| 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 |
![[R logo]](../../../doc/html/Rlogo.svg)
![[Up]](../../../doc/html/left.jpg)
![[Top]](../../../doc/html/up.jpg)