Files in thednainus/senegalHIVmodel

Analysis of HIV data from Senegal

R/data.R R/dating.R R/mcmc_posterior.R R/miscellaneous.R R/prevalence.R README.md analyses/results/README.md analyses/results/Trajectories.R analyses/results/Trajectories_allSubtypes.R analyses/results/compare_mcmc_runs_AllSubtypes.R analyses/results/compare_mcmc_runs_bySubtype.R analyses/results/other_statistics.R analyses/results/other_statistics_PAF2014.R analyses/results/other_statistics_gpf2gpm.R analyses/results/other_statistics_gpf2msm.R analyses/results/other_statistics_gpm2gpf.R analyses/results/other_statistics_msm2gpf.R analyses/results/other_statistics_msm2msm.R analyses/results/plots/README.md analyses/results/plots/mcmc_runs/AllSubtypes_Model2.pdf analyses/results/plots/mcmc_runs/AllSubtypes_Model3.pdf analyses/results/plots/mcmc_runs/AllSubtypes_Model4.pdf analyses/results/plots/mcmc_runs/AllSubtypes_Model5.pdf analyses/results/plots/mcmc_runs/AllSubtypes_Model6.pdf analyses/results/plots/mcmc_runs/AllSubtypes_Model7.pdf analyses/results/plots/mcmc_runs/subtype02_AG_model1.pdf analyses/results/plots/mcmc_runs/subtype02_AG_model2.pdf analyses/results/plots/mcmc_runs/subtype02_AG_model3.pdf analyses/results/plots/mcmc_runs/subtype02_AG_model4.pdf analyses/results/plots/mcmc_runs/subtypeC_model1.pdf analyses/results/plots/mcmc_runs/subtypeC_model2.pdf analyses/results/plots/mcmc_runs/subtypeC_model3.pdf analyses/results/plots/mcmc_runs/subtypeC_model4.pdf analyses/results/plots/plots_withMaleX/AllSubtypes_PAF_and_sizes.pdf analyses/results/plots/plots_withMaleX/AllSubtypes_model2and5_PAF.pdf analyses/results/plots/plots_withMaleX/AllSubtypes_model3and6_PAF.pdf analyses/results/plots/plots_withMaleX/AllSubtypes_models2and5_sizes.pdf analyses/results/plots/plots_withMaleX/AllSubtypes_models3and6_sizes.pdf analyses/results/plots/plots_withMaleX/AllSubtypes_models4and7_sizes.pdf analyses/results/plots/plots_withMaleX/Subtype02AG_PAF.pdf analyses/results/plots/plots_withMaleX/Subtype02AG_sizes.pdf analyses/results/plots/plots_withMaleX/SubtypeC_sizes.pdf analyses/results/plots/plots_withMaleX/bySubtypes_PAF_and_sizes.pdf analyses/results/plots/plots_withMaleX/paper/paper_PAF.pdf analyses/results/plots/plots_withMaleX/paper/paper_PAF_allSubtypes_SI_part1.pdf analyses/results/plots/plots_withMaleX/paper/paper_PAF_allSubtypes_SI_part2.pdf analyses/results/plots/plots_withMaleX/paper/paper_PAF_subtype02AG_SI.pdf analyses/results/plots/plots_withMaleX/paper/paper_PAF_subtypeC_SI.pdf analyses/results/plots/plots_withMaleX/paper/paper_sizes.pdf analyses/results/plots/plots_withMaleX/paper/paper_sizes_allSubtypes_SI_part1.pdf analyses/results/plots/plots_withMaleX/paper/paper_sizes_allSubtypes_SI_part2.pdf analyses/results/plots/plots_withMaleX/paper/paper_sizes_subtype02AG_SI.pdf analyses/results/plots/plots_withMaleX/paper/paper_sizes_subtypeC_SI.pdf analyses/results/plots/plots_withMaleX/subtypeC_model2/C_model2_byGroup_PAF.pdf analyses/results/plots/plots_withMaleX/subtypeC_model2/C_model2_byGroup_Sizes.pdf analyses/results/plots/plots_withMaleX/subtypeC_model2/C_model2_byRep_PAF.pdf analyses/results/plots/plots_withMaleX/subtypeC_model2/C_model2_byRep_Sizes.pdf analyses/results/plots/reproduction_number/AllSubtypes_model2and5_r0.pdf analyses/results/plots/reproduction_number/AllSubtypes_model3and6_r0.pdf analyses/results/plots/reproduction_number/AllSubtypes_model4and7_r0.pdf analyses/results/plots/reproduction_number/Subtype02_AG_r0.pdf analyses/results/plots/reproduction_number/SubtypeC_r0.pdf analyses/results/plots/scripts/PAF_MSM_sensitive_analysis.R analyses/results/plots/scripts/descriptive_plots.R analyses/results/plots/scripts/plot_basicReproductionNumber.R analyses/results/plots/scripts/plot_pafs.R analyses/results/plots/scripts/plot_pafs_Supplementary_Information.R analyses/results/plots/scripts/plot_paper_figure_paf.R analyses/results/plots/scripts/plot_paper_figure_sizes.R analyses/results/plots/scripts/plot_sizes.R analyses/results/plots/scripts/plot_sizes_Supplementary_Information.R analyses/results/read_mcmc_runs.R analyses/scripts/Python-scripts/README.md analyses/scripts/R-scripts/Models/BySubtype/02_AG_m1/1.model.02_AG.R analyses/scripts/R-scripts/Models/BySubtype/02_AG_m1/2.load_data.02_AG.R analyses/scripts/R-scripts/Models/BySubtype/02_AG_m1/3.mcmc.02_AG.R analyses/scripts/R-scripts/Models/BySubtype/02_AG_m1/4.mcmc_zMatrix.02_AG.R analyses/scripts/R-scripts/Models/BySubtype/02_AG_m1/OSG/1.model_osg.02_AG.R analyses/scripts/R-scripts/Models/BySubtype/02_AG_m1/OSG/2.load_data_osg.02_AG.R analyses/scripts/R-scripts/Models/BySubtype/02_AG_m1/OSG/3.mcmc_osg.02_AG.R analyses/scripts/R-scripts/Models/BySubtype/02_AG_m1/OSG/4.mcmc_zMatrix_osg.02_AG.R analyses/scripts/R-scripts/Models/BySubtype/02_AG_m2/1.model.02_AG_m2.R analyses/scripts/R-scripts/Models/BySubtype/02_AG_m2/2.load_data.02_AG_m2.R analyses/scripts/R-scripts/Models/BySubtype/02_AG_m2/3.mcmc.02_AG_m2.R analyses/scripts/R-scripts/Models/BySubtype/02_AG_m2/4.mcmc_zMatrix.02_AG_m2.R analyses/scripts/R-scripts/Models/BySubtype/02_AG_m2/OSG/1.model_osg.02_AG_m2.R analyses/scripts/R-scripts/Models/BySubtype/02_AG_m2/OSG/2.load_data_osg.02_AG_m2.R analyses/scripts/R-scripts/Models/BySubtype/02_AG_m2/OSG/3.mcmc_osg.02_AG_m2.R analyses/scripts/R-scripts/Models/BySubtype/02_AG_m2/OSG/4.mcmc_zMatrix_osg.02_AG_m2.R analyses/scripts/R-scripts/Models/BySubtype/02_AG_m3/1.model.02_AG_m3.R analyses/scripts/R-scripts/Models/BySubtype/02_AG_m3/2.load_data.02_AG_m3.R analyses/scripts/R-scripts/Models/BySubtype/02_AG_m3/3.mcmc.02_AG_m3.R analyses/scripts/R-scripts/Models/BySubtype/02_AG_m3/4.mcmc_zMatrix.02_AG_m3.R analyses/scripts/R-scripts/Models/BySubtype/02_AG_m3/OSG/1.model_osg.02_AG_m3.R analyses/scripts/R-scripts/Models/BySubtype/02_AG_m3/OSG/2.load_data_osg.02_AG_m3.R analyses/scripts/R-scripts/Models/BySubtype/02_AG_m3/OSG/3.mcmc_osg.02_AG_m3.R analyses/scripts/R-scripts/Models/BySubtype/02_AG_m3/OSG/4.mcmc_zMatrix_osg.02_AG_m3.R analyses/scripts/R-scripts/Models/BySubtype/02_AG_m4/1.model.02_AG_m4.R analyses/scripts/R-scripts/Models/BySubtype/02_AG_m4/2.load_data.02_AG_m4.R analyses/scripts/R-scripts/Models/BySubtype/02_AG_m4/3.mcmc.02_AG_m4.R analyses/scripts/R-scripts/Models/BySubtype/02_AG_m4/4.mcmc_zMatrix.02_AG_m4.R analyses/scripts/R-scripts/Models/BySubtype/02_AG_m4/OSG/1.model_osg.02_AG_m4.R analyses/scripts/R-scripts/Models/BySubtype/02_AG_m4/OSG/2.load_data_osg.02_AG_m4.R analyses/scripts/R-scripts/Models/BySubtype/02_AG_m4/OSG/3.mcmc_osg.02_AG_m4.R analyses/scripts/R-scripts/Models/BySubtype/02_AG_m4/OSG/4.mcmc_zMatrix_osg.02_AG_m4.R analyses/scripts/R-scripts/Models/BySubtype/C_m1/1.model.C.R analyses/scripts/R-scripts/Models/BySubtype/C_m1/2.load_data.C.R analyses/scripts/R-scripts/Models/BySubtype/C_m1/3.mcmc.C.R analyses/scripts/R-scripts/Models/BySubtype/C_m1/4.mcmc_zMatrix.C.R analyses/scripts/R-scripts/Models/BySubtype/C_m1/OSG/1.model_osg.C.R analyses/scripts/R-scripts/Models/BySubtype/C_m1/OSG/2.load_data_osg.C.R analyses/scripts/R-scripts/Models/BySubtype/C_m1/OSG/3.mcmc_osg.C.R analyses/scripts/R-scripts/Models/BySubtype/C_m1/OSG/4.mcmc_zMatrix_osg.C.R analyses/scripts/R-scripts/Models/BySubtype/C_m2/1.model.C_m2.R analyses/scripts/R-scripts/Models/BySubtype/C_m2/2.load_data.C_m2.R analyses/scripts/R-scripts/Models/BySubtype/C_m2/3.mcmc.C_m2.R analyses/scripts/R-scripts/Models/BySubtype/C_m2/4.mcmc_zMatrix.C_m2.R analyses/scripts/R-scripts/Models/BySubtype/C_m2/OSG/1.model_osg.C_m2.R analyses/scripts/R-scripts/Models/BySubtype/C_m2/OSG/2.load_data_osg.C_m2.R analyses/scripts/R-scripts/Models/BySubtype/C_m2/OSG/3.mcmc_osg.C_m2.R analyses/scripts/R-scripts/Models/BySubtype/C_m2/OSG/4.mcmc_zMatrix_osg.C_m2.R analyses/scripts/R-scripts/Models/BySubtype/C_m3/1.model.C_m3.R analyses/scripts/R-scripts/Models/BySubtype/C_m3/2.load_data.C_m3.R analyses/scripts/R-scripts/Models/BySubtype/C_m3/3.mcmc.C_m3.R analyses/scripts/R-scripts/Models/BySubtype/C_m3/4.mcmc_zMatrix.C_m3.R analyses/scripts/R-scripts/Models/BySubtype/C_m3/OSG/1.model_osg.C_m3.R analyses/scripts/R-scripts/Models/BySubtype/C_m3/OSG/2.load_data_osg.C_m3.R analyses/scripts/R-scripts/Models/BySubtype/C_m3/OSG/3.mcmc_osg.C_m3.R analyses/scripts/R-scripts/Models/BySubtype/C_m3/OSG/4.mcmc_zMatrix_osg.C_m3.R analyses/scripts/R-scripts/Models/BySubtype/C_m4/1.model.C_m4.R analyses/scripts/R-scripts/Models/BySubtype/C_m4/2.load_data.C_m4.R analyses/scripts/R-scripts/Models/BySubtype/C_m4/3.mcmc.C_m4.R analyses/scripts/R-scripts/Models/BySubtype/C_m4/4.mcmc_zMatrix.C_m4.R analyses/scripts/R-scripts/Models/BySubtype/C_m4/OSG/1.model_osg.C_m4.R analyses/scripts/R-scripts/Models/BySubtype/C_m4/OSG/2.load_data_osg.C_m4.R analyses/scripts/R-scripts/Models/BySubtype/C_m4/OSG/3.mcmc_osg.C_m4.R analyses/scripts/R-scripts/Models/BySubtype/C_m4/OSG/4.mcmc_zMatrix_osg.C_m4.R analyses/scripts/R-scripts/Models/BySubtype/README.md analyses/scripts/R-scripts/Models/README.md analyses/scripts/R-scripts/Models/Subtypes_Combined/Model2/1.model.v2.R analyses/scripts/R-scripts/Models/Subtypes_Combined/Model2/2.load_data.v2.R analyses/scripts/R-scripts/Models/Subtypes_Combined/Model2/3.mcmc.v2.R analyses/scripts/R-scripts/Models/Subtypes_Combined/Model2/4.mcmc_zMatrix.v2.R analyses/scripts/R-scripts/Models/Subtypes_Combined/Model2/OSG/1.model_osg_v2.R analyses/scripts/R-scripts/Models/Subtypes_Combined/Model2/OSG/2.load_data_osg_v2.R analyses/scripts/R-scripts/Models/Subtypes_Combined/Model2/OSG/3.mcmc_osg_v2.R analyses/scripts/R-scripts/Models/Subtypes_Combined/Model2/OSG/4.mcmc_zMatrix_osg.v2.R analyses/scripts/R-scripts/Models/Subtypes_Combined/Model3/1.model.v3.R analyses/scripts/R-scripts/Models/Subtypes_Combined/Model3/2.load_data.v3.R analyses/scripts/R-scripts/Models/Subtypes_Combined/Model3/3.mcmc.v3.R analyses/scripts/R-scripts/Models/Subtypes_Combined/Model3/4.mcmc_zMatrix.v3.R analyses/scripts/R-scripts/Models/Subtypes_Combined/Model3/OSG/1.model_osg.v3.R analyses/scripts/R-scripts/Models/Subtypes_Combined/Model3/OSG/2.load_data_osg.v3.R analyses/scripts/R-scripts/Models/Subtypes_Combined/Model3/OSG/3.mcmc_osg.v3.R analyses/scripts/R-scripts/Models/Subtypes_Combined/Model3/OSG/4.mcmc_zMatrix_osg.v3.R analyses/scripts/R-scripts/Models/Subtypes_Combined/Model4/1.model.v4.R analyses/scripts/R-scripts/Models/Subtypes_Combined/Model4/2.load_data.v4.R analyses/scripts/R-scripts/Models/Subtypes_Combined/Model4/3.mcmc.v4.R analyses/scripts/R-scripts/Models/Subtypes_Combined/Model4/4.mcmc_zMatrix.v4.R analyses/scripts/R-scripts/Models/Subtypes_Combined/Model4/OSG/1.model_osg.v4.R analyses/scripts/R-scripts/Models/Subtypes_Combined/Model4/OSG/2.load_data_osg.v4.R analyses/scripts/R-scripts/Models/Subtypes_Combined/Model4/OSG/3.mcmc.osg_v4.R analyses/scripts/R-scripts/Models/Subtypes_Combined/Model4/OSG/4.mcmc_zMatrix_osg.v4.R analyses/scripts/R-scripts/Models/Subtypes_Combined/Model5/1.model.v5.R analyses/scripts/R-scripts/Models/Subtypes_Combined/Model5/2.load_data.v5.R analyses/scripts/R-scripts/Models/Subtypes_Combined/Model5/3.mcmc.v5.R analyses/scripts/R-scripts/Models/Subtypes_Combined/Model5/4.mcmc_zMatrix.v5.R