AhoCorasickTrie-package

AhoCorasickTrie

Builds an Aho-Corasick trie from one or more keywords and uses it to
 search one or more texts. For a large number of keywords, Aho-Corasick is much faster
 than a naive approach (such as <code>lapply(keywords, gregexpr, text)</code>).

Aho-Corasick is an optimal algorithm for finding many
keywords in a text. It can locate all matches in a text in O(N+M) time; i.e.,
the time needed scales linearly with the number of keywords (N) and the size of
the text (M). Compare this to the naive approach which takes O(N*M) time to loop
through each pattern and scan for it in the text. This implementation builds the
trie (the generic name of the data structure) and runs the search in a single
function call. If you want to search multiple texts with the same trie, the
function will take a list or vector of texts and return a list of matches to
each text. By default, all 128 ASCII characters are allowed in both the keywords
and the text. A more efficient trie is possible if the alphabet size can be
reduced. For example, DNA sequences use at most 19 distinct characters and
usually only 4; protein sequences use at most 26 distinct characters and usually
only 20. UTF-8 (Unicode) matching is not currently supported.

Matt Chambers

Fast Searching for Multiple Keywords in Multiple Texts

Tomas Petricek

Vanderbilt University 

AhoCorasickTrie function

Maintainer: Matt Chambers <a href="/link/matt.chambers42%40gmail.com?package=AhoCorasickTrie&version=0.1.3" data-mini-rdoc="AhoCorasickTrie::matt.chambers42@gmail.com">matt.chambers42@gmail.com</a>
Authors:<ul>
<li>Tomas Petricek [copyright holder]</li>
</ul>Other contributors:<ul>
<li>Vanderbilt University [copyright holder]</li>
</ul>

Author

AhoCorasickTrie: fast searching for multiple keywords in multiple texts — AhoCorasickTrie

Maintainer: Matt Chambers <a href='mailto:matt.chambers42@gmail.com'>matt.chambers42@gmail.com</a>
Authors:<ul>
<li>Tomas Petricek [copyright holder]</li>
</ul>

Other contributors:<ul>
<li>Vanderbilt University [copyright holder]</li>
</ul>

AhoCorasickTrie: AhoCorasickTrie: fast searching for multiple keywords in multiple texts

Description

Arguments

Author

See Also