Data for μ_temperature_response. Species: AnophelesGambiae, LifeStage: Pupa. Source: Abiodun et al (2016).

Data for μ_temperature_response. Species: AedesAegypti, LifeStage: Male, