R/odin.R
In Geidelberg/cotonou:
## Automatically generated by odin - do not edit
.main_model <- odin:::odin_c_class("main_model", list(get_internal = "main_model_get_internal", finalise = "main_model_finalise", create = "main_model_create", initmod_desolve = "main_model_initmod_desolve", contents = "main_model_contents", set_user = "main_model_set_user", metadata = "main_model_metadata", initial_conditions = "main_model_initial_conditions", rhs = "main_model_rhs", rhs_dde = "main_model_rhs_dde", rhs_desolve = "main_model_rhs_desolve", output = "main_model_output_dde", rhs_r = "main_model_rhs_r"), c("above_500_by_group", "alpha01", "alpha02", "alpha03", "alpha04", "alpha05", "alpha11", "alpha22", "alpha23", "alpha24", "alpha25", "alpha32", "alpha33_without_supp", "alpha34_without_supp", "alpha35_without_supp", "alpha42", "alpha43", "alpha44", "alpha45", "art_dropout_interruption_parm_t", "art_dropout_interruption_parm_y", "ART_eligible_CD4_200_349_t", "ART_eligible_CD4_200_349_y", "ART_eligible_CD4_350_500_t", "ART_eligible_CD4_350_500_y", "ART_eligible_CD4_above_500_t", "ART_eligible_CD4_above_500_y", "ART_eligible_CD4_below_200_t", "ART_eligible_CD4_below_200_y", "art_initiation_interruption_parm_t", "art_initiation_interruption_parm_y", "ART_RR", "beta_comm", "beta_noncomm", "c_t_comm", "c_t_noncomm", "c_y_comm", "c_y_noncomm", "cost_1_year_of_ART_government_FSW", "cost_1_year_of_ART_rest_of_population", "cost_1_year_of_ART_study_FSW", "cost_1_year_PrEP_intermediate_adherence_government", "cost_1_year_PrEP_intermediate_adherence_study", "cost_1_year_PrEP_non_adherence_government", "cost_1_year_PrEP_non_adherence_study", "cost_1_year_PrEP_perfect_adherence_government", "cost_1_year_PrEP_perfect_adherence_study", "cost_FSW_1_year_ART_Patient_costs", "cost_FSW_initiation_ART_Patient_costs", "cost_Initiation_ART_rest_of_population", "cost_Initiation_of_ART_government_FSW", "cost_Initiation_of_ART_study_FSW", "cost_Initiation_of_PrEP_government", "cost_Initiation_of_PrEP_study", "cost_PREP_1_year_ART_Patient_costs", "cost_PREP_initiation_Patient_costs", "count_PrEP_1a", "count_PrEP_1b", "count_PrEP_1c", "cumuInf_init", "dur_FSW", "ec", "eP", "eP0", "eP1a", "eP1b", "eP1c", "eP1d", "epsilon_t", "epsilon_y", "fc_t_comm", "fc_t_noncomm", "fc_y_comm", "fc_y_noncomm", "fP_t_comm", "fP_t_noncomm", "fP_y_comm", "fP_y_noncomm", "fPa", "fPb", "fPc", "fraction_FSW_foreign", "FSW_ONLY", "gamma01", "gamma02", "gamma03", "gamma04", "gamma11", "gamma22", "gamma23", "gamma24", "gamma32_without_supp", "gamma33_without_supp", "gamma34_without_supp", "gamma42", "gamma43", "gamma44", "I01_init", "I02_init", "I03_init", "I04_init", "I05_init", "I11_init", "I22_init", "I23_init", "I24_init", "I25_init", "I32_init", "I33_init", "I34_init", "I35_init", "I42_init", "I43_init", "I44_init", "I45_init", "infect_acute", "infect_AIDS", "infect_ART_t", "infect_ART_y", "infected_FSW_incoming", "intervention_ART_increase", "intervention_testing_increase", "iota", "kappa1", "kappaa", "kappab", "kappac", "M_comm", "M_noncomm", "mu", "n_t_comm", "n_t_noncomm", "n_y_comm", "n_y_noncomm", "Nage", "Ncat", "nu", "old_VS_assumption", "omega", "pfFSW_t", "pfFSW_y", "phi2", "phi3", "phi4", "phi5", "prep_efficacious_t", "prep_efficacious_y", "prep_intervention_t", "prep_intervention_y", "PrEP_reinit_OnOff_t", "PrEP_reinit