DOI: 10.5061/dryad.vk7t0
title: Data from: A stochastic rate-calibrated method for time-scaling phylogenies of fossil taxa

description: 1.) Applying phylogeny-based analyses of trait evolution and
 diversification in the fossil record generally involves transforming an
 unscaled cladogram into a phylogeny scaled to geologic time. Current
 methods produce single time-scaled phylogenies with artificial zero-length
 branches and no indication of the uncertainty in the temporal
 relationships. 2.) Here I present a stochastic algorithm for time-scaling
 phylogenies of fossil taxa by randomly sampling node ages from a
 constrained distribution, with the ultimate goal of producing large
 samples of time-scaled phylogenies for a given dataset as the basis for
 phylogeny-based analyses. I describe how this stochastic approach can be
 extended to consider potential ancestral relationships and resolve
 polytomies. 3) The stochastic selection of node ages in this algorithm is
 weighted by the probability density of the total inferable unobserved
 evolutionary history at single divergence events in a tree, a distribution
 dependent on rates of branching, extinction and sampling in the fossil
 record. 4) The combined time-scaling method must be calibrated with
 explicit estimates of three rates: branching, extinction and sampling, and
 thus is named the cal3 time-scaling method, included in the R library
 paleotree. I test the time-scaling capabilities of the cal3 and older
 time-scaling methods in simulations. cal3 produces samples of time-scaled
 trees that better bracket the uncertainty in the true node ages than
 existing time-scaling methods. This is true even in simulations under a
 ‘terminal-taxon’ model of differentiation that violates many of the
 assumptions of the cal3 method. 5) The cal3 method provides a new approach
 for time-scaling paleontological cladograms, calibrated to estimated
 sampling and diversification rates, allowing for better estimates of
 uncertainty in the phylogenetic time-scaling. The cal3 method is robust to
 relaxation of at least some model assumptions. Additional work is needed
 to analyze the impact of time-scaling approaches on macroevolutionary
 analyses and to integrate time-scaling with phylogenetic inference.
description: R script for methods
 comparison simulations under buddingThis R script will
 execute the methods comparison simulations shown in the paper under
 budding differentiation, given that appropriate libraries are
 installed.timeTest_budd_r0.1_in5_LAD_11-05-12.RR script for methods comparison simulations under terminal-taxon differentiationThis R script will execute the methods comparison simulations shown in the paper under terminal-taxon differentiation, given that appropriate libraries are installed.timeTest_candle_r0.1_in5_LAD_11-05-12.RR Workspace for methods comparisons with buddingWorkspace file containing methods comparison simulation data generated under budding differentiation.timeTest_budd_r0.1_in5_LAD_11-05-12.RdataR Workspace for methods comparisons with terminal-taxon differentiationWorkspace file containing methods comparison simulation data generated under terminal-taxon differentiation.timeTest_candle_r0.1_in5_LAD_11-05-12.RdataR script for plotting methods comparison figuresThis 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.plot_Fig12_Fig13_Fig14_Fig15_11-12-12.RR script for testing Ps derivation with simulationsR script for simulating Ps under various rates to compare to the value calculated by the solved derivation.testing_Ps_09-21-12.RR Workspace for testing PsWorkspace file that contains all the simulation data necessary for creating the figure showing the comparison of simulated and calculated values of Ps.testing_Ps_09-22-12.RdataR script for plotting Ps comparison figureR 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.plot_testing_Ps.RR script for simulating cap-delta distributions (Budding, set A)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).testing_gap_models_A_09-21-12.RR script for simulating cap-delta distributions (Budding, set B)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).testing_gap_models_B_09-21-12.RR script for simulating cap-delta distributions (Budding, set C)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).testing_gap_models_C_09-21-12.RR script for simulating cap-delta distributions (Bifurcation)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).testing_gap_models_bifurc_09-21-12.RR workspace for simulated cap-delta distributions (Budding, set A)This contains simulated cap-delta values generated under a budding scenario with equal branching, extinction and sampling rates.gaptest_data_A_09-22-12.RdataR workspace for simulated cap-delta distributions (Budding, set B)This contains simulated cap-delta values generated under a budding scenario with branching and extinction rates greater than the sampling rates.gaptest_data_B_09-22-12.RdataR workspace for simulated cap-delta distributions (Budding, set C)This contains simulated cap-delta values generated under a budding scenario with branching and extinction rates less than the sampling rates.gaptest_data_C_09-22-12.RdataR workspace for simulated cap-delta distributions (Bifurcation)This contains simulated cap-delta values generated under a bifurcating cladogenesis scenario with equal branching, extinction and sampling rates.gaptest_data_bifurc_09-22-12.RdataR script for plotting cap-delta comparison figuresThis 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.plot_gaptest_Fig10_abc&bifurc.R