Bioarchaeology of the Near East, 5:41-44 (2011)

Technical Note: An R script for Smith's Mean Measure of Divergence

Arkadiusz Soltysiak
Department of Bioarchaeology,
Institute of Archaeology, University of Warsaw,
ul. Krakowskie Przedmiescie 26/28, 00-927 Warszawa, Poland
email: a.soltysiak@uw.edu.pl

Abstract: The present paper introduces a script written in R language that generates a matrix of Smith's Measure of Divergence (MMD) for a set of non-metric trait frequencies. The script uses either the Anscombe or Freeman & Tukey transformation to obtain theta values, and a choice of the Freeman & Tukey or Grewal correction for small sample size to yield an MMD matrix. A matrix of standard deviations, using Sjovold's formula, and statistical significance for each value are also calculated.

Key words: R language, distance matrix, non-metric traits

Received 24 January 2012; accepted 12 February 2012; published online 16 February 2012.

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