Data from: Topology, divergence dates, and macroevolutionary inferences vary between different tip-dating approaches applied to fossil theropods (Dinosauria)

Bapst DW, Wright AM, Matzke NJ, Lloyd GT

Date Published: June 21, 2016

DOI: http://dx.doi.org/10.5061/dryad.n2g80

 

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Title README
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Description README file describes the file type and contents of all files in this data repository.
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Title B2noSA_inputFile
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Description BEAST2 Input file for noSA analysis
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Title B2noSA_majrule_burn03
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Description Half-compatibility summary for noSA BEAST2 analysis
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Title B2noSA_mcc_burn03
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Description Maximum clade credibility summary for noSA BEAST2 analysis
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Title B2noSA_treelog
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Description Posterior sampled tree file from BEAST2 noSA analysis
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Title B2SA_inputFile
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Description BEAST2 Input file for SA analysis
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Title B2SA_majrule_burn03
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Description Half-compatibility summary for SA BEAST2 analysis
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Title B2SA_mcc_burn03
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Description Maximum clade credibility summary for SA BEAST2 analysis
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Title B2SA_treelog
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Description Posterior sampled tree file from BEAST2 SA analysis
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Title birdtree_workspace_03-07-2016
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Description Saved R Environment from executing RMarkdown script.
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Title birdtreecomparison_03-07-16
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Description PDF created by executing RMarkdown script.
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Title birdtreecomparison_03-07-16
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Description RMarkDown script containing all post-inference analyses.
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Title figures_theropod_06-17-16
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Description R script which, if executed from within the saved R environment, produces all figures in the manuscript and supplemental.
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Title makeBEAST2_majRule_02-05-16
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Description An R script for obtaining half-compatibility trees with posterior probabilities on the edges from BEAST2 treelogs, albeit without branch lengths.
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Title mass_data_for_PCMs_BensonEtal14_10-27-14
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Description Datafile of mass estimates for taxa, as obtained from the dataset supplied by Benson et al., 2014.
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Title MrBayesSA_100treeSample_burn03
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Description The Posterior tree sample from MrBayes analysis.
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Title MrBayesSA_input_script
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Description NEXUS input with MrBayes block for our MrBayes analysis.
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Title MrBayesSA_majrule_burn03
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Description Half-compatibility summary for the MrBayes analysis
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Title MrBayesSA_mcc_burn03
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Description Maximum clade compatibility summary for the MrBayes analysis
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Title theropod_tree_LeeWorthy2011_RAXML_02-01-16
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Description NEXUS file containing an unscaled topology matching the RAXML tree presented in Lee & Worthy, 2011.
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Title theropod_tree_XuEtAll2011_FigS6_02-01-16
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Description NEXUS file containing an unscaled topology matching the tree presented in Figure S6 of Xu et al., 2011.
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Title timeList_sorted_asIs_theropods_DWB_11-05-14
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Description A timeList object for these taxa, structured as is necessary for use with paleotree, describing their stratigraphic ranges in discrete intervals.
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Title TNT_most_parsimonious_trees
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Description Sample of 100 most parsimonious trees taken from our TNT analysis.
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When using this data, please cite the original publication:

Bapst DW, Wright AM, Matzke NJ, Lloyd GT (2016) Topology, divergence dates, and macroevolutionary inferences vary between different tip-dating approaches applied to fossil theropods (Dinosauria). Biology Letters 12(7): 20160237. http://dx.doi.org/10.1098/rsbl.2016.0237

Additionally, please cite the Dryad data package:

Bapst DW, Wright AM, Matzke NJ, Lloyd GT (2016) Data from: Topology, divergence dates, and macroevolutionary inferences vary between different tip-dating approaches applied to fossil theropods (Dinosauria). Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.n2g80
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