Data from: Age-dependent speciation can explain the shape of empirical phylogenies

Hagen O, Hartmann K, Steel M, Stadler T

Date Published: August 24, 2015

DOI: http://dx.doi.org/10.5061/dryad.31227.2

 

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Title Data-set empirical trees
Downloaded 36 times
Description The input file” treebase_input.rda” has the trees cached from TreeBase by the R-package treebase (Sanderson, M.J., Donoghue, M.J., et al. 1994). The file was later treated for specific statistics and compared with simulated trees, as described in out methodology. For that the “processing_treebase.R” R-script was used, being the file “treebaselist_output.RData” the final output. We would like to stress that this is not a complete catalogue of all R-scripts used in our study, especially regarding plotting and investigation of model behavior, once much was simulated with a cluster computer involving multiple outputs, code files and csv parameter tables that changed over time. If you plan to run similar experiments, we strongly encourage the reading of our TreeSimGM R-package help material.
Download data-set_empirical_trees.zip (10.20 Mb)
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Title Empirical trees parameter estimation based on simulated trees
Downloaded 44 times
Description “SBFUSED_input.RData” is the main input data that was generated from simulations using the central high-performance computer cluster of ETH Zurich (Brutus) and the R-package TreeSimGM (Hagen, O., Stadler, T. 2013). Inputs from “treebase_output.RData” (that can be found at “data-set_empirical_trees.zip”) are also used, once we use here empirical trees for the fitting. For more details please consult the respective R-package tutorials. All other files are the sub products of the “procedure_rscript.R” script. More details can be found at the methodology section. Figure 3 originates mainly from “SBep_output.RData”, “SBleast.square_output.RData” and “plot_script.R”. We would like to stress that this is not a complete catalogue of all R-scripts used in our study, especially regarding plotting and investigation of model behavior, once much was simulated with a cluster computer involving multiple outputs, code files and csv parameter tables that changed over time. If you plan to run similar experiments, we strongly encourage the reading of our TreeSimGM R-package help material.
Download empirical_trees_parameter_estimation_base...es.zip (976.3 Kb)
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Title Reliable estimates of shape on simulated phylogenies
Downloaded 44 times
Description Data and scripts used to test our procedure for parameter estimation over the three sets of simulated phylogenies (SI_Fig 6, 7, and 8). We would like to stress that this is not a complete catalogue of all R-scripts used in our study, especially regarding plotting and investigation of model behavior, once much was simulated with a cluster computer involving multiple outputs, code files and csv parameter tables that changed over time. If you plan to run similar experiments, we strongly encourage the reading of our TreeSimGM R-package help material.
Download reliable_estimates_of_shape_on_simulated_...es.zip (694.5 Kb)
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Title Supplementary Figures 1-10
Downloaded 51 times
Download SupplementaryFigures1-10.pdf (784.9 Kb)
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Title Supplementary Analytic Results
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Download SupplementaryAnalyticResults.pdf (431.4 Kb)
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When using this data, please cite the original publication:

Hagen O, Hartmann K, Steel M, Stadler T (2015) Age-dependent speciation can explain the shape of empirical phylogenies. Systematic Biology 64(3): 432-440. http://dx.doi.org/10.1093/sysbio/syv001

Additionally, please cite the Dryad data package:

Hagen O, Hartmann K, Steel M, Stadler T (2015) Data from: Age-dependent speciation can explain the shape of empirical phylogenies. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.31227.2
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