Data from: Automatic detection of key innovations, rate shifts, and diversity-dependence on phylogenetic trees

Rabosky DL

Date Published: March 4, 2014

DOI: http://dx.doi.org/10.5061/dryad.hn1vn

 

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Title Phylogenetic trees simulated under multi-process macroevolutionary models for analysis with BAMM
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Description This file contains simulated datasets analyzed as part of Rabosky (2014). There are 6 general simulation scenarios, described at length in the manuscript. These include 500 phylogenetic trees simulated under each macroevolutionary scenario. Each batch of simulated datasets was analyzed with BAMM. This dataset contains the simulated datasets, and also the parameters underlying the simulations. For example, the subdirectory "constant" contains the 500 constant-rate birth-death process phylogenies that were analyzed with BAMM. These trees are stored in the fild "simtrees.txt". Another file in this directory, "cr_truerates.txt", contains the actual simulation parameters. For example, the first row of that file gives the speciation and extinction parameters that were used to simulate the first tree in the "simtrees.txt" file. The same general idea holds for the other subdirectories. dd_k1 for example is a pure-birth background process with a shift to a single diversity-dependent regime on one descendant lineage. The simulation scenarios are detailed in the master file "DESCRIPTION.txt".
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When using this data, please cite the original publication:

Rabosky DL (2014) Automatic detection of key innovations, rate shifts, and diversity-dependence on phylogenetic trees. PLoS ONE 9(2): e89543. http://dx.doi.org/10.1371/journal.pone.0089543

Additionally, please cite the Dryad data package:

Rabosky DL (2014) Data from: Automatic detection of key innovations, rate shifts, and diversity-dependence on phylogenetic trees. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.hn1vn
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