture.length")[i, ] - 1)
  }))
  colnames(m) <- attr(result, "capture.names")
  m
}
parse.one(notables, parsed)

## Decompose a URL into its components.
## Example by LT (http://www.cs.uiowa.edu/~luke/R/regexp.html).
x <- "http://stat.umn.edu:80/xyz"
m <- regexec("^(([^:]+)://)?([^:/]+)(:([0-9]+))?(/.*)", x)
m
regmatches(x, m)
## Element 3 is the protocol, 4 is the host, 6 is the port, and 7
## is the path.  We can use this to make a function for extracting the
## parts of a URL:
URL_parts <- function(x) {
    m <- regexec("^(([^:]+)://)?([^:/]+)(:([0-9]+))?(/.*)", x)
    parts <- do.call(rbind,
                     lapply(regmatches(x, m), `[`, c(3L, 4L, 6L, 7L)))
    colnames(parts) <- c("protocol","host","port","path")
    parts
}
URL_parts(x)

## gregexec() may match multiple times within a single string.
pattern <- "([[:alpha:]]+)([[:digit:]]+)"
s <- "Test: A1 BC23 DEF456"
m <- gregexec(pattern, s)
m
regmatches(s, m)

## Before gregexec() was implemented, one could emulate it by running
## regexec() on the regmatches obtained via gregexpr().  E.g.:
lapply(regmatches(s, gregexpr(pattern, s)),
       function(e) regmatches(e, regexec(pattern, e)))