stringdist: An R repository from nijibabulu

stringdist

Approximate matching, fuzzy text search, and string distance calculations for R.
All distance and matching operations are system- and encoding-independent.
Built for speed, using openMP for parallel computing.

Citing

@article{RJ-2014-011,
  author = {Mark P.J. van der Loo},
  title = {{The stringdist Package for Approximate String Matching}},
  year = {2014},
  journal = {{The R Journal}},
  doi = {10.32614/RJ-2014-011},
  url = {https://doi.org/10.32614/RJ-2014-011},
  pages = {111--122},
  volume = {6},
  number = {1}
}

Functionality

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
afind finds the location of fuzzy matches of a short string in a long string.
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-Winkler 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.

C API

As of version 0.9.5.0 you can call a number of stringdist functions directly from the C code of your R package. The description of the API can be found

By typing ?stringdist_api in the R console
By browsing the package's help index to User guides, package vignettes and other documentation and clicking on doc/stringdist_api.pdf.
Or you can find the file's location as follows

system.file("doc/stringdist_api.pdf", package="stringdist")

Examples of packages that link to stringdist can be found here and here.

Installation

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

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 removed as of version 0.9.5.0

The following arguments have been obsolete since 2015 and have been removed in the 0.9.5.0 release (spring 2018)

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

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

nijibabulu/stringdist