| Type: | Package |
| Title: | Abbreviate Strings to Short, Unique Identifiers |
| Version: | 1.0.1 |
| Description: | For each string in a set of strings, determine a unique tag that is a substring of fixed size k unique to that string, if it has one. If no such unique substring exists, the least frequent substring is used. If multiple unique substrings exist, the lexicographically smallest substring is used. This lexicographically smallest substring of size k is called the "UniqTag" of that string. |
| License: | MIT + file LICENSE |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.1.2 |
| URL: | https://github.com/sjackman/uniqtag |
| BugReports: | https://github.com/sjackman/uniqtag/issues |
| Suggests: | testthat |
| NeedsCompilation: | no |
| Packaged: | 2022-05-10 21:34:38 UTC; shaun.jackman |
| Author: | Shaun Jackman [aut, cph, cre] |
| Maintainer: | Shaun Jackman <sjackman@gmail.com> |
| Repository: | CRAN |
| Date/Publication: | 2022-06-10 06:10:02 UTC |
Abbreviate strings to short, unique identifiers.
Description
For each string in a set of strings, determine a unique tag that is a substring of fixed size k unique to that string, if it has one. If no such unique substring exists, the least frequent substring is used. If multiple unique substrings exist, the lexicographically smallest substring is used. This lexicographically smallest substring of size k is called the "UniqTag" of that string.
Author(s)
Shaun Jackman sjackman@gmail.com
Cumulative count of strings.
Description
Return an integer vector counting the number of occurrences of each string up to that position in the vector.
Usage
cumcount(xs)
Arguments
xs |
a character vector |
Value
an integer vector of the cumulative string counts
Examples
cumcount(abbreviate(state.name, 3, strict = TRUE))
Return the k-mers of a string.
Description
Return the k-mers (substrings of size k) of the string x, or
return the string x itself if it is shorter than k.
Usage
kmers_of(x, k)
vkmers_of(xs, k)
Arguments
x |
a character string |
k |
the size of the substrings, an integer |
xs |
a character vector |
Value
kmers_of: a character vector of the k-mers of x
vkmers_of: a list of character vectors of the k-mers of xs
Functions
-
kmers_of: Return the k-mers of the stringx. -
vkmers_of: Return the k-mers of the stringsxs.
Make character strings unique.
Description
Append sequence numbers to duplicate elements to make all elements of a character vector unique.
Usage
make_unique(xs, sep = "-")
make_unique_duplicates(xs, sep = "-")
make_unique_all(xs, sep = "-")
make_unique_all_or_none(xs, sep = "-")
Arguments
xs |
a character vector |
sep |
a character string used to separate a duplicate string from its sequence number |
Functions
-
make_unique: Append a sequence number to duplicated elements, including the first occurrence. -
make_unique_duplicates: Append a sequence number to duplicated elements, except the first occurrence.This function behaves similarly to make.unique
-
make_unique_all: Append a sequence number to every element. -
make_unique_all_or_none: Append a sequence number to every element or no elements.Return
xsunchanged if the elements of the character vectorxsare already unique. Otherwise append a sequence number to every element.
See Also
make.unique
Examples
abcb <- c("a", "b", "c", "b")
make_unique(abcb)
make_unique_duplicates(abcb)
make_unique_all(abcb)
make_unique_all_or_none(abcb)
make_unique_all_or_none(c("a", "b", "c"))
x <- make_unique(abbreviate(state.name, 3, strict = TRUE))
x[grep("-", x)]
Abbreviate strings to short, unique identifiers.
Description
Abbreviate strings to unique substrings of k characters.
Usage
uniqtag(xs, k = 9, uniq = make_unique_all_or_none, sep = "-")
Arguments
xs |
a character vector |
k |
the size of the identifier, an integer |
uniq |
a function to make the abbreviations unique, such as make_unique, make_unique_duplicates, make_unique_all_or_none, make_unique_all, make.unique, or to disable this function, identity or NULL |
sep |
a character string used to separate a duplicate string from its sequence number |
Details
For each string in a set of strings, determine a unique tag that is a substring of fixed size k unique to that string, if it has one. If no such unique substring exists, the least frequent substring is used. If multiple unique substrings exist, the lexicographically smallest substring is used. This lexicographically smallest substring of size k is called the UniqTag of that string.
The lexicographically smallest substring depend on the locale's sort order.
You may wish to first call Sys.setlocale("LC_COLLATE", "C")
Value
a character vector of the UniqTags of the strings x
See Also
abbreviate, locales, make.unique
Examples
Sys.setlocale("LC_COLLATE", "C")
states <- sub(" ", "", state.name)
uniqtags <- uniqtag(states)
uniqtags4 <- uniqtag(states, k = 4)
uniqtags3 <- uniqtag(states, k = 3)
uniqtags3x <- uniqtag(states, k = 3, uniq = make_unique)
table(nchar(states))
table(nchar(uniqtags))
table(nchar(uniqtags4))
table(nchar(uniqtags3))
table(nchar(uniqtags3x))
uniqtags3[grep("-", uniqtags3x)]