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10 Commits
posterior_distributions_admixture
posterior_distributions_admixture
 
 
#Arguello_parameters.py#
#Arguello_parameters.py#
 
 
#qsub_admixture_bottleneck_mode_theta0#
#qsub_admixture_bottleneck_mode_theta0#
 
 
#qsub_admixture_mode_Garud_2015_theta0#
#qsub_admixture_mode_Garud_2015_theta0#
 
 
Arguello_parameters.py
Arguello_parameters.py
 
 
Arguello_parameters.py~
Arguello_parameters.py~
 
 
DaDi_compute_S_Pi_TajD.py
DaDi_compute_S_Pi_TajD.py
 
 
DaDi_compute_S_Pi_TajD.py~
DaDi_compute_S_Pi_TajD.py~
 
 
Figure3_Jensen_response.R
Figure3_Jensen_response.R
 
 
H12_H2H1_fixedWinOption.py
H12_H2H1_fixedWinOption.py
 
 
H12_H2H1_simulations.py
H12_H2H1_simulations.py
 
 
Jensen_response_plots.R
Jensen_response_plots.R
 
 
Jensen_response_publication.R
Jensen_response_publication.R
 
 
Jensen_response_revision.R
Jensen_response_revision.R
 
 
LD_MAF_simulations.py
LD_MAF_simulations.py
 
 
Pi_MS_TajD.py
Pi_MS_TajD.py
 
 
Pi_MS_TajD_perBp.py
Pi_MS_TajD_perBp.py
 
 
Pi_per_shortIntron.py
Pi_per_shortIntron.py
 
 
README.md
README.md
 
 
SNPdensity.py
SNPdensity.py
 
 
SNPdensity2.py
SNPdensity2.py
 
 
_Pi_S_TajD_perBp.txt
_Pi_S_TajD_perBp.txt
 
 
admixture_parameters_jointDistn.py
admixture_parameters_jointDistn.py
 
 
admixture_parameters_mode.py
admixture_parameters_mode.py
 
 
admixture_parameters_mode_DuchenRhoTheta.py
admixture_parameters_mode_DuchenRhoTheta.py
 
 
admixture_parameters_mode_MS.py
admixture_parameters_mode_MS.py
 
 
admixture_parameters_mode_diffProps.py
admixture_parameters_mode_diffProps.py
 
 
admixture_parameters_mode_fixedPopSize.py
admixture_parameters_mode_fixedPopSize.py
 
 
admixture_parameters_mode_fixedPopSize_MS.py
admixture_parameters_mode_fixedPopSize_MS.py
 
 
admixture_parameters_mode_fixedPopSize_MS_trajectoryTest.py
admixture_parameters_mode_fixedPopSize_MS_trajectoryTest.py
 
 
admixture_parameters_mode_fixedPopSize_MS_trajectoryTest.py~
admixture_parameters_mode_fixedPopSize_MS_trajectoryTest.py~
 
 
admixture_parameters_mode_migration.py
admixture_parameters_mode_migration.py
 
 
admixture_parameters_mode_varyGrowth.py
admixture_parameters_mode_varyGrowth.py
 
 
admixture_parameters_posteriorDistn.py
admixture_parameters_posteriorDistn.py
 
 
admixture_parameters_posteriorDistn_95CI.py
admixture_parameters_posteriorDistn_95CI.py
 
 
admixture_parameters_posteriorDistn_95CI_DuchenRhoTheta.py
admixture_parameters_posteriorDistn_95CI_DuchenRhoTheta.py
 
 
admixture_parameters_posteriorDistn_95CI_DuchenRhoTheta_Xchr.py
admixture_parameters_posteriorDistn_95CI_DuchenRhoTheta_Xchr.py
 
 
admixture_parameters_posteriorDistn_95CI_MS.py
admixture_parameters_posteriorDistn_95CI_MS.py
 
 
admixture_parameters_posteriorDistn_DuchenRhoTheta.py
admixture_parameters_posteriorDistn_DuchenRhoTheta.py
 
 
admixture_parameters_posteriorDistn_DuchenRhoTheta_Xchr.py
admixture_parameters_posteriorDistn_DuchenRhoTheta_Xchr.py
 
 
admixture_parameters_posteriorDistn_outside_95CI.py
admixture_parameters_posteriorDistn_outside_95CI.py
 