_OnOff_y", "PrEPOnOff", "psia", "psib", "R", "rate_leave_pro_FSW", "rate_move_in", "rate_move_out", "rate_move_out_PrEP", "re_init_interruption_parm_t", "re_init_interruption_parm_y", "replaceDeaths", "rho", "rho_intervention_t", "rho_intervention_y", "RR_test_CD4200", "S0_init", "S1a_init", "S1b_init", "S1c_init", "S1d_init", "sigma", "TasP_testing", "tau_intervention_t", "tau_intervention_y", "test_rate_prep", "testing_prob_t", "testing_prob_y", "theta", "viral_supp_t", "viral_supp_y", "W0", "W1", "W2", "W3", "who_believe_comm"), list(discrete = FALSE, has_array = TRUE, has_output = TRUE, has_user = TRUE, has_delay = FALSE, has_interpolate = TRUE, has_stochastic = FALSE, has_include = TRUE, initial_time_dependent = FALSE), "cotonou", "odin/main_model.json", TRUE)
main_model <- structure(function (above_500_by_group, alpha01, alpha02, alpha03,
alpha04, alpha05, alpha11, alpha22, alpha23, alpha24, alpha25,
alpha32, alpha33_without_supp, alpha34_without_supp, alpha35_without_supp,
alpha42, alpha43, alpha44, alpha45, art_dropout_interruption_parm_t,
art_dropout_interruption_parm_y, ART_eligible_CD4_200_349_t,
ART_eligible_CD4_200_349_y, ART_eligible_CD4_350_500_t, ART_eligible_CD4_350_500_y,
ART_eligible_CD4_above_500_t, ART_eligible_CD4_above_500_y,
ART_eligible_CD4_below_200_t, ART_eligible_CD4_below_200_y,
art_initiation_interruption_parm_t, art_initiation_interruption_parm_y,
ART_RR, beta_comm, beta_noncomm, c_t_comm, c_t_noncomm, c_y_comm,
c_y_noncomm, cost_1_year_of_ART_government_FSW, cost_1_year_of_ART_rest_of_population,
cost_1_year_of_ART_study_FSW, cost_1_year_PrEP_intermediate_adherence_government,
cost_1_year_PrEP_intermediate_adherence_study, cost_1_year_PrEP_non_adherence_government,
cost_1_year_PrEP_non_adherence_study, cost_1_year_PrEP_perfect_adherence_government,
cost_1_year_PrEP_perfect_adherence_study, cost_FSW_1_year_ART_Patient_costs,
cost_FSW_initiation_ART_Patient_costs, cost_Initiation_ART_rest_of_population,
cost_Initiation_of_ART_government_FSW, cost_Initiation_of_ART_study_FSW,
cost_Initiation_of_PrEP_government, cost_Initiation_of_PrEP_study,
cost_PREP_1_year_ART_Patient_costs, cost_PREP_initiation_Patient_costs,
count_PrEP_1a, count_PrEP_1b, count_PrEP_1c, cumuInf_init,
dur_FSW, ec, eP, eP0, eP1a, eP1b, eP1c, eP1d, epsilon_t,
epsilon_y, fc_t_comm, fc_t_noncomm, fc_y_comm, fc_y_noncomm,
fP_t_comm, fP_t_noncomm, fP_y_comm, fP_y_noncomm, fPa, fPb,
fPc, fraction_FSW_foreign, FSW_ONLY, gamma01, gamma02, gamma03,
gamma04, gamma11, gamma22, gamma23, gamma24, gamma32_without_supp,
gamma33_without_supp, gamma34_without_supp, gamma42, gamma43,
gamma44, I01_init, I02_init, I03_init, I04_init, I05_init,
I11_init, I22_init, I23_init, I24_init, I25_init, I32_init,
I33_init, I34_init, I35_init, I42_init, I43_init, I44_init,
I45_init, infect_acute, infect_AIDS, infect_ART_t, infect_ART_y,
infected_FSW_incoming, intervention_ART_increase, intervention_testing_increase,
iota, kappa1, kappaa, kappab, kappac, M_comm, M_noncomm,
mu, n_t_comm, n_t_noncomm, n_y_comm, n_y_noncomm, Nage, Ncat,
nu, old_VS_assumption, omega, pfFSW_t, pfFSW_y, phi2, phi3,
phi4, phi5, prep_efficacious_t, prep_efficacious_y, prep_intervention_t,
prep_intervention_y, PrEP_reinit_OnOff_t, PrEP_reinit_OnOff_y,
PrEPOnOff, psia, psib, R, rate_leave_pro_FSW, rate_move_in,
