The R Journal: accepted article

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alineR: an R Package for Optimizing Feature-Weighted Alignments and Linguistic Distances
Sean S. Downey, Guowei Sun and Peter Norquest

Abstract Linguistic distance measurements are commonly used in anthropology and biology when quantitative and statistical comparisons between words are needed. This is common, for example, when analyzing linguistic and genetic data. Such comparisons can provide insight into historical population patterns and they provide general insight into evolutionary processes. However, the most commonly used linguistic distances are derived from edit distances, which do not weight phonetic features that may, for example, represent smaller-scale patterns in linguistic evolution. Thus, computational methods for calculating feature-weighted linguistic distances are needed for linguistic, biological, and evolutionary applications; additionally, the linguistic distances presented here are generic and may have broader applications in fields such as text mining and search, as well as applications in psycholinguistics and morphology. To facilitate this research, we are making our software available as an open-source R software package that performs feature-weighted linguistic distance calculations. The package includes a supervised learning methodology that uses a genetic algorithm and manually determined alignments to estimate 13 linguistic parameters including feature weights and a skip penalty. Here we present the package and use it to demonstrate a supervised learning methodology to estimate the optimal linguistic parameters for a sample of Austronesian languages. Our results show that the methodology can estimate these parameters for both simulated language data and for real language data, that optimizing feature weights improves alignment accuracy by approximately 29%, and that optimization and significantly affects the resulting distance measurements. Availability: alineR is available on CRAN.

Received: 2016-04-18; online 2017-03-27
CRAN packages: alineR, stringdist, RecordLinkage, doMC , CRAN Task Views implied by cited CRAN packages: OfficialStatistics, HighPerformanceComputing , Bioconductor packages: Biostrings

CC BY 4.0
This article is licensed under a Creative Commons Attribution 4.0 International license.

  author = {Sean S. Downey and Guowei Sun and Peter Norquest},
  title = {{alineR: an R Package for Optimizing Feature-Weighted
          Alignments and Linguistic Distances}},
  year = {2017},
  journal = {{The R Journal}},
  url = {}