FossilSim: An r package for simulating fossil occurrence data under mechanistic models of preservation and recovery
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Author / Producer
Date
2019-06
Publication Type
Journal Article
ETH Bibliography
yes
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OPEN ACCESS
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Abstract
1.Key features of the fossil record that present challenges for integrating palaeontological and phylogenetic datasets include (i) non‐uniform fossil recovery, (ii) stratigraphic age uncertainty and (iii) inconsistencies in the definition of species origination and taxonomy.
2.We present an r package FossilSim that can be used to simulate and visualise fossil data for phylogenetic analysis under a range of flexible models. The package includes interval‐, environment‐ and lineage‐dependent models of fossil recovery that can be combined with models of stratigraphic age uncertainty and species evolution.
3.The package input and output can be used in combination with the wide range of existing phylogenetic and palaeontological r packages. We also provide functions for converting between FossilSim and paleotree objects.
4. Simulated datasets provide enormous potential to assess the performance of phylogenetic methods and to explore the impact of using fossil occurrence databases on parameter estimation in macroevolution.
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Publication status
published
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Book title
Journal / series
Volume
10 (6)
Pages / Article No.
835 - 840
Publisher
Wiley
Event
Edition / version
Methods
Software
Geographic location
Date collected
Date created
Subject
fossil preservation; macroevolution; phylogeny; sampling biases; simulation
Organisational unit
09490 - Stadler, Tanja / Stadler, Tanja