rate_move_out, rate_move_out_PrEP, re_init_interruption_parm_t,
re_init_interruption_parm_y, replaceDeaths, rho, rho_intervention_t,
rho_intervention_y, RR_test_CD4200, S0_init, S1a_init, S1b_init,
S1c_init, S1d_init, sigma, TasP_testing, tau_intervention_t,
tau_intervention_y, test_rate_prep, testing_prob_t, testing_prob_y,
theta, viral_supp_t, viral_supp_y, W0, W1, W2, W3, who_believe_comm,
user = list(above_500_by_group = above_500_by_group, alpha01 = alpha01,
alpha02 = alpha02, alpha03 = alpha03, alpha04 = alpha04,
alpha05 = alpha05, alpha11 = alpha11, alpha22 = alpha22,
alpha23 = alpha23, alpha24 = alpha24, alpha25 = alpha25,
alpha32 = alpha32, alpha33_without_supp = alpha33_without_supp,
alpha34_without_supp = alpha34_without_supp, alpha35_without_supp = alpha35_without_supp,
alpha42 = alpha42, alpha43 = alpha43, alpha44 = alpha44,
alpha45 = alpha45, art_dropout_interruption_parm_t = art_dropout_interruption_parm_t,
art_dropout_interruption_parm_y = art_dropout_interruption_parm_y,
ART_eligible_CD4_200_349_t = ART_eligible_CD4_200_349_t,
ART_eligible_CD4_200_349_y = ART_eligible_CD4_200_349_y,
ART_eligible_CD4_350_500_t = ART_eligible_CD4_350_500_t,
ART_eligible_CD4_350_500_y = ART_eligible_CD4_350_500_y,
ART_eligible_CD4_above_500_t = ART_eligible_CD4_above_500_t,
ART_eligible_CD4_above_500_y = ART_eligible_CD4_above_500_y,
ART_eligible_CD4_below_200_t = ART_eligible_CD4_below_200_t,
ART_eligible_CD4_below_200_y = ART_eligible_CD4_below_200_y,
art_initiation_interruption_parm_t = art_initiation_interruption_parm_t,
art_initiation_interruption_parm_y = art_initiation_interruption_parm_y,
ART_RR = ART_RR, beta_comm = beta_comm, beta_noncomm = beta_noncomm,
c_t_comm = c_t_comm, c_t_noncomm = c_t_noncomm, c_y_comm = c_y_comm,
c_y_noncomm = c_y_noncomm, cost_1_year_of_ART_government_FSW = cost_1_year_of_ART_government_FSW,
cost_1_year_of_ART_rest_of_population = cost_1_year_of_ART_rest_of_population,
cost_1_year_of_ART_study_FSW = cost_1_year_of_ART_study_FSW,
cost_1_year_PrEP_intermediate_adherence_government = cost_1_year_PrEP_intermediate_adherence_government,
cost_1_year_PrEP_intermediate_adherence_study = cost_1_year_PrEP_intermediate_adherence_study,
cost_1_year_PrEP_non_adherence_government = cost_1_year_PrEP_non_adherence_government,
cost_1_year_PrEP_non_adherence_study = cost_1_year_PrEP_non_adherence_study,
cost_1_year_PrEP_perfect_adherence_government = cost_1_year_PrEP_perfect_adherence_government,
cost_1_year_PrEP_perfect_adherence_study = cost_1_year_PrEP_perfect_adherence_study,
cost_FSW_1_year_ART_Patient_costs = cost_FSW_1_year_ART_Patient_costs,
cost_FSW_initiation_ART_Patient_costs = cost_FSW_initiation_ART_Patient_costs,
cost_Initiation_ART_rest_of_population = cost_Initiation_ART_rest_of_population,
cost_Initiation_of_ART_government_FSW = cost_Initiation_of_ART_government_FSW,
cost_Initiation_of_ART_study_FSW = cost_Initiation_of_ART_study_FSW,
cost_Initiation_of_PrEP_government = cost_Initiation_of_PrEP_government,
cost_Initiation_of_PrEP_study = cost_Initiation_of_PrEP_study,
cost_PREP_1_year_ART_Patient_costs = cost_PREP_1_year_ART_Patient_costs,
cost_PREP_initiation_Patient_costs = cost_PREP_initiation_Patient_costs,
count_PrEP_1a = count_PrEP_1a, count_PrEP_1b = count_PrEP_1b,
count_PrEP_1c = count_PrEP_1c, cumuInf_init = cumuInf_init,
dur_FSW = dur_FSW, ec = ec, eP = eP, eP0 = eP0, eP1a = eP1a,
