Files in EvoNetHIV/Test_and_Treat

Evonet: Integrated Bio-Social Models for HIV Epidemiology

R/ErgmTerms.R R/RcppExports.R R/adherence.R R/aging.R R/assign_ai_prop.R R/births.R R/cd4_update.R R/cd4_update2.R R/coital_acts.R R/deaths.R R/deaths_tx_time_adjusted.R R/evonet-package.R R/evonet_deprecated.R R/evonet_run.R R/evonet_setup.R R/evoplot.R R/evorun.R 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_process.R R/input_parameters_qa_qc.R R/input_params.R R/model_fit.R R/netsim_restart.R R/nw_setup.R R/plot_age_hist.R R/plot_aim3_drug_muts.R R/plot_disc_coital_acts_history.R R/plot_donors_cd4.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_output.R R/plots_popsumm.R R/plots_popsumm_deprecated.R R/plots_summary_timeseries.R R/remove_offset_relationships.R R/restart_module.R R/risk_group_changes.R R/risk_heterogeneity_module.R R/setup_epimodel_control_object.R R/setup_initialize_nw.R R/social_2nd_line_treatment_module.R R/social_act_type_het.R R/social_bring_new_groups_into_care_module.R R/social_coital_acts.R R/social_condom_use.R R/social_discord_edgelist.R R/social_discord_edgelist_df.R R/social_dropout_module.R R/social_generic_attribute_transition.R R/social_increased_testing_defined_groups.R R/social_increased_testing_selected_groups_module.R R/social_increased_testing_selected_groups_module_in_progress.R R/social_relationship_dur_length_calcs.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_eligibles_only_module_.R R/social_testing_diagnosis_with_enhancements_module_.R R/social_treatment_dropout.R R/social_treatment_module_PrEP.R R/social_treatment_module_john.R R/social_treatment_module_john_v3.R R/social_treatment_module_multiple_criteria.R R/social_treatment_prep.R R/social_treatment_prep_SES.R R/social_treatment_ranked.R R/social_treatment_sex_age.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_modlue.R R/summary_partner_list.R R/summary_popsumm.R R/summary_popsumm_deprec.R R/summary_popsumm_fxns.R R/summary_popsumm_mat.R R/summary_popsumm_vars.R R/summary_viral_lineage.R R/summary_vl_list.R R/targeted_treatment.R R/targeted_treatment2.R R/targeted_treatment6.R R/testing.R R/transmission.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/treatment.R R/treatment_dropout.R R/utilities.R R/vaccination.R R/viral_cd4_helper_fxns.R R/viral_cd4_udate_initial_pop.R R/viral_cd4_update_daily_aids_var.R R/viral_cd4_update_daily_with_age.R R/viral_update.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_delayed_rebound.R R/viral_update_gamma.R R/viral_update_gamma_dropout.R R/viral_update_gamma_treated.R R/vital_births_bookkeeping_misc.R R/vital_births_bookkeeping_pop.R R/vital_births_calculate_new.R R/vital_death_aged_out.R R/vital_death_aids.R R/vital_death_aids_john.R R/vital_death_non_aids.R R/vital_initial_age_dist.R R/vital_new_additions.R README.md