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

Code can be traced from documentation_Jensen_response_publication.doc

Name		Name	Last commit message	Last commit date
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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Code can be traced from documentation_Jensen_response_publication.doc

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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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