 
admixture_paramters_uniformPrior.py
admixture_paramters_uniformPrior.py
 
 
alldata_averaged_sorted
alldata_averaged_sorted
 
 
averageLD_realData.py
averageLD_realData.py
 
 
averageLD_realData.py~
averageLD_realData.py~
 
 
averageLD_realData2.py
averageLD_realData2.py
 
 
averageLD_realData2.py~
averageLD_realData2.py~
 
 
cleanOutput.py
cleanOutput.py
 
 
cleanOutput.py~
cleanOutput.py~
 
 
compute_Bayes_factors.py
compute_Bayes_factors.py
 
 
compute_short_intron_lengths.py
compute_short_intron_lengths.py
 
 
constNeZI_LD_H.sh
constNeZI_LD_H.sh
 
 
convertFile.py
convertFile.py
 
 
convertMS.py
convertMS.py
 
 
convertMS_noSegSites.py
convertMS_noSegSites.py
 
 
count_fields.py
count_fields.py
 
 
count_fields_Pi_S.py
count_fields_Pi_S.py
 
 
count_fields_Pi_S_TajD.py
count_fields_Pi_S_TajD.py
 
 
count_fields_any.py
count_fields_any.py
 
 
documentation_Jensen_response.doc
documentation_Jensen_response.doc
 
 
documentation_Jensen_response.doc~
documentation_Jensen_response.doc~
 
 
documentation_Jensen_response_publication.doc
documentation_Jensen_response_publication.doc
 
 
documentation_Jensen_response_publication.doc~
documentation_Jensen_response_publication.doc~
 
 
generate_MS_commands.py
generate_MS_commands.py
 
 
generate_MS_commands.py~
generate_MS_commands.py~
 
 
hapSpectrum_viz_JensenResponse.R
hapSpectrum_viz_JensenResponse.R
 
 
loc_AER_new_noHeader.txt
loc_AER_new_noHeader.txt
 
 
plot_admixture_diffProps.py
plot_admixture_diffProps.py
 
 
plot_admixture_fixedPopSize.py
plot_admixture_fixedPopSize.py
 
 
plot_admixture_fixedPopSize.py~
plot_admixture_fixedPopSize.py~
 
 
plot_admixture_migration.py
plot_admixture_migration.py
 
 
plot_admixture_varyGrowth.py
plot_admixture_varyGrowth.py
 
 
plot_original_models.py
plot_original_models.py
 
 
plot_original_models.py~
plot_original_models.py~
 
 
plot_trajectories.py
plot_trajectories.py
 
 
plot_trajectories.py~
plot_trajectories.py~
 
 
qsub_Arguello
qsub_Arguello
 
 
qsub_Arguello_tmp
qsub_Arguello_tmp
 
 
qsub_Arguello_tmp~
qsub_Arguello_tmp~
 
 
qsub_Arguello~
qsub_Arguello~
 
 
qsub_admixture_95CI_DuchenRhoTheta_exactLength_theta0
qsub_admixture_95CI_DuchenRhoTheta_exactLength_theta0
 
 
qsub_admixture_95CI_DuchenRhoTheta_exactLength_theta0_Xchr
qsub_admixture_95CI_DuchenRhoTheta_exactLength_theta0_Xchr
 
 
qsub_admixture_bot_mode_Garud2015_theta0_shortIntron
qsub_admixture_bot_mode_Garud2015_theta0_shortIntron
 
 
qsub_admixture_bot_mode_Garud_2015_theta0
qsub_admixture_bot_mode_Garud_2015_theta0
 
 
qsub_admixture_bot_mode_Garud_2015_theta0~
qsub_admixture_bot_mode_Garud_2015_theta0~
 
 
qsub_admixture_bot_mode_theta0_shortIntron
qsub_admixture_bot_mode_theta0_shortIntron
 
 
qsub_admixture_bottleneck_mode_theta0
qsub_admixture_bottleneck_mode_theta0
 
 
qsub_admixture_bottleneck_mode_theta0_400SNPs
qsub_admixture_bottleneck_mode_theta0_400SNPs
 
 
qsub_admixture_bottleneck_mode_theta0_400SNPs_MS
qsub_admixture_bottleneck_mode_theta0_400SNPs_MS
 
 
qsub_admixture_bottleneck_mode_theta0_MS
qsub_admixture_bottleneck_mode_theta0_MS
 
 
qsub_admixture_fullPosterior_DuchenRhoTheta_exactLength_theta0_Xchr
qsub_admixture_fullPosterior_DuchenRhoTheta_exactLength_theta0_Xchr
 
 
qsub_admixture_joint_theta0
qsub_admixture_joint_theta0
 
 
qsub_admixture_mode_DuchenRhoTheta_exactLength_theta0
qsub_admixture_mode_DuchenRhoTheta_exactLength_theta0
 
 
qsub_admixture_mode_Garud2015_theta0_shortIntron
qsub_admixture_mode_Garud2015_theta0_shortIntron
 
 
qsub_admixture_mode_Garud_2015_theta0
qsub_admixture_mode_Garud_2015_theta0
 
 
qsub_admixture_mode_Garud_2015_theta0~
qsub_admixture_mode_Garud_2015_theta0~
 
 
qsub_admixture_mode_corrected_theta0
qsub_admixture_mode_corrected_theta0
 
 
qsub_admixture_mode_hardcoded_theta0
qsub_admixture_mode_hardcoded_theta0
 
 
qsub_admixture_mode_rho5e-7_theta0
qsub_admixture_mode_rho5e-7_theta0
 
 
qsub_admixture_mode_theta0
qsub_admixture_mode_theta0
 
 

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Readme for response to Harris et al. 2018 PLoS Genetics.

Code can be traced from documentation_Jensen_response_publication.doc

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