eP1b = eP1b, eP1c = eP1c, eP1d = eP1d, epsilon_t = epsilon_t,
epsilon_y = epsilon_y, fc_t_comm = fc_t_comm, fc_t_noncomm = fc_t_noncomm,
fc_y_comm = fc_y_comm, fc_y_noncomm = fc_y_noncomm, fP_t_comm = fP_t_comm,
fP_t_noncomm = fP_t_noncomm, fP_y_comm = fP_y_comm, fP_y_noncomm = fP_y_noncomm,
fPa = fPa, fPb = fPb, fPc = fPc, fraction_FSW_foreign = fraction_FSW_foreign,
FSW_ONLY = FSW_ONLY, gamma01 = gamma01, gamma02 = gamma02,
gamma03 = gamma03, gamma04 = gamma04, gamma11 = gamma11,
gamma22 = gamma22, gamma23 = gamma23, gamma24 = gamma24,
gamma32_without_supp = gamma32_without_supp, gamma33_without_supp = gamma33_without_supp,
gamma34_without_supp = gamma34_without_supp, gamma42 = gamma42,
gamma43 = gamma43, gamma44 = gamma44, I01_init = I01_init,
I02_init = I02_init, I03_init = I03_init, I04_init = I04_init,
I05_init = I05_init, I11_init = I11_init, I22_init = I22_init,
I23_init = I23_init, I24_init = I24_init, I25_init = I25_init,
I32_init = I32_init, I33_init = I33_init, I34_init = I34_init,
I35_init = I35_init, I42_init = I42_init, I43_init = I43_init,
I44_init = I44_init, I45_init = I45_init, infect_acute = infect_acute,
infect_AIDS = infect_AIDS, infect_ART_t = infect_ART_t,
infect_ART_y = infect_ART_y, infected_FSW_incoming = infected_FSW_incoming,
intervention_ART_increase = intervention_ART_increase,
intervention_testing_increase = intervention_testing_increase,
iota = iota, kappa1 = kappa1, kappaa = kappaa, kappab = kappab,
kappac = kappac, M_comm = M_comm, M_noncomm = M_noncomm,
mu = mu, n_t_comm = n_t_comm, n_t_noncomm = n_t_noncomm,
n_y_comm = n_y_comm, n_y_noncomm = n_y_noncomm, Nage = Nage,
Ncat = Ncat, nu = nu, old_VS_assumption = old_VS_assumption,
omega = omega, pfFSW_t = pfFSW_t, pfFSW_y = pfFSW_y,
phi2 = phi2, phi3 = phi3, phi4 = phi4, phi5 = phi5, prep_efficacious_t = prep_efficacious_t,
prep_efficacious_y = prep_efficacious_y, prep_intervention_t = prep_intervention_t,
prep_intervention_y = prep_intervention_y, PrEP_reinit_OnOff_t = PrEP_reinit_OnOff_t,
PrEP_reinit_OnOff_y = PrEP_reinit_OnOff_y, PrEPOnOff = PrEPOnOff,
psia = psia, psib = psib, R = R, rate_leave_pro_FSW = rate_leave_pro_FSW,
rate_move_in = rate_move_in, rate_move_out = rate_move_out,
rate_move_out_PrEP = rate_move_out_PrEP, re_init_interruption_parm_t = re_init_interruption_parm_t,
re_init_interruption_parm_y = re_init_interruption_parm_y,
replaceDeaths = replaceDeaths, rho = rho, rho_intervention_t = rho_intervention_t,
rho_intervention_y = rho_intervention_y, RR_test_CD4200 = RR_test_CD4200,
S0_init = S0_init, S1a_init = S1a_init, S1b_init = S1b_init,
S1c_init = S1c_init, S1d_init = S1d_init, sigma = sigma,
TasP_testing = TasP_testing, tau_intervention_t = tau_intervention_t,
tau_intervention_y = tau_intervention_y, test_rate_prep = test_rate_prep,
testing_prob_t = testing_prob_t, testing_prob_y = testing_prob_y,
theta = theta, viral_supp_t = viral_supp_t, viral_supp_y = viral_supp_y,
W0 = W0, W1 = W1, W2 = W2, W3 = W3, who_believe_comm = who_believe_comm),
unused_user_action = NULL, use_dde = FALSE)
{
.main_model$new(user, unused_user_action, use_dde)
}, ir = "odin/main_model.json", class = "odin_generator")
class(main_model) <- "odin_generator"
attr(main_model, "ir") <- .main_model$public_fields$ir
Geidelberg/cotonou documentation built on Aug. 29, 2020, 4:22 a.m.
