| age_strat_fit_mod | Model to feed to 'rootSolve::multiroot()' to estimate key... |
| age_strat_get_pars | Function taking 'age_strat_fit_mod' and implementing within... |
| augment_age_strat_parameters | Augment parameter set for age stratified schisto model with... |
| beta_from_eggs | Function to estimate beta from egg output and other... |
| cheever_eggs_to_females | Cheever eggs to females function |
| convert_burden_egg_to_worm | Function to get solutions for worm burden and clumping... |
| cvrg_from_pars | Estimate MDA coverage necessary to reach breakpoint as a... |
| cvrg_from_W_bp | Estimate MDA coverage necessary to reach breakpoint as a... |
| dWdt_W | Get rate of change of mean worm burden as function of W,... |
| eggs_kap_get_W | Function to estimate worm burden given mean egg burden and... |
| egg_to_worm_fx | Function used in multiroot to estimate worm burden and... |
| eqbm_snails_fit_mod | Solve for equilibrium susceptible snail and total snail... |
| eq_W_get_alpha | Function to estimate probability of worm establishment per... |
| eq_Ws_get_Omega_Lambda0 | Function to estimate miracidial invasion rate and relative... |
| est_prev_W_k | Estimate prevalence as function of clumping parameter and... |
| exp_seq | Function to generate log transformed sequence evenly... |
| fit_pars_from_eq_vals | Uses 'W_Ip_eq_solns' within 'multiroot' to solve for unkown... |
| gam_Wxi | Schistosomiasis acquired immunity |
| garch_discrete_mod | Garchitorena discrete time simulator |
| garch_discrete_mod_dd | Garchitorena discrete time simulator with density dependence |
| garch_mod | Garchitorena et al model for environmentally transmitted... |
| garch_mod_dd | Garchitorena et al model for environmentally transmitted... |
| garch_r0 | Garchitorena et al $R_0$ estimation |
| gen_force_fx | Generate seasonal model forcing function |
| get_breakpoint_W_N | Worm burden breakpoint estimation |
| get_Ip_W_bp | Get breakpoint snail infection prevalence and mean worm... |
| get_R0 | Estimate R_0 from model parameters |
| I_get_E | Estimate exposed snail fraction from infected snail... |
| I_get_Lambda | Function to estimate Lambda (snail-to-man FOI) as function of... |
| infection_inputs_get_pars | Function to input observed equilibrium infection values and... |
| I_P_get_W_eq | Estimate endemic equilibrium given infected snail prevalence |
| k_w_fx | Estimate clumping parameter as a function of log worm burden |
| Lambda_get_N_eq | Function to estimate equilibirum snail population size, N_eq,... |
| Lambda_Wij | Estimate saturating form of man-to-snail FOI |
| Lambda_Wij_linear | Estimate linear form of man-to-snail FOI |
| latexImg | Function to insert latex equations into .md dox |
| load_csv_from_googledrive | Function that takes a google drive file id and loads the file... |
| nil_1 | Return 1 |
| phi_Wk | Schistosomiasis mating probability |
| prev_get_W | Estimate mean worm burden and clumping parameter as function... |
| prev_intensity_to_clump | Estimate clumping parameter as function of prevalence and... |
| prev_kap_get_W | Estimate mean worm burden from egg prevalence and clumping... |
| prev_W_get_k | Estimate clumping parameter, kappa, as function of mean... |
| R0_egg_kap_gamma_m | Estimate R_0 from input egg burden and density dependence... |
| Reff_W | Get Reff as function of W, model parameters, and DDs |
| R_eff_W_I | Estimate effective reproduction number as product of W, I and... |
| Reff_Wij | Estimate effective reproduction number |
| Reff_Wij_I_P | Estimate effective reproduction number as function of mean... |
| Reff_W_kap | Get Reff as function of W, model parameters, kappa, and DDs |
| rho_Wk | Schistosomiasis density dependent fecundity |
| schisto_age_strat_mod | Age-stratified schistosomiasis model |
| schisto_base_mod | Basic schistosomiasis model |
| schisto_mod | Barebones schistosomiasis model |
| schisto_stoch_mod | Stochastic version of the age stratified schistosomiasis... |
| sim_discrete_mod | Garchitorena discrete time model simulation |
| sim_garch_mod | Simulate the garchitorena model |
| sim_int_choice | Garchitorena discrete time model simulation with intervention... |
| sim_opt_choice | Implement an optimal policy identified with MDPtoolbox... |
| sim_schisto_mod | Simulate a schistosomiasis model |
| sim_schisto_stoch_mod | Simulate the stochastic version of age-stratified... |
| sim_w_inputs | Simulate transmission and intervention through time with... |
| wbp_fx | Worm burden breakpoint equations for use in multiroot |
| W_bp_I_P | Estimate breakpoint as function of I_P and parameters |
| W_bp_N_solver | Model to feed to 'rootSolve::multiroot()' to estimate... |
| W_bp_R_0 | Estimate W_bp from R_0 |
| W_ij_get_N_S_E_I | Estimate Snail infection class distribution given mean worm... |
| W_Ip_eq_solns | Function used in 'multiroot" to fit transmission parameters |
| w_start_get_r0 | Estimate R0 from starting worm burden and density dependence... |
