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paleotree: an R package for paleontological and phylogenetic analyses of evolution
Article first published online: 18 JUN 2012
DOI: 10.1111/j.2041-210X.2012.00223.x
© 2012 The Authors. Methods in Ecology and Evolution © 2012 British Ecological Society
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How to Cite
Bapst, D. W. (2012), paleotree: an R package for paleontological and phylogenetic analyses of evolution. Methods in Ecology and Evolution, 3: 803–807. doi: 10.1111/j.2041-210X.2012.00223.x
Publication History
- Issue published online: 5 OCT 2012
- Article first published online: 18 JUN 2012
- Received 23 February 2012; accepted 27 April 2012 Handling Editor: Robert Freckleton
- Abstract
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- References
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Keywords:
- birth-death models;
- comparative methods;
- diversification;
- macroevolution;
- paleobiology
Summary
1. paleotree is a library of functions for the R statistical computing environment dedicated to analyses that combine paleontological and phylogenetic data sets, particularly the time-scaling of phylogenetic trees, which include extinct fossil lineages.
2. The functions included in this library focus on simulating paleontological data sets, measuring sampling rates, time-scaling cladograms of fossil taxa and plotting historical diversity curves.
3. I describe the capabilities and analytical basis of the functions in paleotree by presenting two examples. The first example showcases the simulation capabilities and plotting the output as diversity curves. The second example demonstrates time-scaling a cladogram of fossil taxa and estimating sampling rates and completeness from temporal ranges.