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## Automatically generated by odin - do not edit
.main_model <- odin:::odin_c_class("main_model", list(get_internal = "main_model_get_internal", finalise = "main_model_finalise", create = "main_model_create", initmod_desolve = "main_model_initmod_desolve", contents = "main_model_contents", set_user = "main_model_set_user", metadata = "main_model_metadata", initial_conditions = "main_model_initial_conditions", rhs = "main_model_rhs", rhs_dde = "main_model_rhs_dde", rhs_desolve = "main_model_rhs_desolve", output = "main_model_output_dde", rhs_r = "main_model_rhs_r"), c("above_500_by_group", "alpha01", "alpha02", "alpha03", "alpha04", "alpha05", "alpha11", "alpha22", "alpha23", "alpha24", "alpha25", "alpha32", "alpha33_without_supp", "alpha34_without_supp", "alpha35_without_supp", "alpha42", "alpha43", "alpha44", "alpha45", "art_dropout_interruption_parm_t", "art_dropout_interruption_parm_y", "ART_eligible_CD4_200_349_t", "ART_eligible_CD4_200_349_y", "ART_eligible_CD4_350_500_t", "ART_eligible_CD4_350_500_y", "ART_eligible_CD4_above_500_t", "ART_eligible_CD4_above_500_y", "ART_eligible_CD4_below_200_t", "ART_eligible_CD4_below_200_y", "art_initiation_interruption_parm_t", "art_initiation_interruption_parm_y", "ART_RR", "beta_comm", "beta_noncomm", "c_t_comm", "c_t_noncomm", "c_y_comm", "c_y_noncomm", "cost_1_year_of_ART_government_FSW", "cost_1_year_of_ART_rest_of_population", "cost_1_year_of_ART_study_FSW", "cost_1_year_PrEP_intermediate_adherence_government", "cost_1_year_PrEP_intermediate_adherence_study", "cost_1_year_PrEP_non_adherence_government", "cost_1_year_PrEP_non_adherence_study", "cost_1_year_PrEP_perfect_adherence_government", "cost_1_year_PrEP_perfect_adherence_study", "cost_FSW_1_year_ART_Patient_costs", "cost_FSW_initiation_ART_Patient_costs", "cost_Initiation_ART_rest_of_population", "cost_Initiation_of_ART_government_FSW", "cost_Initiation_of_ART_study_FSW", "cost_Initiation_of_PrEP_government", "cost_Initiation_of_PrEP_study", "cost_PREP_1_year_ART_Patient_costs", "cost_PREP_initiation_Patient_costs", "count_PrEP_1a", "count_PrEP_1b", "count_PrEP_1c", "cumuInf_init", "dur_FSW", "ec", "eP", "eP0", "eP1a", "eP1b", "eP1c", "eP1d", "epsilon_t", "epsilon_y", "fc_t_comm", "fc_t_noncomm", "fc_y_comm", "fc_y_noncomm", "fP_t_comm", "fP_t_noncomm", "fP_y_comm", "fP_y_noncomm", "fPa", "fPb", "fPc", "fraction_FSW_foreign", "FSW_ONLY", "gamma01", "gamma02", "gamma03", "gamma04", "gamma11", "gamma22", "gamma23", "gamma24", "gamma32_without_supp", "gamma33_without_supp", "gamma34_without_supp", "gamma42", "gamma43", "gamma44", "I01_init", "I02_init", "I03_init", "I04_init", "I05_init", "I11_init", "I22_init", "I23_init", "I24_init", "I25_init", "I32_init", "I33_init", "I34_init", "I35_init", "I42_init", "I43_init", "I44_init", "I45_init", "infect_acute", "infect_AIDS", "infect_ART_t", "infect_ART_y", "infected_FSW_incoming", "intervention_ART_increase", "intervention_testing_increase", "iota", "kappa1", "kappaa", "kappab", "kappac", "M_comm", "M_noncomm", "mu", "n_t_comm", "n_t_noncomm", "n_y_comm", "n_y_noncomm", "Nage", "Ncat", "nu", "old_VS_assumption", "omega", "pfFSW_t", "pfFSW_y", "phi2", "phi3", "phi4", "phi5", "prep_efficacious_t", "prep_efficacious_y", "prep_intervention_t", "prep_intervention_y", "PrEP_reinit_OnOff_t", "PrEP_reinit_OnOff_y", "PrEPOnOff", "psia", "psib", "R", "rate_leave_pro_FSW", "rate_move_in", "rate_move_out", "rate_move_out_PrEP", "re_init_interruption_parm_t", "re_init_interruption_parm_y", "replaceDeaths", "rho", "rho_intervention_t", "rho_intervention_y", "RR_test_CD4200", "S0_init", "S1a_init", "S1b_init", "S1c_init", "S1d_init", "sigma", "TasP_testing", "tau_intervention_t", "tau_intervention_y", "test_rate_prep", "testing_prob_t", "testing_prob_y", "theta", "viral_supp_t", "viral_supp_y", "W0", "W1", "W2", "W3", "who_believe_comm"), list(discrete = FALSE, has_array = TRUE, has_output = TRUE, has_user = TRUE, has_delay = FALSE, has_interpolate = TRUE, has_stochastic = FALSE, has_include = TRUE, initial_time_dependent = FALSE), "cotonou", "odin/main_model.json", TRUE)
main_model <- structure(function (above_500_by_group, alpha01, alpha02, alpha03,
alpha04, alpha05, alpha11, alpha22, alpha23, alpha24, alpha25,
alpha32, alpha33_without_supp, alpha34_without_supp, alpha35_without_supp,
alpha42, alpha43, alpha44, alpha45, art_dropout_interruption_parm_t,
art_dropout_interruption_parm_y, ART_eligible_CD4_200_349_t,
ART_eligible_CD4_200_349_y, ART_eligible_CD4_350_500_t, ART_eligible_CD4_350_500_y,
ART_eligible_CD4_above_500_t, ART_eligible_CD4_above_500_y,
ART_eligible_CD4_below_200_t, ART_eligible_CD4_below_200_y,
art_initiation_interruption_parm_t, art_initiation_interruption_parm_y,
ART_RR, beta_comm, beta_noncomm, c_t_comm, c_t_noncomm, c_y_comm,
c_y_noncomm, cost_1_year_of_ART_government_FSW, cost_1_year_of_ART_rest_of_population,
cost_1_year_of_ART_study_FSW, cost_1_year_PrEP_intermediate_adherence_government,
cost_1_year_PrEP_intermediate_adherence_study, cost_1_year_PrEP_non_adherence_government,
cost_1_year_PrEP_non_adherence_study, cost_1_year_PrEP_perfect_adherence_government,
cost_1_year_PrEP_perfect_adherence_study, cost_FSW_1_year_ART_Patient_costs,
cost_FSW_initiation_ART_Patient_costs, cost_Initiation_ART_rest_of_population,
cost_Initiation_of_ART_government_FSW, cost_Initiation_of_ART_study_FSW,
cost_Initiation_of_PrEP_government, cost_Initiation_of_PrEP_study,
cost_PREP_1_year_ART_Patient_costs, cost_PREP_initiation_Patient_costs,
count_PrEP_1a, count_PrEP_1b, count_PrEP_1c, cumuInf_init,
dur_FSW, ec, eP, eP0, eP1a, eP1b, eP1c, eP1d, epsilon_t,
epsilon_y, fc_t_comm, fc_t_noncomm, fc_y_comm, fc_y_noncomm,
fP_t_comm, fP_t_noncomm, fP_y_comm, fP_y_noncomm, fPa, fPb,
fPc, fraction_FSW_foreign, FSW_ONLY, gamma01, gamma02, gamma03,
gamma04, gamma11, gamma22, gamma23, gamma24, gamma32_without_supp,
gamma33_without_supp, gamma34_without_supp, gamma42, gamma43,
gamma44, I01_init, I02_init, I03_init, I04_init, I05_init,
I11_init, I22_init, I23_init, I24_init, I25_init, I32_init,
I33_init, I34_init, I35_init, I42_init, I43_init, I44_init,
I45_init, infect_acute, infect_AIDS, infect_ART_t, infect_ART_y,
infected_FSW_incoming, intervention_ART_increase, intervention_testing_increase,
iota, kappa1, kappaa, kappab, kappac, M_comm, M_noncomm,
mu, n_t_comm, n_t_noncomm, n_y_comm, n_y_noncomm, Nage, Ncat,
nu, old_VS_assumption, omega, pfFSW_t, pfFSW_y, phi2, phi3,
phi4, phi5, prep_efficacious_t, prep_efficacious_y, prep_intervention_t,
prep_intervention_y, PrEP_reinit_OnOff_t, PrEP_reinit_OnOff_y,
PrEPOnOff, psia, psib, R, rate_leave_pro_FSW, rate_move_in,
