String distance functions for R
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Latest commit bddbf04 Apr 30, 2017 @markvanderloo committed on GitHub Merge pull request #54 from nirmalpatel/master
Edited seq_distmatrix for case when b is not provided

README.md

Build Status Coverage Status CRAN DownloadsResearch software impact

stringdist

  • Approximate matching and string distance calculations for R.
  • All distance and matching operations are system- and encoding-independent.

The package offers the following main functions:

  • stringdist computes pairwise distances between two input character vectors (shorter one is recycled)
  • stringdistmatrix computes the distance matrix for one or two vectors
  • stringsim computes a string similarity between 0 and 1, based on stringdist
  • amatch is a fuzzy matching equivalent of R's native match function
  • ain is a fuzzy matching equivalent of R's native %in% operator
  • seq_dist, seq_distmatrix, seq_amatch and seq_ain for distances between, and matching of integer sequences. (see also the hashr package).

These functions are built upon C-code that re-implements some common (weighted) string distance functions. Distance functions include:

  • Hamming distance;
  • Levenshtein distance (weighted);
  • Restricted Damerau-Levenshtein distance (weighted, a.k.a. Optimal String Alignment);
  • Full Damerau-Levenshtein distance (weighted);
  • Longest Common Substring distance;
  • Q-gram distance
  • cosine distance for q-gram count vectors (= 1-cosine similarity)
  • Jaccard distance for q-gram count vectors (= 1-Jaccard similarity)
  • Jaro, and Jaro-Winker distance
  • Soundex-based string distance.

Also, there are some utility functions:

  • qgrams() tabulates the qgrams in one or more character vectors.
  • seq_qrams() tabulates the qgrams (somtimes called ngrams) in one or more integer vectors.
  • phonetic() computes phonetic codes of strings (currently only soundex)
  • printable_ascii() is a utility function that detects non-printable ascii or non-ascii characters.

Installation

To install the latest release from CRAN, open an R terminal and type

install.packages('stringdist')

Beta versions are released through my drat repository. These versions build and pass all current tests correctly on Linux but builds have not been tested on all architectures that CRAN supports. Windows users will also need to have rtools installed.

drat::addRepo("markvanderloo")
install.packages("stringdist")

To obtain the package from the very latest source code open a bash terminal (or git bash if you work under Windows with msysgit) and type

git clone https://github.com/markvanderloo/stringdist.git
cd stringdist
bash ./build.bash
R CMD INSTALL output/stringdist_*.tar.gz

Warning: the github version can change any time and may not even build properly. As most of the code is written in C, the development version may crash your R-session.

Resources

  • A paper on stringdist has been published in the R-journal
  • Slides of te useR!2014 conference.

Note to users: deprecated arguments as of >= 0.9.0, >= 0.9.2

Parallelization used to be based on R's parallel package, that works by spawning several R sessions in the background. As of version 0.9.0, stringdist uses the more efficient openMP protocol to parallelize everything under the hood.

The following arguments have become obsolete and will be removed somewhere in 2016:

  • Argument cluster for function stringdistmatrix.
  • Argument maxDist for functions stringdist and stringdistmatrix (not amatch).
  • Argument ncores for function stringdistmatrix