analyses/scripts/R-scripts/Models/Subtypes_Combined/Model5/OSG/1.model_osg_v5.R analyses/scripts/R-scripts/Models/Subtypes_Combined/Model5/OSG/2.load_data_osg_v5.R analyses/scripts/R-scripts/Models/Subtypes_Combined/Model5/OSG/3.mcmc_osg_v5.R analyses/scripts/R-scripts/Models/Subtypes_Combined/Model5/OSG/4.mcmc_zMatrix_osg.v5.R analyses/scripts/R-scripts/Models/Subtypes_Combined/Model6/1.model.v6.R analyses/scripts/R-scripts/Models/Subtypes_Combined/Model6/2.load_data.v6.R analyses/scripts/R-scripts/Models/Subtypes_Combined/Model6/3.mcmc.v6.R analyses/scripts/R-scripts/Models/Subtypes_Combined/Model6/4.mcmc_zMatrix.v6.R analyses/scripts/R-scripts/Models/Subtypes_Combined/Model6/OSG/1.model_osg.v6.R analyses/scripts/R-scripts/Models/Subtypes_Combined/Model6/OSG/2.load_data_osg.v6.R analyses/scripts/R-scripts/Models/Subtypes_Combined/Model6/OSG/3.mcmc_osg.v6.R analyses/scripts/R-scripts/Models/Subtypes_Combined/Model6/OSG/4.mcmc_zMatrix_osg.v6.R analyses/scripts/R-scripts/Models/Subtypes_Combined/Model7/1.model.v7.R analyses/scripts/R-scripts/Models/Subtypes_Combined/Model7/2.load_data.v7.R analyses/scripts/R-scripts/Models/Subtypes_Combined/Model7/3.mcmc.v7.R analyses/scripts/R-scripts/Models/Subtypes_Combined/Model7/4.mcmc_zMatrix.v7.R analyses/scripts/R-scripts/Models/Subtypes_Combined/Model7/OSG/1.model_osg.v7.R analyses/scripts/R-scripts/Models/Subtypes_Combined/Model7/OSG/2.load_data_osg.v7.R analyses/scripts/R-scripts/Models/Subtypes_Combined/Model7/OSG/3.mcmc.osg_v7.R analyses/scripts/R-scripts/Models/Subtypes_Combined/Model7/OSG/4.mcmc_zMatrix_osg.v7.R analyses/scripts/R-scripts/Models/Subtypes_Combined/README.md analyses/scripts/R-scripts/Processing/README.md analyses/scripts/R-scripts/Processing/merge_trees.R analyses/scripts/R-scripts/Processing/treedater_HIV_CGR_byCodon.R analyses/scripts/R-scripts/README.md inst/data/README.md inst/data/alignments/by_codon/README.md inst/data/trees_by_subtype/README.md man/beast_phydyn.Rd man/bindTree_for_phydynBeast.Rd man/births_mq.Rd man/births_newCases.Rd man/births_pafs.Rd man/calculate_newCases.Rd man/calculate_pafs.Rd man/data_format.Rd man/deme2deme.Rd man/df_newCases.Rd man/df_pafs.Rd man/df_r0.Rd man/df_sizes.Rd man/df_sizes_prop.Rd man/get_posterior.Rd man/gpspline.Rd man/median_and_quantiles.Rd man/mq_prop.Rd man/mq_r0.Rd man/msmspline.Rd man/organize_metadata.Rd man/organize_metadata_bySubtype.Rd man/post_traj.Rd man/post_traj_mx.Rd man/posterior_trajectories.Rd man/prPrevalenceStat.Rd man/prop_infected.Rd man/read_mcmc_rds.Rd man/reorganize_deme_sizes.Rd man/replace_values.Rd man/root_drop_tips.Rd man/set_prev_state_parameters.Rd man/setup.model.equations.Rd man/tfgy2prevalenceStat.Rd tests/testthat.R tests/testthat/test-model_equations.R vignettes/SenegalHIVmodel.Rmd