Function reference • VivaxModelR

All functions
`calculate_h1_rcd()`	Calculate h1 from aggregated incidence data
`calculate_r0_rc_fromdata()`	Calculate R0 and Rc on an incidence dataset
`calculate_r0_rc_fromdata_delay()`	Calculate R0 and Rc on an incidence dataset
`calculate_r0_rc_fromdata_delay_rcd()`	Calculate R0 and Rc on an incidence dataset with delays and RCD
`calculate_r0_rc_fromdata_rcd()`	Calculate R0 and Rc on an incidence dataset with RCD
`calculate_tau_rcd()`	Calculate the targeting ratio from incidence data with information on RCD
`calibrate_vivax_equilibrium()`	Calibrate the vivax model
`create_approximation()`	Creates linear interpolation
`format_data_simulation()`	Formating intervention parameters within a database
`get_equilibrium_states_vivax()`	Calculate equilibrium state variables
`get_equilibrium_states_vivax_delay()`	Calculate equilibrium state variables, in model with delay to treatment
`get_equilibrium_states_vivax_rcd()`	Calculate equilibrium state variables
`get_equilibrium_states_vivax_rcd_no_referral()`	Calculate equilibrium state variables, RCD model (no referral)
`get_equilibrium_states_vivax_rcd_referral()`	Calculate equilibrium state variables, RCD model (referral)
`get_prop_relapse()`	Calculate proportion of relapses
`get_r0_vivax()`	R0 calculation
`get_rc_vivax()`	Rc calculation, with case management and vector control
`get_rc_vivax_delay()`	Rc calculation, with case management and vector control and delay to treatment
`get_validity_condition_vivax()`	Checks validity condition
`incidence_day2year()`	Converts daily incidence to annual
`incidence_year2day()`	Converts annual incidence to daily
`model_sto_vivax_delay()`	Reaction associated with the vivax model with delays, in stochastic version
`model_sto_vivax_delay_mda()`	Reaction associated with the vivax model with delays and MDA during prophylaxis, in stochastic version
`model_sto_vivax_delay_rcd_no_referral()`	Reaction associated with the vivax model with delays and RCD, in stochastic version
`model_sto_vivax_delay_rcd_no_referral_mda()`	Reaction associated with the vivax model with delays, RCD and MDA during prophylaxis, in stochastic version
`model_sto_vivax_delay_rcd_referral()`	Reaction associated with the vivax model with delays and RCD, in stochastic version
`model_sto_vivax_delay_rcd_referral_mda()`	Reaction associated with the vivax model with delays, RCD and MDA during prophylaxis, in stochastic version
`ode_vivax_cm_importation_vc()`	ODE vivax model with case management, importation and vector control
`ode_vivax_delay()`	ODE vivax model with case management, importation and vector control, including delay to treatment
`ode_vivax_delay_mda()`	ODE vivax model with case management, importation and vector control, including delay to treatment, during MDA prophylaxis
`ode_vivax_delay_rcd_no_referral()`	ODE vivax model with case management, RCD without referral, importation and vector control, including delay to treatment
`ode_vivax_delay_rcd_no_referral_mda()`	ODE vivax model with case management, RCD without referral, importation and vector control, including delay to treatment, during MDA prophylaxis
`ode_vivax_delay_rcd_referral()`	ODE vivax model with case management, RCD with referral, importation and vector control, including delay to treatment
`ode_vivax_delay_rcd_referral_mda()`	ODE vivax model with case management, RCD with referral, importation and vector control, including delay to treatment, during PDA prophylaxis
`ode_vivax_mda()`	ODE vivax model with case management, importation and vector control, during MDA prophylaxis
`ode_vivax_rcd()`	ODE vivax model with case management, RCD, importation and vector control, including delay to treatment
`ode_vivax_rcd_mda()`	ODE vivax model with case management, RCD, importation and vector control, during MDA prophylaxis
`sample_uncertainty_incidence_import()`	Samples uncertainty in incidence and importation data
`sanity_checks_inputs_calculate()`	Check on the database input for calculating lambda at baseline
`sanity_checks_inputs_simulate()`	Check on the database input for simulating the model on a database of values
`simulate_from_data()`	Simulate the model for several values in a database
`simulate_from_data_delay()`	Simulate from equilibrium, with delays in treatment
`simulate_vivax_delay_mda_ode()`	Simulate vivax model with delay to treatment and MDA
`simulate_vivax_delay_mda_sto()`	Simulate vivax model with delay to treatment and MDA, with stochastic model
`simulate_vivax_delay_ode()`	Simulate vivax model with delay to treatment
`simulate_vivax_delay_sto()`	Simulate vivax model with delay to treatment, with stochastic model
`simulate_vivax_interventions()`	Simulate the effect of several interventions
`simulate_vivax_mda_ode()`	Simulate vivax model with MDA
`simulate_vivax_ode()`	Simulate vivax model
`solve_lambda_vivax()`	Transmission rate calculation
`solve_lambda_vivax_delay()`	Transmission rate calculation, in model with delay to treatment
`solve_lambda_vivax_rcd()`	Transmission rate calculation
`solve_lambda_vivax_rcd_no_referral()`	Transmission rate calculation
`solve_lambda_vivax_rcd_referral()`	Transmission rate calculation
`varying_tau()`	Function for time varying tau
`vector_control_exponential_decay()`	Creates vector control exponential decay

Reference

All functions