| Read global configuration options | api_config_global |
| Check if two numeric values are approximately equal | approx_equal |
| Compute bloodmeals taken by mosquitoes on hosts | compute_bloodmeal |
| Compute bloodmeals taken by mosquitoes on hosts in simple models | compute_bloodmeal_simple |
| Compute number of newly emerging adults (lambda) | compute_emergents |
| Compute number of newly emerging adults from Beverton-Holt dynamics | compute_emergents.BH |
| Compute number of newly emerging adults from forcing term | compute_emergents.trace |
| Compute number of newly emerging adults from forcing term (deterministic) | compute_emergents.trace_deterministic |
| Compute number of newly emerging adults from forcing term (stochastic) | compute_emergents.trace_stochastic |
| Compute mosquito feeding rate (f) | compute_f |
| Compute mosquito feeding rate for BQ model (f) | compute_f.BQ |
| Compute mosquito feeding rate for RM model (f) | compute_f.RM |
| Compute null mosquito feeding rate (f) | compute_f.trace |
| Compute human population strata sizes (H) | compute_H |
| Compute human population strata sizes for MOI model (H) | compute_H.MOI |
| Compute human population strata sizes for SIP model (H) | compute_H.SIP |
| Compute human population strata sizes for SIR model (H) | compute_H.SIR |
| Compute human population strata sizes for SIS model (H) | compute_H.SIS |
| Compute available alternative blood hosts (O) | compute_O |
| Compute available alternative blood hosts for trace model (O) | compute_O.trace |
| Compute number of eggs laid from oviposition for each patch | compute_oviposit |
| Compute number of eggs laid from oviposition for each aquatic habitat for BQ model | compute_oviposit.BQ |
| Compute number of eggs laid from oviposition for each patch for deterministic RM model | compute_oviposit.BQ_deterministic |
| Compute number of eggs laid from oviposition for each patch for stochastic RM model | compute_oviposit.BQ_stochastic |
| Compute number of eggs laid from oviposition for each patch for RM model | compute_oviposit.RM |
| Compute number of eggs laid from oviposition for each patch for deterministic RM model | compute_oviposit.RM_deterministic |
| Compute number of eggs laid from oviposition for each patch for stochastic RM model | compute_oviposit.RM_stochastic |
| Compute number of eggs laid from oviposition for each patch for null model | compute_oviposit.trace |
| Compute time at risk matrix (Psi) | compute_Psi |
| Compute time at risk matrix for MOI model (Psi) | compute_Psi.MOI |
| Compute time at risk matrix for SIP model (Psi) | compute_Psi.SIP |
| Compute time at risk matrix for SIR model (Psi) | compute_Psi.SIR |
| Compute time at risk matrix for SIS model (Psi) | compute_Psi.SIS |
| Compute human blood feeding fraction (q) | compute_q |
| Compute human blood feeding fraction for BQ model (q) | compute_q.BQ |
| Compute human blood feeding fraction for RM model (q) | compute_q.RM |
| Compute null human blood feeding fraction (q) | compute_q.trace |
| Compute available visitors (W_{delta}) | compute_Wd |
| Compute available visitors for trace model (W_{delta}) | compute_Wd.trace |
| Compute human biting weights (w_{f}) | compute_wf |
| Compute human biting weights for MOI model (w_{f}) | compute_wf.MOI |
| Compute human biting weights for SIP model (w_{f}) | compute_wf.SIP |
| Compute human biting weights for SIR model (w_{f}) | compute_wf.SIR |
| Compute human biting weights for SIS model (w_{f}) | compute_wf.SIS |
| Compute net infectiousness of humans (x) | compute_x |
| Compute net infectiousness for MOI model (x) | compute_x.MOI |
| Compute net infectiousness for SIP model (x) | compute_x.SIP |
| Compute net infectiousness for SIR model (x) | compute_x.SIR |
