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Description: The code here underlies the paper "Re-examing the use of the LSI technique in Zooarchaeology", published in Journal of Archaeological Science (DOI: https://doi.org/10.1016/j.jas.2020.105254) focused on re-examining three central tenets of LSI analyses in zooarchaeology: (1) the logarithm base for these analyes, (2) critiques based on the distribution of LSI values and their relationship to original measurements, and (3) arguments cerntering on aggregation choices. The code is designed to reproduce all findings and figures from the paper as well as provide code for applying multilevel LSI models to other zooarchaeological datasets. The dataset used in this project comes the Supplemental Information of Popkin, et al. (2012): Popkin, Peter R.W., Polydora Baker, Fay Worley, Sebastian Payne, and Andy Hammond 2012. The Sheep Project (1): determining skeletal growth, timing of epiphyseal fusion and morphometric variation in unimproved Shetland sheep of known age, sex, castration status and nutrition. Journal of Archaeological Science 39(6): 1775-1792. https://doi.org/10.1016/j.jas.2012.01.018