rate_move_out, rate_move_out_PrEP, re_init_interruption_parm_t,
re_init_interruption_parm_y, replaceDeaths, rho, rho_intervention_t,
rho_intervention_y, RR_test_CD4200, S0_init, S1a_init, S1b_init,
S1c_init, S1d_init, sigma, TasP_testing, tau_intervention_t,
tau_intervention_y, test_rate_prep, testing_prob_t, testing_prob_y,
theta, viral_supp_t, viral_supp_y, W0, W1, W2, W3, who_believe_comm,
user = list(above_500_by_group = above_500_by_group, alpha01 = alpha01,
alpha02 = alpha02, alpha03 = alpha03, alpha04 = alpha04,
alpha05 = alpha05, alpha11 = alpha11, alpha22 = alpha22,
alpha23 = alpha23, alpha24 = alpha24, alpha25 = alpha25,
alpha32 = alpha32, alpha33_without_supp = alpha33_without_supp,
alpha34_without_supp = alpha34_without_supp, alpha35_without_supp = alpha35_without_supp,
alpha42 = alpha42, alpha43 = alpha43, alpha44 = alpha44,
alpha45 = alpha45, art_dropout_interruption_parm_t = art_dropout_interruption_parm_t,
art_dropout_interruption_parm_y = art_dropout_interruption_parm_y,
ART_eligible_CD4_200_349_t = ART_eligible_CD4_200_349_t,
ART_eligible_CD4_200_349_y = ART_eligible_CD4_200_349_y,
ART_eligible_CD4_350_500_t = ART_eligible_CD4_350_500_t,
ART_eligible_CD4_350_500_y = ART_eligible_CD4_350_500_y,
ART_eligible_CD4_above_500_t = ART_eligible_CD4_above_500_t,
ART_eligible_CD4_above_500_y = ART_eligible_CD4_above_500_y,
ART_eligible_CD4_below_200_t = ART_eligible_CD4_below_200_t,
ART_eligible_CD4_below_200_y = ART_eligible_CD4_below_200_y,
art_initiation_interruption_parm_t = art_initiation_interruption_parm_t,
art_initiation_interruption_parm_y = art_initiation_interruption_parm_y,
ART_RR = ART_RR, beta_comm = beta_comm, beta_noncomm = beta_noncomm,
c_t_comm = c_t_comm, c_t_noncomm = c_t_noncomm, c_y_comm = c_y_comm,
c_y_noncomm = c_y_noncomm, cost_1_year_of_ART_government_FSW = cost_1_year_of_ART_government_FSW,
cost_1_year_of_ART_rest_of_population = cost_1_year_of_ART_rest_of_population,
cost_1_year_of_ART_study_FSW = cost_1_year_of_ART_study_FSW,
cost_1_year_PrEP_intermediate_adherence_government = cost_1_year_PrEP_intermediate_adherence_government,
cost_1_year_PrEP_intermediate_adherence_study = cost_1_year_PrEP_intermediate_adherence_study,
cost_1_year_PrEP_non_adherence_government = cost_1_year_PrEP_non_adherence_government,
cost_1_year_PrEP_non_adherence_study = cost_1_year_PrEP_non_adherence_study,
cost_1_year_PrEP_perfect_adherence_government = cost_1_year_PrEP_perfect_adherence_government,
cost_1_year_PrEP_perfect_adherence_study = cost_1_year_PrEP_perfect_adherence_study,
cost_FSW_1_year_ART_Patient_costs = cost_FSW_1_year_ART_Patient_costs,
cost_FSW_initiation_ART_Patient_costs = cost_FSW_initiation_ART_Patient_costs,
cost_Initiation_ART_rest_of_population = cost_Initiation_ART_rest_of_population,
cost_Initiation_of_ART_government_FSW = cost_Initiation_of_ART_government_FSW,
cost_Initiation_of_ART_study_FSW = cost_Initiation_of_ART_study_FSW,
cost_Initiation_of_PrEP_government = cost_Initiation_of_PrEP_government,
cost_Initiation_of_PrEP_study = cost_Initiation_of_PrEP_study,
cost_PREP_1_year_ART_Patient_costs = cost_PREP_1_year_ART_Patient_costs,
cost_PREP_initiation_Patient_costs = cost_PREP_initiation_Patient_costs,
count_PrEP_1a = count_PrEP_1a, count_PrEP_1b = count_PrEP_1b,
count_PrEP_1c = count_PrEP_1c, cumuInf_init = cumuInf_init,
