Reference

Petri net & Hazards

Functions to construct the Petri net, and generate the hazard functions.

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_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_lifecycle_network()

Make Transitions (T) For a Network (Mosquitoes only)

spn_T_lifecycle_node()

Make Transitions (T) For a Node (Mosquitoes only)

spn_hazards()

Make Hazards (Lambda) For a MGDrivE2: Node and Network Simulations

Equilibrium & Parameters

Functions that are helpful to calculate equilibrium solutions as initial conditions or construct parameter sets for simulation.

calc_move_rate()

Calculate Outbound Movement Rate

movement_prob2rate()

Convert Stochastic Matrix to Rate Matrix

solve_muAqua()

Solve for Constant Aquatic Mortality

get_shape()

Calculate Erlang shape parameter

equilibrium_SEI_SEIR()

Calculate Equilibrium for Mosquito SEI - Human SEIR Model

equilibrium_SEI_SIS()

Calculate Equilibrium for Mosquito SEI - Human SIS Model

equilibrium_lifeycle()

Calculate Equilibrium for Lifecycle Model (Logistic or Lotka-Volterra)

batch_migration()

Sample Batch Migration Events

Simulation

These are the interfaces for sampling trajectories from a fully constructed Petri net model.

sim_trajectory_CSV()

Simulate Trajectory From a SPN Model

sim_trajectory_R()

Simulate Trajectory From a SPN Model

track_hinf()

Make tracking matrix for human infection events

Output Processing

These functions help users summarize output, either arrays returned to R or CSV files.

split_aggregate_CSV()

Split CSV output by Patch and Aggregate by Mate or Dwell-Stage

summarize_stats_CSV()

Summary Statistics for MGDrivE2

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_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