Data from: A stochastic rate-calibrated method for time-scaling phylogenies of fossil taxa

Bapst DW

Date Published: August 12, 2013

DOI: http://dx.doi.org/10.5061/dryad.vk7t0

 

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Title R script for methods comparison simulations under budding
Downloaded 18 times
Description This R script will execute the methods comparison simulations shown in the paper under budding differentiation, given that appropriate libraries are installed.
Download timeTest_budd_r0.1_in5_LAD_11-05-12.R (20.21 Kb)
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Title R script for methods comparison simulations under terminal-taxon differentiation
Downloaded 11 times
Description This R script will execute the methods comparison simulations shown in the paper under terminal-taxon differentiation, given that appropriate libraries are installed.
Download timeTest_candle_r0.1_in5_LAD_11-05-12.R (20.21 Kb)
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Title R Workspace for methods comparisons with budding
Downloaded 9 times
Description Workspace file containing methods comparison simulation data generated under budding differentiation.
Download timeTest_budd_r0.1_in5_LAD_11-05-12.Rdata (1.035 Mb)
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Title R Workspace for methods comparisons with terminal-taxon differentiation
Downloaded 8 times
Description Workspace file containing methods comparison simulation data generated under terminal-taxon differentiation.
Download timeTest_candle_r0.1_in5_LAD_11-05-12.Rdata (1.396 Mb)
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Title R script for plotting methods comparison figures
Downloaded 13 times
Description This R script, when executed with the two R workspace files for methods comparisons (see first few lines) will recreate the various methods comparison plots from the paper. Note that the figure numbers in the actual paper have shifted since this script was written, with one figure even being moved to the supplement.
Download plot_Fig12_Fig13_Fig14_Fig15_11-12-12.R (3.097 Kb)
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Title R script for testing Ps derivation with simulations
Downloaded 11 times
Description R script for simulating Ps under various rates to compare to the value calculated by the solved derivation.
Download testing_Ps_09-21-12.R (8.089 Kb)
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Title R Workspace for testing Ps
Downloaded 6 times
Description Workspace file that contains all the simulation data necessary for creating the figure showing the comparison of simulated and calculated values of Ps.
Download testing_Ps_09-22-12.Rdata (443.8 Kb)
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Title R script for plotting Ps comparison figure
Downloaded 7 times
Description R script which, given the workspace file that contains all the simulation data from the Ps comparison, will create the figure showing the comparison of simulated and calculated values of Ps.
Download plot_testing_Ps.R (241 bytes)
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Title R script for simulating cap-delta distributions (Budding, set A)
Downloaded 9 times
Description This R script, when executed, generates simulated phylogenies and fossil records under a budding scenario with branching, extinction and sampling rates equal, saving the cap-delta values at the root (as defined in the manuscript).
Download testing_gap_models_A_09-21-12.R (1.822 Kb)
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Title R script for simulating cap-delta distributions (Budding, set B)
Downloaded 10 times
Description This R script, when executed, generates simulated phylogenies and fossil records under a budding scenario with branching and extinction rates greater than sampling rates, saving the cap-delta values at the root (as defined in the manuscript).
Download testing_gap_models_B_09-21-12.R (1.822 Kb)
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Title R script for simulating cap-delta distributions (Budding, set C)
Downloaded 7 times
Description This R script, when executed, generates simulated phylogenies and fossil records under a budding scenario with branching and extinction rates less than sampling rates, saving the cap-delta values at the root (as defined in the manuscript).
Download testing_gap_models_C_09-21-12.R (1.822 Kb)
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Title R script for simulating cap-delta distributions (Bifurcation)
Downloaded 11 times
Description This R script, when executed, generates simulated phylogenies and fossil records under a bifurcating cladogenesis scenario with equal branching, extinction and sampling rates, saving the cap-delta values at the root (as defined in the manuscript).
Download testing_gap_models_bifurc_09-21-12.R (3.892 Kb)
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Title R workspace for simulated cap-delta distributions (Budding, set A)
Downloaded 7 times
Description This contains simulated cap-delta values generated under a budding scenario with equal branching, extinction and sampling rates.
Download gaptest_data_A_09-22-12.Rdata (1.189 Mb)
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Title R workspace for simulated cap-delta distributions (Budding, set B)
Downloaded 5 times
Description This contains simulated cap-delta values generated under a budding scenario with branching and extinction rates greater than the sampling rates.
Download gaptest_data_B_09-22-12.Rdata (3.333 Mb)
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Title R workspace for simulated cap-delta distributions (Budding, set C)
Downloaded 6 times
Description This contains simulated cap-delta values generated under a budding scenario with branching and extinction rates less than the sampling rates.
Download gaptest_data_C_09-22-12.Rdata (1.215 Mb)
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Title R workspace for simulated cap-delta distributions (Bifurcation)
Downloaded 5 times
Description This contains simulated cap-delta values generated under a bifurcating cladogenesis scenario with equal branching, extinction and sampling rates.
Download gaptest_data_bifurc_09-22-12.Rdata (1.476 Mb)
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Title R script for plotting cap-delta comparison figures
Downloaded 18 times
Description This R script, when executed with the four workspaces containing simulated cap-delta values, will generate the histogram and q-q plots shown in the supplement which compare the simulated values against different derivations of the cap-delta function.
Download plot_gaptest_Fig10_abc&bifurc.R (11.90 Kb)
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When using this data, please cite the original publication:

Bapst DW (2013) A stochastic rate-calibrated method for time-scaling phylogenies of fossil taxa. Methods in Ecology and Evolution 4(8): 724-733. http://dx.doi.org/10.1111/2041-210X.12081

Additionally, please cite the Dryad data package:

Bapst DW (2013) Data from: A stochastic rate-calibrated method for time-scaling phylogenies of fossil taxa. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.vk7t0
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