Files in EvoNetHIV/Goodreau_et_al_Behavior_-_SPVL
Evonet: Integrated Bio-Social Models for HIV Epidemiology
DESCRIPTION
NAMESPACE
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/Acute Infection Heightened Infectiousness/Network.Estimation.R
Simulation scripts/Acute Infection Heightened Infectiousness/Sim.R
Simulation scripts/Coital Cessation in AIDS Stage/Network.Estimation.R
Simulation scripts/Coital Cessation in AIDS Stage/Sim.R
Simulation scripts/Coital Frequency/Network.Estimation.R
Simulation scripts/Coital Frequency/Sim.R
Simulation scripts/Default/Default.Network.Estimation.R
Simulation scripts/Default/Default.Sim.R
Simulation scripts/Heritability/Network.Estimation.R
Simulation scripts/Heritability/Sim.R
Simulation scripts/Increasing vs Plateauing Transmission Function/Increasing.Network.Estimation.R
Simulation scripts/Increasing vs Plateauing Transmission Function/Increasing.Sim.R
Simulation scripts/Increasing vs Plateauing Transmission Function/Plateauing.Network.Estimation.R
Simulation scripts/Increasing vs Plateauing Transmission Function/Plateauing.Sim.R
Simulation scripts/Relational Duration/Network.Estimation.R
Simulation scripts/Relational 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
