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

Abstract

1. 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. 2. 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.3. 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. 4. The modular and fast implementation of published methods ensures traceability, reproducibility, and comparability of future studies.

Climate change and the latitudinal selectivity of ancient marine extinctions

“…All analyses were performed in the R statistical computing environment (R Development Core Team 2018). Analytical code for the core functions noted above is available in the R package ‘divDyn’ (Kocsis et al 2018).…”

Nonequilibrium evolution of volatility in origination and extinction explains fat-tailed fluctuations in Phanerozoic biodiversity

“…We opted not to use subsampling methods ( 12 , 51 , 57 ) because these approaches would not be advisable for clades with few genera. However, our new method achieves similar results to subsampling procedures at the global scale across all clades.…”