# Mosquito Gene Drive Explorer 2

## Documentation for package ‘MGDrivE2’ version 2.1.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

add_interventions | This set of functions modifies mosquito life history parameters in the presence of adult interventions - indoor residual spraying (IRS) and insecticide treated nets (ITN) This is based on the work of Le Menach et al (2007) and Griffin et al (2010). We vary three parameters in the presence of interventions: Egg laying rate (beta), Adult mortality (muF), Mosquito biting rate (av0)
base_aquatic_geno | Base Aquatic Function for Genotype Summary
base_aquatic_stage | Base Aquatic Function for Erlang-Stage Summary
base_erlang | Base Summary of Erlang Stages for Aquatic Life Stages
base_erlang_F | Base Summary of Erlang Stages for Adult Females
base_gen | Base Summary for Eggs, Larvae, Pupae, Susceptible Females, and Infectious Females
base_gen_FE | Base Summary for Latent Females
base_MQ | Base Summary Function
base_MUH | Base Summary for Males, Unmated Females, and Humans
base_summarize_humans | Base Function for Human Summary
base_sum_F | Base Summary of Infection (SEI) Stages for Adult Females
batch_migration | Sample Batch Migration Events
batch_migration_stage | Internal function to sample and set up data structure for batch migration
calc_move_rate | Calculate Outbound Movement Rate
convert_prevalence_to_eir | Generally, pathogen prevalence is a more accesible metric for users, but the Imperial equilibrium function requires an annual EIR. This function converts a given pathogen prevalence to an EIR
equilibrium_Imperial_decoupled | This function calculates the human and mosquito equilibrium values for the decoupled Imperial model. Currently this only works in one node.
equilibrium_Imperial_decoupled_human | This function calculates the human equilibrium values for the decoupled Imperial model. Requires the age structure of the population Currently this only works in one node.
equilibrium_lifeycle | Calculate Equilibrium for Lifecycle Model (Logistic or Lotka-Volterra)
equilibrium_SEI_decoupled_human | This function calculates the equilibrium values for the decoupled SIS human states. Currently this only works in one node.
equilibrium_SEI_decoupled_mosy | Calculate Equilibrium for Decoupled Mosquito SEI model. Human states will be handled separately.
equilibrium_SEI_Imperial | Calculate Equilibrium for Mosquito SEI - Human Imperial Model
equilibrium_SEI_SEIR | Calculate Equilibrium for Mosquito SEI - Human SEIR Model
equilibrium_SEI_SIS | Calculate Equilibrium for Mosquito SEI - Human SIS Model
get_shape | Calculate Erlang shape parameter
human_Imperial_ODE | ODE describing the age-structured Imperial model used in decoupled sampling, which will pass in values of I_V and return the human states for usein the mosquito portion of the model
imperial_model_param_list_create | Model Parameter List Creation
make_Q_Imperial | Rate Matrix (Q) for Adult Mosquito SEI Dynamics
make_Q_SEI | Rate Matrix (Q) for Adult Mosquito SEI Dynamics
movement_prob2rate | Convert Stochastic Matrix to Rate Matrix
mu_ts | Mosquito Death Rates, Comoros Islands
sim_trajectory_base_CSV | Simulate Trajectory From one SPN Model
sim_trajectory_base_CSV_decoupled | Simulate Trajectory From one SPN Model
sim_trajectory_base_R | Simulate Trajectory From one SPN Model
sim_trajectory_base_R_decoupled_Imperial | Simulate Trajectory From one SPN Model using Imperial Malaria model
sim_trajectory_base_R_decoupled_SIS | Simulate Trajectory From one SPN Model using Human SIS model
sim_trajectory_CSV | Simulate Trajectory From a SPN Model
sim_trajectory_CSV_decoupled | Simulate Trajectory From a SPN Model
sim_trajectory_R | Simulate Trajectory From a SPN Model
sim_trajectory_R_decoupled | Simulate Trajectory From a SPN Model
solve_muAqua | Solve for Constant Aquatic Mortality
split_aggregate_CSV | Split CSV output by Patch and Aggregate by Mate or Dwell-Stage
split_aggregate_CSV_decoupled | Split CSV output for decoupled sampling with Imperial malaria model
spn_hazards | Make Hazards (Lambda) For a MGDrivE2: Node and Network Simulations
spn_hazards_decoupled | Make Hazards (Lambda) For a MGDrivE2: Node and Network Simulations
spn_Post | Make Post Matrix For a Petri Net
spn_Pre | Make Pre Matrix For a Petri Net
spn_P_epiSEIR_network | Make Places (P) For a Network (SEI Mosquitoes - SEIR Humans)
spn_P_epiSEIR_node | Make Places (P) For a Node (SEI Mosquitoes - SEIR Humans)
spn_P_epiSIS_network | Make Places (P) For a Network (SEI Mosquitoes - SIS Humans)
spn_P_epiSIS_node | Make Places (P) For a Node (SEI Mosquitoes - SIS Humans)
spn_P_epi_decoupled_node | Make Places (P) For a Node (SEI Mosquitoes). Note in the v2 epi module, we only use the SPN framework for the mosquito component of the model. The human compoenent will be handled separately in the sampler, and will be formulated as an ODE. This function makes the set of places (P) for a SPN. It is used alone if our model is a single-node metapopulation for mosquito SEI and dynamics; This is used by both SIS and Imperial transmission models.
spn_P_lifecycle_network | Make Places (P) For a Network (Mosquitoes only)
spn_P_lifecycle_node | Make Places (P) For a Node (Mosquitoes only)
spn_S | Make stoichiometry Matrix For a Petri Net
spn_T_epiSEIR_network | Make Transitions (T) For a Network (SEI Mosquitoes - SEIR Humans)
spn_T_epiSEIR_node | Make Transitions (T) For a Node (SEI Mosquitoes - SEIR Humans)
spn_T_epiSIS_network | Make Transitions (T) For a Network (SEI Mosquitoes - SIS Humans)
spn_T_epiSIS_node | Make Transitions (T) For a Node (SEI Mosquitoes - SIS Humans)
spn_T_epi_decoupled_node | Make Transitions (T) For a Node (SEI Mosquitoes)
spn_T_lifecycle_network | Make Transitions (T) For a Network (Mosquitoes only)
spn_T_lifecycle_node | Make Transitions (T) For a Node (Mosquitoes only)
step_CLE | Make Chemical Langevin (CLE) Sampler for a SPN model
step_DM | Make Gillespie's Direct Method (DM) Sampler for a SPN model
step_ODE | Make Mean-field Approximation (ODE) Numerical Integrator for a SPN Model
step_ODE_decoupled | Make Mean-field Approximation (ODE) Numerical Integrator for a SPN Model for Decoupled Epi Dynamics
step_PTS | Make Poisson Time-Step (PTS) Sampler for a SPN Model
step_PTS_decoupled | Make Poisson Time-Step (PTS) Sampler for a SPN Model
summarize_eggs_geno | Summarize Eggs by Genotype
summarize_eggs_stage | Summarize Eggs by Erlang-Stage
summarize_females | Summarize Adult Females (One Node or Metapopulation Network, Lifecycle Model)
summarize_females_epi | Summarize Adult Females (One Node or Metapopulation Network, SEI Mosquitoes)
summarize_humans_epiImperial | Summarize Humans for Imperial Model
summarize_humans_epiSEIR | Summarize Humans (One Node or Metapopulation Network, SEI Mosquitoes - SEIR Humans)
summarize_humans_epiSIS | Summarize Humans (One Node or Metapopulation Network, SEI Mosquitoes - SIS Humans)
summarize_larvae_geno | Summarize Larvae by Genotype
summarize_larvae_stage | Summarize Larval by Erlang-Stage
summarize_males | Summarize Adult Males (One Node or Metapopulation Network)
summarize_pupae_geno | Summarize Pupal by Genotype
summarize_pupae_stage | Summarize Pupal by Erlang-Stage
summarize_stats_CSV | Summary Statistics for MGDrivE2
summarize_stats_CSV_decoupled | Summary Statistics for MGDrivE2 - Decoupled samples
track_hinf | Make tracking matrix for human infection events