The distance matrices used in the analyses are: -Linguistic distance, which is based on the Levenshtein algorithm as calculated through GABMAP -Time since divergence, which is based on Lee and Hasegawa's 2011 maximum clade credibility tree -Geographic distance, which is based on the geospatial data of the language varieties -Separation by water, which is a binary variable indicating the presence of an oceanic barrier These distance matrices are combined into a single long-format file for the mixed model analysis. The accompanying R script file provides the syntax for the analyses reported: -Cluster analysis of Japonic based on linguistic distance -Simple Mantel correlations between the predictors of linguistic distance -Partial Mantel correlations between linguistic distance and its predictors -Multiple regression over distances matrices for linguistic distance -Linear mixed effects model analysis for linguistic distance that controls for language variety as a random variable