Data from: Recommendations for using msBayes to incorporate uncertainty in selecting an ABC model prior: a response to Oaks et al.

 

Files in this package

Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Title table_S1 _01272013
Downloaded 7 times
Description Supplemental 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.
Download table_S1 _01272013.csv (9.275 Kb)
Details View File Details
Title table_S2_01272013
Downloaded 3 times
Description Supplemental 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.
Download table_S2_01272013.csv (7.467 Kb)
Details View File Details
Title table_S3_01272013
Downloaded 11 times
Description Supplemental 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.
Download table_S3_01272013.csv (5.63 Kb)
Details View File Details
Title batch_table1_prior
Downloaded 16 times
Description batch 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_M7
Download batch_table1_prior.txt (3.282 Kb)
Details View File Details
Title scripts_table1_posterior_rejectionsample
Downloaded 15 times
Description see #comments
Download scripts_table1_posterior_rejectionsample.txt (3.466 Kb)
Details View File Details
Title scripts_Fig1_posterior_rejectionsample
Downloaded 13 times
Description read #comments
Download scripts_Fig1_posterior_rejectionsample.txt (2.109 Kb)
Details View File Details
Title scripts_Fig2
Downloaded 12 times
Download scripts_Fig2.r (6.528 Kb)
Details View File Details
Title scripts_FigS1
Downloaded 11 times
Download scripts_FigS1.r (923 bytes)
Details View File Details
Title HU_IB_batchNEWpars_psi18_ne0.5_taumax0.75
Downloaded 9 times
Description batch 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 PODS
Download HU_IB_batchNEWpars_psi18_ne0.5_taumax0.75.txt (2.96 Kb)
Details View File Details
Title Script_Table2_HUIB_PODS_PARSnewPsi18_3M_HUIBPODStest_neuralnet_psi_omega_et_tol0.1_110812_ne0.5_taumax0.75
Downloaded 12 times
Description script for generating PODS (Table 2)
Download Script_Table2_HUIB_PODS_PARSnewPsi18_3M_HU...75.sh (1.827 Kb)
Details View File Details
Title HUIB_PODS_PARSnewPsi18_3M_HUIBPODStest_neuralnet_psi_omega_et_tol0.1_061512_ne0.5_taumax0.75
Downloaded 7 times
Description to 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.sh
Download HUIB_PODS_PARSnewPsi18_3M_HUIBPODStest_neur...75.r (2.172 Kb)
Details View File Details
Title HUIBObsTAIL_columnReduction_ne0.5_taumax0.75
Downloaded 2 times
Description 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.sh
Download HUIBObsTAIL_columnReduction_ne0.5_taumax0.75.r (127 bytes)
Details View File Details
Title HU_IB_psi18_BFCalculation_110812
Downloaded 7 times
Description R script for calculating Bayes Factors given the PODS data (Table 2)
Download HU_IB_psi18_BFCalculation_110812.r (4.023 Kb)
Details View File Details
Title batchPulse1_26
Downloaded 5 times
Description batch file for generating prior sample for estimates in Table S4 (data Table S1)
Download batchPulse1_26.BirdCOI_II (3.515 Kb)
Details View File Details
Title batchPulse2_23
Downloaded 9 times
Description batch file for generating prior sample for estimates in Table S4 (data Table S2)
Download batchPulse2_23.BirdCOI_II (3.167 Kb)
Details View File Details
Title batchPulse3_22
Downloaded 3 times
Description batch file for generating prior sample for estimates in Table S4 (data Table S3)
Download batchPulse3_22.BirdCOI_II (3.156 Kb)
Details View File Details
Title BirdCOI R scripts_psi3
Downloaded 2 times
Description R scripts for generating estimates in table S4
Download BirdCOI R scripts_psi3.txt (3.877 Kb)
Details View File Details

When using this data, please cite the original publication:

Hickerson MJ, Stone GN, Lohse K, Demos TC, Xie X, Landerer C, Takebayashi N (2013) Recommendations for using msBayes to incorporate uncertainty in selecting an ABC model prior: a response to Oaks et al. Evolution 68(1): 284–294. http://dx.doi.org/10.1111/evo.12241

Additionally, please cite the Dryad data package:

Hickerson MJ, Stone GN, Lohse K, Demos TC, Xie X, Landerer C, Takebayashi N (2013) Data from: Recommendations for using msBayes to incorporate uncertainty in selecting an ABC model prior: a response to Oaks et al. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.17f8v
Cite | Share
Download the data package citation in the following formats:
   RIS (compatible with EndNote, Reference Manager, ProCite, RefWorks)
   BibTex (compatible with BibDesk, LaTeX)

Search for data

Be part of Dryad

We encourage organizations to: