README.md

In evolucionario/cladeage: CladeAge: Estimating Clade Age Using The Fossil Record

CladeAge: Empirical Priors of Clade Age Using the Fossil Record

Santiago Claramunt

Department of Natural History, Royal Ontario Museum, and Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada.

E-mail: [e-mail]

An example simulation using the Solow (2003) method incorporating fossil age uncertainty.

Overview

Given a set of fossil ages for a specific clade, these functions model the uncertainty about the crown age of the clade. The basic method is based on the model of Strauss & Sadler (1989) and assumes a uniform distribution of precisely known fossil ages but there are options for incorporating fossil age uncertainty (Claramunt & Cracraft, 2015) and non-uniform fossil age distributions (Solow, 2003). The original version of this code aimed at generating probability density functions, but the current version instead implements a more efficient strategy involving the generation of random samples of possible clade ages using quantile functions. These numbers can then be used to generate a histogram and fit probability functions for using as priors in Bayesian time tree estimation (Claramunt & Cracraft, 2015).

Installation

install.packages("devtools");
devtools::install_github("evolucionario/cladeage", dependencies=TRUE);

References

Claramunt S, Cracraft J. 2015. A new time tree reveals Earth history’s imprint on the evolution of modern birds. Science Advances, 1(11), e1501005. doi: 10.1126/sciadv.1501005.

Gingerich PD, Uhen MD. 1998. Likelihood estimation of the time of origin of Cetacea and the time of divergence of Cetacea and Artiodactyla. Palaeontologia Electronica, 1(2), 47.

Norris RW, Strope CL, McCandlish DM, Stoltzfus A. 2015. Bayesian priors for tree calibration: Evaluating two new approaches based on fossil intervals. bioRxiv, 014340. doi: 10.1101/014340.

Solow AR. 2003. Estimation of stratigraphic ranges when fossil finds are not randomly distributed. Paleobiology, 29(2), 181–185. doi: 10.1666/0094-8373(2003)029<0181:EOSRWF>2.0.CO;2.

Strauss D, Sadler PM. 1989. Classical confidence intervals and Bayesian probability estimates for ends of local taxon ranges. Mathematical Geology, 21(4), 411–427. doi: 10.1007/BF00897326.

Wang SC, Everson PJ. 2007. Confidence intervals for pulsed mass extinction events. Paleobiology, 33(2), 324–336. doi: 10.1666/06056.1.

Wang SC, Chudzicki DJ, Everson PJ. 2009. Optimal estimators of the position of a mass extinction when recovery potential is uniform. Paleobiology, 35(3), 447–459. doi: 10.1666/0094-8373-35.3.447.

Wang SC. 2010. Principles of statistical inference: likelihood and the Bayesian paradigm. The Paleontological Society Papers, 16, 1–18. doi: 10.1017/S1089332600001790.

evolucionario/cladeage documentation built on Dec. 31, 2021, 8:48 a.m.