dur_FSW = dur_FSW, ec = ec, eP = eP, eP0 = eP0, eP1a = eP1a,
eP1b = eP1b, eP1c = eP1c, eP1d = eP1d, epsilon_t = epsilon_t,
epsilon_y = epsilon_y, fc_t_comm = fc_t_comm, fc_t_noncomm = fc_t_noncomm,
fc_y_comm = fc_y_comm, fc_y_noncomm = fc_y_noncomm, fP_t_comm = fP_t_comm,
fP_t_noncomm = fP_t_noncomm, fP_y_comm = fP_y_comm, fP_y_noncomm = fP_y_noncomm,
fPa = fPa, fPb = fPb, fPc = fPc, fraction_FSW_foreign = fraction_FSW_foreign,
FSW_ONLY = FSW_ONLY, gamma01 = gamma01, gamma02 = gamma02,
gamma03 = gamma03, gamma04 = gamma04, gamma11 = gamma11,
gamma22 = gamma22, gamma23 = gamma23, gamma24 = gamma24,
gamma32_without_supp = gamma32_without_supp, gamma33_without_supp = gamma33_without_supp,
gamma34_without_supp = gamma34_without_supp, gamma42 = gamma42,
gamma43 = gamma43, gamma44 = gamma44, I01_init = I01_init,
I02_init = I02_init, I03_init = I03_init, I04_init = I04_init,
I05_init = I05_init, I11_init = I11_init, I22_init = I22_init,
I23_init = I23_init, I24_init = I24_init, I25_init = I25_init,
I32_init = I32_init, I33_init = I33_init, I34_init = I34_init,
I35_init = I35_init, I42_init = I42_init, I43_init = I43_init,
I44_init = I44_init, I45_init = I45_init, infect_acute = infect_acute,
infect_AIDS = infect_AIDS, infect_ART_t = infect_ART_t,
infect_ART_y = infect_ART_y, infected_FSW_incoming = infected_FSW_incoming,
intervention_ART_increase = intervention_ART_increase,
intervention_testing_increase = intervention_testing_increase,
iota = iota, kappa1 = kappa1, kappaa = kappaa, kappab = kappab,
kappac = kappac, M_comm = M_comm, M_noncomm = M_noncomm,
mu = mu, n_t_comm = n_t_comm, n_t_noncomm = n_t_noncomm,
n_y_comm = n_y_comm, n_y_noncomm = n_y_noncomm, Nage = Nage,
Ncat = Ncat, nu = nu, old_VS_assumption = old_VS_assumption,
omega = omega, pfFSW_t = pfFSW_t, pfFSW_y = pfFSW_y,
phi2 = phi2, phi3 = phi3, phi4 = phi4, phi5 = phi5, prep_efficacious_t = prep_efficacious_t,
prep_efficacious_y = prep_efficacious_y, prep_intervention_t = prep_intervention_t,
prep_intervention_y = prep_intervention_y, PrEP_reinit_OnOff_t = PrEP_reinit_OnOff_t,
PrEP_reinit_OnOff_y = PrEP_reinit_OnOff_y, PrEPOnOff = PrEPOnOff,
psia = psia, psib = psib, R = R, rate_leave_pro_FSW = rate_leave_pro_FSW,
rate_move_in = rate_move_in, rate_move_out = rate_move_out,
rate_move_out_PrEP = rate_move_out_PrEP, re_init_interruption_parm_t = re_init_interruption_parm_t,
re_init_interruption_parm_y = re_init_interruption_parm_y,
replaceDeaths = replaceDeaths, rho = rho, rho_intervention_t = rho_intervention_t,
rho_intervention_y = rho_intervention_y, RR_test_CD4200 = RR_test_CD4200,
S0_init = S0_init, S1a_init = S1a_init, S1b_init = S1b_init,
S1c_init = S1c_init, S1d_init = S1d_init, sigma = sigma,
TasP_testing = TasP_testing, tau_intervention_t = tau_intervention_t,
tau_intervention_y = tau_intervention_y, test_rate_prep = test_rate_prep,
testing_prob_t = testing_prob_t, testing_prob_y = testing_prob_y,
theta = theta, viral_supp_t = viral_supp_t, viral_supp_y = viral_supp_y,
W0 = W0, W1 = W1, W2 = W2, W3 = W3, who_believe_comm = who_believe_comm),
unused_user_action = NULL, use_dde = FALSE)
{
.main_model$new(user, unused_user_action, use_dde)
}, ir = "odin/main_model.json", class = "odin_generator")
class(main_model) <- "odin_generator"
attr(main_model, "ir") <- .main_model$public_fields$ir
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