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The R package divDyn for quantifying diversity dynamics using fossil sampling data

By Kocsis Á. T., Reddin C. J., Alroy J., Kiessling W.

Posted 23 Sep 2018
bioRxiv DOI: 10.1101/423780 (published DOI: 10.1111/2041-210x.13161)

Unbiased time series of diversity dynamics are vital for quantifying the grand history of life. Applications include identifying ancient mass extinctions and inferring both biotic and abiotic controls on diversification rates. We introduce divDyn, a new R package that facilitates the calculation of taxonomic richness, extinction and origination rates from time-binned fossil sampling data. State-of-the-art sampling completeness metrics, counting protocols, and sampling standardisation functions permit the reconstruction of biologically meaningful time series. Additional functions permit the partitioning of turnover rates by trait and environmental affinity. We display Phanerozoic-scale diversity dynamics of marine invertebrates using the divDyn package. Using the core function and standard subsampling options, we revisit earlier assessments of declining extinction and origination rates over time and of equilibrial diversity dynamics to assess their methodological dependency. The modular and fast implementation of published methods ensures traceability, reproducibility, and comparability of future studies.

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