DOI: 10.5061/dryad.17f8v
title: Data from: Recommendations for using msBayes to incorporate uncertainty in selecting an ABC model prior: a response to Oaks et al.

description: Prior specification is an essential component of parameter estimation and
 model comparison in Approximate Bayesian computation (ABC). Oaks et al.
 present a simulation-based power analysis of msBayes and conclude that
 msBayes has low power to detect genuinely random divergence times across
 taxa, and suggest the cause is Lindley's paradox. Although the
 predictions are similar, we show that their findings are more
 fundamentally explained by insufficient prior sampling that arises with
 poorly chosen wide priors that critically undersample nonsimultaneous
 divergence histories of high likelihood. In a reanalysis of their data on
 Philippine Island vertebrates, we show how this problem can be
 circumvented by expanding upon a previously developed procedure that
 accommodates uncertainty in prior selection using Bayesian model
 averaging. When these procedures are used, msBayes supports recent
 divergences without support for synchronous divergence in the Oaks et al.
 data and we further present a simulation analysis that demonstrates that
 msBayes can have high power to detect asynchronous divergence under
 narrower priors for divergence time. Our findings highlight the need for
 exploration of plausible parameter space and prior sampling efficiency for
 ABC samplers in high dimensions. We discus potential improvements to
 msBayes and conclude that when used appropriately with model averaging,
 msBayes remains an effective and powerful tool.
description: table_S1
 _01272013Supplemental 1. Genbank
 accession numbers and species names of data used to test for synchronous
 divergence with msBayes versions 20120222 and 20120510 given 25
 species-pairs. Each pair of species has the same genus
 name.table_S2_01272013Supplemental 2. Genbank accession numbers and species names of data used to test for synchronous divergence with msBayes versions 20120222 and 20120510 given 23 species-pairs. Each pair of species has the same genus name.table_S3_01272013Supplemental 3. Genbank accession numbers and species names of data used to test for synchronous divergence with msBayes versions 20120222 and 20120510 given 23 species-pairs. Each pair of species has the same genus name.batch_table1_priorbatch file to be used with msBayes to generate simulated draws from priors M1 through M8. The values for prior bounds upperTheta, lowerTheta, upperTau, and upperAncPopSize will have to be changed accordingly depending on which of the 8 prior models (M7 in this example). IMPORTANT, if running in multiple parallel jobs, make sure the start times are different by more than a second to assure different random number seeds. To generate each set of prior simulations (M7 in this example), use command line: cd $HOME/msbayes/trunk/src ./msbayes.pl -c batch_table1_prior -r 500000 -o prior_M7scripts_table1_posterior_rejectionsamplesee #commentsscripts_Fig1_posterior_rejectionsampleread #commentsscripts_Fig2scripts_FigS1HU_IB_batchNEWpars_psi18_ne0.5_taumax0.75batch file for generating PODS (used within Script_Table2_HUIB_PODS_PARSnewPsi18_3M_HUIBPODStest_neuralnet_psi_omega_et_tol0.1_110812_ne0.5_taumax0.75.sh). By changing appropriate prior settings, this batch file can also be used for obtaining the prior sample (ie Reference Table) used to generate the PODSScript_Table2_HUIB_PODS_PARSnewPsi18_3M_HUIBPODStest_neuralnet_psi_omega_et_tol0.1_110812_ne0.5_taumax0.75script for generating PODS (Table 2)HUIB_PODS_PARSnewPsi18_3M_HUIBPODStest_neuralnet_psi_omega_et_tol0.1_061512_ne0.5_taumax0.75to be used for generating PODS (table 2). Used within shell script Script_Table2_HUIB_PODS_PARSnewPsi18_3M_HUIBPODStest_neuralnet_psi_omega_et_tol0.1_110812_ne0.5_taumax0.75.shHUIBObsTAIL_columnReduction_ne0.5_taumax0.75used for generating PODS (Table 2). Used within shell script Script_Table2_HUIB_PODS_PARSnewPsi18_3M_HUIBPODStest_neuralnet_psi_omega_et_tol0.1_110812_ne0.5_taumax0.75.shHU_IB_psi18_BFCalculation_110812R script for calculating Bayes Factors given the PODS data (Table 2)batchPulse1_26batch file for generating prior sample for estimates in Table S4 (data Table S1)batchPulse2_23batch file for generating prior sample for estimates in Table S4 (data Table S2)batchPulse3_22batch file for generating prior sample for estimates in Table S4 (data Table S3)BirdCOI R scripts_psi3R scripts for generating estimates in table S4