| add_interventions | This set of functions modifies mosquito life history... |
| 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,... |
| base_gen_FE | Base Summary for Latent Females |
| base_MQ | Base Summary Function |
| base_MUH | Base Summary for Males, Unmated Females, and Humans |
| base_sum_F | Base Summary of Infection (SEI) Stages for Adult Females |
| base_summarize_humans | Base Function for Human Summary |
| batch_migration | Sample Batch Migration Events |
| batch_migration_stage | Internal function to sample and set up data structure for... |
| calc_move_rate | Calculate Outbound Movement Rate |
| convert_prevalence_to_eir | Generally, pathogen prevalence is a more accesible metric for... |
| equilibrium_Imperial_decoupled | This function calculates the human and mosquito equilibrium... |
| equilibrium_Imperial_decoupled_human | This function calculates the human equilibrium values for the... |
| equilibrium_lifeycle | Calculate Equilibrium for Lifecycle Model (Logistic or... |
| equilibrium_SEI_decoupled_human | This function calculates the equilibrium values for the... |
| equilibrium_SEI_decoupled_mosy | Calculate Equilibrium for Decoupled Mosquito SEI model. Human... |
| 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... |
| 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... |
| 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... |
| split_aggregate_CSV_decoupled | Split CSV output for decoupled sampling with Imperial malaria... |
| spn_hazards | Make Hazards (Lambda) For a MGDrivE2: Node and Network... |
| spn_hazards_decoupled | Make Hazards (Lambda) For a MGDrivE2: Node and Network... |
| spn_P_epi_decoupled_node | Make Places (P) For a Node (SEI Mosquitoes). Note in the v2... |
| 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_lifecycle_network | Make Places (P) For a Network (Mosquitoes only) |
| spn_P_lifecycle_node | Make Places (P) For a Node (Mosquitoes only) |
| spn_Post | Make Post Matrix For a Petri Net |
| spn_Pre | Make Pre Matrix For a Petri Net |
| spn_S | Make stoichiometry Matrix For a Petri Net |
| spn_T_epi_decoupled_node | Make Transitions (T) For a Node (SEI Mosquitoes) |
| spn_T_epiSEIR_network | Make Transitions (T) For a Network (SEI Mosquitoes - SEIR... |
| spn_T_epiSEIR_node | Make Transitions (T) For a Node (SEI Mosquitoes - SEIR... |
| spn_T_epiSIS_network | Make Transitions (T) For a Network (SEI Mosquitoes - SIS... |
| spn_T_epiSIS_node | Make Transitions (T) For a Node (SEI Mosquitoes - SIS Humans) |
| 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... |
| step_ODE_decoupled | Make Mean-field Approximation (ODE) Numerical Integrator for... |
| 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,... |
| summarize_females_epi | Summarize Adult Females (One Node or Metapopulation Network,... |
| summarize_humans_epiImperial | Summarize Humans for Imperial Model |
| summarize_humans_epiSEIR | Summarize Humans (One Node or Metapopulation Network, SEI... |
| summarize_humans_epiSIS | Summarize Humans (One Node or Metapopulation Network, SEI... |
| 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 |
