mrc-ide/malariasimulation
An individual based model for malaria

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Search the mrc-ide/malariasimulation package
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262
Source code
84
Man pages
51
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mrc-ide/malariasimulation: An individual based model for malaria
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API

API for mrc-ide/malariasimulation
An individual based model for malaria

Global functions
.human_blood_meal_rate Source code
AL_params Man page
CQ_PQ_params_vivax Man page
CQ_TQ_params_vivax Man page
CQ_params_vivax Man page
CorrelationParameters Man page
DHA_PQP_params Man page
SP_AQ_params Man page
account_for_tbv Source code
adult_mosquito_model_restore_state Source code
adult_mosquito_model_save_state Source code
adult_mosquito_model_update Source code
anti_parasite_immunity Source code
approx_sum Source code
aquatic_mosquito_model_update Source code
arab_params Man page
asymptomatic_infectivity Source code
attach_pev_dose_listeners Source code
average_p_repelled Source code
average_p_successful Source code
bednet_decay Source code
bernoulli Source code
bernoulli_multi_p Source code
bernoulli_multi_p_cpp Source code
between Source code
biting_effects_individual Source code
bitset_at Source code
bitset_index Source code
bitset_index_cpp Source code
blood_immunity Source code
blood_meal_rate Source code
boost_immunity Source code
calculate_R_bar Source code
calculate_TBA Source code
calculate_TRA Source code
calculate_asymptomatic_detectable Source code
calculate_carrying_capacity Man page Source code
calculate_clinical_infections Source code
calculate_eir Source code
calculate_eq Source code
calculate_falciparum_infections Source code
calculate_foim Source code
calculate_infectious Source code
calculate_infectious_compartmental Source code
calculate_infectious_individual Source code
calculate_initial_ages Source code
calculate_initial_counts Source code
calculate_lm_det_infections Source code
calculate_omega Source code
calculate_pev_antibodies Source code
calculate_pev_efficacy Source code
calculate_successful_treatments Source code
calculate_tbv_antibodies Source code
calculate_treated Source code
calculate_vivax_infections Source code
calculate_zeta Source code
carrying_capacity Source code
clinical_immunity Source code
create_adult_mosquito_model Source code
create_adult_solver Source code
create_age_group_renderer Source code
create_age_variable_mean_renderer_process Source code
create_aquatic_mosquito_model Source code
create_aquatic_solver Source code
create_biting_process Source code
create_compartmental_rendering_process Source code
create_dosage_renderer Source code
create_epi_pev_process Source code
create_events Source code
create_exponential_decay_process Source code
create_export_variable Source code
create_hypnozoite_batch_decay_process Source code
create_lagged_eir Source code
create_lagged_infectivity Source code
create_mass_pev_listener Source code
create_mda_listeners Source code
create_mortality_process Source code
create_mosquito_emergence_process Source code
create_n_with_hypnozoites_age_renderer_process Source code
create_n_with_hypnozoites_renderer_process Source code
create_pev_booster_listener Source code
create_pev_efficacy_listener Source code
create_pev_profile Man page Source code
create_pmc_process Source code
create_prevalence_renderer Source code
create_processes Source code
create_progress_process Man page Source code
create_progression_rates_process Source code
create_seasonal_booster_scheduler Source code
create_solver_stepping_process Source code
create_tbv_listener Source code
create_timeseries Source code
create_total_M_renderer_compartmental Source code
create_transmission_mixer Source code
create_variable_mean_renderer_process Source code
create_variables Source code
create_vector_count_renderer_individual Source code
death_rate Source code
distribute_nets Source code
effective_biting_rates Source code
eggs_laid Source code
equilibrium_total_M Source code
exponential_process_cpp Source code
falciparum_infection_outcome_process Source code
fast_weighted_sample Source code
find_birthrates Man page Source code
fun_params Man page
gamb_params Man page
get_age Source code
get_antimalarial_resistance_parameters Man page Source code
get_correlation_parameters Man page Source code
get_equilibrium_population Source code
get_gonotrophic_cycle Source code
get_human_population Source code
get_init_carrying_capacity Man page Source code
get_parameters Man page Source code
get_treatment_coverages Source code
human_blood_meal_rate Source code
human_pi Source code
in_age_range Source code
incidence_probability_renderer Source code
incidence_renderer Source code
indoor_spraying Source code
initial_immunity Source code
initial_mosquito_counts Source code
initial_state Source code
initial_state_vivax Source code
intervention_coefficient Source code
inverse_param Source code
invlogit Source code
itexp Source code
kol_params Man page
log_uniform Source code
ls_treatment_prophylaxis_efficacy Source code
match_timestep Source code
mean_param Source code
merged_named_lists Source code
net_usage_renderer Source code
parameter_draws_pf Man page
parameter_draws_pv Man page
parameterise_mosquito_equilibrium Man page Source code
parameterise_mosquito_models Source code
parameterise_solvers Source code
parameterise_total_M Man page Source code
parasite_parameters Man page
peak_season_offset Man page Source code
pev_efficacy Source code
populate_incidence_rendering_columns Source code
populate_metapopulation_incidence_rendering_columns Source code
prob_bitten Source code
prob_repelled_bednets Source code
prob_spraying_repels Source code
prob_survives_bednets Source code
prob_survives_spraying Source code
prob_to_rate Source code
probability_of_detection Source code
product_param Source code
progression_outcome_process Source code
r21_booster_profile Man page
r21_profile Man page
rainfall Source code
random_restore_state Source code
random_save_state Source code
random_seed Source code
rate_to_prob Source code
rcondmvnorm Source code
rdt_detectable Source code
relapse_bite_infection_hazard_resolution Source code
remove_keys Source code
remove_unused_equilibrium Source code
render_initial_incidence Source code
reset_target Source code
rtexp Source code
rtss_booster_profile Man page
rtss_profile Man page
run_metapop_simulation Man page Source code
run_resumable_simulation Man page Source code
run_simulation Man page Source code
run_simulation_with_repetitions Man page
sample_bitset Source code
sample_intervention Source code
sample_maternal_immunity Source code
sample_pev_param Source code
schedule_infections Source code
schedule_vaccination Source code
set_antimalarial_resistance Man page Source code
set_bednets Man page Source code
set_carrying_capacity Man page Source code
set_clinical_treatment Man page Source code
set_demography Man page Source code
set_drugs Man page Source code
set_epi_outputs Man page Source code
set_equilibrium Man page Source code
set_mass_pev Man page Source code
set_mda Man page Source code
set_parameter_draw Man page Source code
set_pev_epi Man page Source code
set_pmc Man page Source code
set_smc Man page Source code
set_species Man page Source code
set_spraying Man page Source code
set_tbv Man page Source code
severe_immunity Source code
simulate_bites Source code
simulate_infection Source code
solver_get_states Source code
solver_set_states Source code
solver_step Source code
spraying_decay Source code
steph_params Man page
throw_away_nets Source code
time_cached Source code
timeseries_at Source code
timeseries_push Source code
timeseries_restore_state Source code
timeseries_save_state Source code
to_char_vector Source code
translate_equilibrium Source code
translate_parameters Source code
translate_vivax_parameters Source code
treatment_prophylaxis_efficacy Source code
unique_biting_rate Source code
update_infection Source code
update_mass_drug_admin Source code
update_severe_disease Source code
update_to_asymptomatic_infection Source code
vcapply Source code
vivax_infection_outcome_process Source code
vlapply Source code
vnapply Source code
weibull_survival Source code
mrc-ide/malariasimulation documentation built on Feb. 18, 2025, 8:43 a.m.

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