| Compute net infectiousness for SIS model (x) | compute_x.SIS |
| Compute net infectiousness of visitors (x_{delta}) | compute_xd |
| Compute net infectiousness of visitors for trace model (x_{delta}) | compute_xd.trace |
| Compute density of infective mosquitoes (Z) | compute_Z |
| Compute density of infective mosquitoes for BQ model (Z) | compute_Z.BQ |
| Compute density of infective mosquitoes for RM model (Z) | compute_Z.RM |
| Compute null density of infective mosquitoes (Z) | compute_Z.trace |
| Distribute items into bins as evenly as possible | distribute |
| Division of integers | divmod |
| Draw a multinomially distributed random vector | draw_multinom |
| Get parameters for trace driven alternative blood hosts | get_config_alternative_trace |
| Get parameters for aquatic (immature) model with Beverton-Holt dynamics | get_config_aqua_BH |
| Get parameters for aquatic (immature) model with forced emergence | get_config_aqua_trace |
| Get parameters for MOI human model | get_config_humans_MOI |
| Get parameters for SIR human model | get_config_humans_SIR |
| Get parameters for SIS human model | get_config_humans_SIS |
| Get parameters for generalized Ross-Macdonald mosquito model | get_config_mosquito_RM |
| Get parameters for null mosquito model | get_config_mosquito_trace |
| Get parameters for trace driven visitors | get_config_visitor_trace |
| Get extrinsic incubation period for Ross-Macdonald mosquito model | get_eip_mosquito_RM |
| Get feeding rate for Ross-Macdonald mosquito model | get_f_mosquito_RM |
| Get carrying capacity for Beverton-Holt aquatic mosquito model | get_K_aqua_BH |
| Get kappa for Ross-Macdonald mosquito model | get_kappa_mosquito_RM |
| Get daily emergence for Beverton-Holt aquatic mosquito model | get_lambda_aqua_trace |
| Get daily maturation probability for Beverton-Holt aquatic mosquito model | get_molt_aqua_BH |
| Get number of eggs laid per oviposition for Ross-Macdonald mosquito model | get_nu_mosquito_RM |
| Get daily survival probability for Ross-Macdonald mosquito model | get_p_mosquito_RM |
| Get mosquito dispersal matrix for Ross-Macdonald mosquito model | get_psi_mosquito_RM |
| Get human blood feeding fraction for Ross-Macdonald mosquito model | get_q_mosquito_RM |
| Get daily survival probability for Beverton-Holt aquatic mosquito model | get_surv_aqua_BH |
| Get maximum time of simulation from model object | get_tmax |
| Get current time of simulation from model object | get_tnow |
| Does a numeric object consist of only zeros and ones? | is_binary |
| Make a model object | make_MicroMoB |
| MicroMoB: Microsimulation for mosquito-borne pathogens | MicroMoB-package MicroMoB |
| Observe PfPR in human strata | observe_pfpr |
| Observe PfPR in human strata for SIP model | observe_pfpr.SIP |
| Observe PfPR in human strata for SIS model | observe_pfpr.SIS |
| Get output for aquatic (immature) mosquito populations | output_aqua |
| Get output for aquatic (immature) mosquito populations with Beverton-Holt dynamics | output_aqua.BH |
| Get output for aquatic (immature) mosquito populations with forced emergence | output_aqua.trace |
| Get output for mosquito populations | output_mosquitoes |
| Get output for Ross-Macdonald mosquito populations | output_mosquitoes.RM |
| Get output for null mosquito populations | output_mosquitoes.trace |
| Sample a stochastic matrix | sample_stochastic_matrix |
| Sample a stochastic vector | sample_stochastic_vector |
| Set extrinsic incubation period for Ross-Macdonald mosquito model | set_eip_mosquito_RM |
| Set feeding rate for Ross-Macdonald mosquito model | set_f_mosquito_RM |
| Set carrying capacity for Beverton-Holt aquatic mosquito model | set_K_aqua_BH |
| Set kappa for Ross-Macdonald mosquito model | set_kappa_mosquito_RM |
| Set daily emergence for trace (forced) aquatic mosquito model | set_lambda_aqua_trace |
| Set daily maturation probability for Beverton-Holt aquatic mosquito model | set_molt_aqua_BH |
| Set number of eggs laid per oviposition for Ross-Macdonald mosquito model | set_nu_mosquito_RM |
| Set daily survival probability for Ross-Macdonald mosquito model | set_p_mosquito_RM |
| Set mosquito dispersal matrix for Ross-Macdonald mosquito model | set_psi_mosquito_RM |
| Set human blood feeding fraction for Ross-Macdonald mosquito model | set_q_mosquito_RM |
| Set daily survival probability for Beverton-Holt aquatic mosquito model | set_surv_aqua_BH |
| Setup trace driven alternative blood hosts | setup_alternative_trace |
| Setup aquatic (immature) mosquito model with Beverton-Holt dynamics | setup_aqua_BH |
| Setup aquatic (immature) mosquito model with trace (forced) emergence | setup_aqua_trace |
| Setup humans with MOI (multiplicity of infection) pathogen model | setup_humans_MOI |
| Setup humans with SIP pathogen model | setup_humans_SIP |
| Setup humans with SIR infection model | setup_humans_SIR |
| Setup humans with SIS pathogen model | setup_humans_SIS |
| Setup blood feeding & oviposition (BQ) behavioral state mosquito model | setup_mosquito_BQ |
| Setup generalized Ross-Macdonald mosquito model | setup_mosquito_RM |
| Setup null mosquito model | setup_mosquito_trace |
| Setup trace driven visitors | setup_visitor_trace |
| Update aquatic (immature) mosquito populations | step_aqua |
| Update aquatic (immature) mosquito populations for Beverton-Holt dynamics | step_aqua.BH |
| Update aquatic (immature) mosquito populations for deterministic Beverton-Holt dynamics | step_aqua.BH_deterministic |
| Update aquatic (immature) mosquito populations for stochastic Beverton-Holt dynamics | step_aqua.BH_stochastic |
| Update aquatic (immature) mosquito populations for forced emergence | step_aqua.trace |
| Update human population | step_humans |
| Update MOI human model | step_humans.MOI |
| Update MOI human model (deterministic) | step_humans.MOI_deterministic |
| Update MOI human model (stochastic) | step_humans.MOI_stochastic |
| Update SIP human model | step_humans.SIP |
| Update SIP human model (deterministic) | step_humans.SIP_deterministic |
| Update SIP human model (stochastic) | step_humans.SIP_stochastic |
| Update SIR human model | step_humans.SIR |
| Update SIR human model (deterministic) | step_humans.SIR_deterministic |
| Update SIR human model (stochastic) | step_humans.SIR_stochastic |
| Update SIS human model | step_humans.SIS |
| Update SIS human model (deterministic) | step_humans.SIS_deterministic |
| Update SIS human model (stochastic) | step_humans.SIS_stochastic |
| Update mosquito population | step_mosquitoes |
| Update blood feeding & oviposition (BQ) behavioral state mosquitoes | step_mosquitoes.BQ |
| Update blood feeding & oviposition (BQ) behavioral state mosquitoes (deterministic) | step_mosquitoes.BQ_deterministic |
| Update blood feeding & oviposition (BQ) behavioral state mosquitoes (stochastic) | step_mosquitoes.BQ_stochastic |
| Update Ross-Macdonald mosquitoes | step_mosquitoes.RM |
| Update Ross-Macdonald mosquitoes (deterministic) | step_mosquitoes.RM_deterministic |
| Update Ross-Macdonald mosquitoes (stochastic) | step_mosquitoes.RM_stochastic |
| Update null mosquito population | step_mosquitoes.trace |
| Helper function for lumped population strata (counts) | strata_to_residency_counts |
| Helper function for lumped population strata (proportional assignment) | strata_to_residency_proportion |
| Input parameters that may vary by time and patch | time_patch_varying_parameter |
| Input parameters that may vary by time | time_varying_parameter |
