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