R: Discrete Time Simulation of Mosquito-Borne Pathogen Transmission

# Discrete Time Simulation of Mosquito-Borne Pathogen Transmission

## Documentation for package ‘MicroMoB’ version 0.1.2

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

A C D G I M O S T

MicroMoB-package | MicroMoB: Microsimulation for mosquito-borne pathogens

## -- A --

api_config_global | Read global configuration options
approx_equal | Check if two numeric values are approximately equal

## -- C --

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_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_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_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_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_Wd | Compute available visitors (W_{delta})
compute_Wd.trace | Compute available visitors for trace model (W_{delta})
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})
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)

## -- D --

distribute | Distribute items into bins as evenly as possible
divmod | Division of integers
draw_multinom | Draw a multinomially distributed random vector

## -- G --

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_K_aqua_BH | Get carrying capacity for Beverton-Holt aquatic 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_psi_mosquito_RM | Get mosquito dispersal matrix for Ross-Macdonald mosquito model
get_p_mosquito_RM | Get daily survival probability 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

## -- I --

is_binary | Does a numeric object consist of only zeros and ones?

## -- M --

make_MicroMoB | Make a model object
MicroMoB | MicroMoB: Microsimulation for mosquito-borne pathogens

## -- O --

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

## -- S --

sample_stochastic_matrix | Sample a stochastic matrix
sample_stochastic_vector | Sample a stochastic vector
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
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_K_aqua_BH | Set carrying capacity for Beverton-Holt aquatic 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_psi_mosquito_RM | Set mosquito dispersal matrix for Ross-Macdonald mosquito model
set_p_mosquito_RM | Set daily survival probability 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
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)

## -- T --

time_patch_varying_parameter | Input parameters that may vary by time and patch
time_varying_parameter | Input parameters that may vary by time