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)
batch_migration         Sample Batch Migration Events
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_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
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_lifeycle    Calculate Equilibrium for Lifecycle Model
                        (Logistic or Lotka-Volterra)
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_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
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
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_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_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_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)
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
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
