Files in EvoNetHIV/RoleSPVL

Evonet: Integrated Bio-Social Models for HIV Epidemiology

R/initialize_agents.R R/initialize_evonet_misc.R R/initialize_infecteds_cd4.R R/initialize_infecteds_vl.R R/initialize_module.R R/initialize_popsumm_dynamics.R R/initialize_restart.R R/initialize_vl_cd4_list.R R/input_parameters_age_distribution.R R/input_parameters_agent_attributes.R R/input_parameters_asmr.R R/input_parameters_cd4.R R/input_parameters_derived.R R/input_parameters_popsumm_stats.R R/input_parameters_primary.R R/input_parameters_qa_qc.R R/input_paramters_asmr.R R/plot_age_hist.R R/plot_disc_coital_acts_history.R R/plot_end_epidemic_values.R R/plot_heritability_quarters.R R/plot_incidence_rate.R R/plot_network.R R/plot_popsumm_multi_models.R R/plot_relationship_duration.R R/plot_relationship_history.R R/plot_table_parameters.R R/plot_time_to_removal.R R/plot_time_to_removal_spvl.R R/plot_vl_trajectories.R R/plot_vl_trajectories_aim2.R R/plot_vl_trajectories_aim3.R R/plots_infection_history_coital_acts_table.R R/plots_infection_history_plot.R R/plots_infection_history_vl_plots.R R/plots_infection_summary_table.R R/plots_initial_diagnostic.R R/plots_output.R R/plots_popsumm.R R/plots_summary_timeseries.R R/setup_epimodel_control_object.R R/setup_initialize_nw.R R/social_2nd_line_treatment_module.R R/social_adherence.R R/social_attribute_transition_module.R R/social_coital_acts.R R/social_coital_acts_module.R R/social_condom_use.R R/social_discord_edgelist.R R/social_discord_edgelist_df.R R/social_generic_attribute_transition.R R/social_resistance_testing_module.R R/social_role_msm.R R/social_set_generic_attribute_on_nw.R R/social_set_msm_role_on_nw.R R/social_testing_diagnosis_module.R R/social_treatment_module.R R/social_treatment_module_john.R R/social_treatment_ranked.R R/social_treatment_vaccination.R R/social_viral_load_testing_module.R R/summary_end_epidemic_values.R R/summary_evo_newick.R R/summary_misc.R R/summary_module.R R/summary_popsumm.R R/summary_popsumm_fxns.R R/summary_viral_lineage.R R/summary_vl_list.R R/transmission_bookkeeping_module.R R/transmission_cd4_module.R R/transmission_hill_fxn.R R/transmission_hughes_and_exp.R R/transmission_main_module.R R/utilities.R R/viral_cd4_helper_fxns.R R/viral_cd4_udate_initial_pop.R R/viral_cd4_update_daily.R R/viral_update_aim3.R R/viral_update_aim3_args_list_1.R R/viral_update_aim3_args_list_2.R R/viral_update_aim3_cd4.R R/viral_update_aim3_rcpp_output.R R/viral_update_cd4_diff_eqn.R R/viral_update_cd4_simple_diff_eqn.R R/viral_update_gamma.R R/vital_aging_module.R R/vital_births_bookkeeping_misc.R R/vital_births_bookkeeping_pop.R R/vital_births_calculate_new.R R/vital_births_module.R R/vital_death_aged_out.R R/vital_death_aids.R R/vital_death_non_aids.R R/vital_deaths_module.R R/vital_initial_age_dist.R R/vital_new_additions.R R/vital_new_additions_both.R README.md Simulation scripts/parameters.R Simulation scripts/relationship_duration_sim.R man/coital_acts_table_fxn.Rd man/incidence_rate_plot.Rd man/infection_history_plot.Rd man/infection_history_vl_cd4_plot.Rd man/infection_summary_table_fxn.Rd man/initialize_agents.Rd man/initialize_evonet_misc.Rd man/initialize_infecteds_cd4.Rd man/initialize_infecteds_vl.Rd man/initialize_module.Rd man/initialize_popsumm_dynamics.Rd man/initialize_restart.Rd man/initialize_vl_cd4_list.Rd man/input_parameters_age_distribution.Rd man/input_parameters_agent_attributes.Rd man/input_parameters_asmr.Rd man/input_parameters_cd4_data.Rd man/input_parameters_derived.Rd man/input_parameters_popsumm_stats.Rd man/input_parameters_primary.Rd man/input_parameters_qaqc.Rd man/new_additions_fxn.Rd man/new_additions_fxn_both.Rd man/output_plots_fxn.Rd man/plot_age_hist.Rd man/plot_disc_coital_acts_history.Rd man/plot_end_epidemic_values.Rd man/plot_heritability_quarters.Rd man/plot_network_fxn.Rd man/plot_relationship_duration.Rd man/plot_relationship_history.Rd man/plot_summary_timeseries.Rd man/plot_table_parameters.Rd man/plot_time_to_removal.Rd man/plot_time_to_removal_by_spvl.Rd man/plot_vl_trajectories.Rd man/plot_vl_trajectories_aim2.Rd man/plot_vl_trajectories_aim3.Rd man/plots_initial_diagnostic.Rd man/plots_popsumm_multi_models.Rd man/plots_popsumm_ymin_ymax.Rd man/setup_epimodel_control_object.Rd man/setup_initialize_network.Rd man/social_2nd_line_treatment_module.Rd man/social_adherence.Rd man/social_attribute_transition_module.Rd man/social_coital_acts.Rd man/social_coital_acts_module.Rd man/social_condom_use.Rd man/social_discord_edgelist.Rd man/social_discord_edgelist_df.Rd man/social_generic_attribute_transition.Rd man/social_resistance_testing_module.Rd man/social_role_msm.Rd man/social_set_generic_attribute_on_nw.Rd man/social_set_msm_role_on_nw.Rd man/social_testing_diagnosis_module.Rd man/social_treatment_module.Rd man/social_treatment_module_john.Rd man/social_treatment_ranked.Rd man/social_treatment_vaccination.Rd man/social_viral_load_testing_module.Rd man/summary_end_epidemic_values.Rd man/summary_evo_newick.Rd man/summary_misc.Rd man/summary_module.Rd man/summary_popsumm.Rd man/summary_popsumm_fxns.Rd man/summary_viral_lineage.Rd man/summary_vl_list.Rd man/transmission_bookkeeping_module.Rd man/transmission_cd4_module.Rd man/transmission_hill_fxn.Rd man/transmission_hughes_and_exp.Rd man/transmission_main_module.Rd man/utilities_apportion.lr.Rd man/viral_spvl_cat_fxn.Rd man/viral_update_aim3.Rd man/viral_update_aim3_args_list_1.Rd man/viral_update_aim3_args_list_2.Rd man/viral_update_aim3_cd4.Rd man/viral_update_aim3_rcpp_output.Rd man/viral_update_cd4_daily.Rd man/viral_update_cd4_diff_eqn.Rd man/viral_update_cd4_intial_pop.Rd man/viral_update_cd4_simple_diff_eqn.Rd man/viral_update_gamma.Rd man/vital_aging_module.Rd man/vital_births_bookkeeping_misc.Rd man/vital_births_bookkeeping_pop.Rd man/vital_births_calculate_new.Rd man/vital_births_module.Rd man/vital_death_aged_out.Rd man/vital_death_aids.Rd man/vital_death_non_aids.Rd man/vital_deaths_module.Rd man/vital_initial_age_dist.Rd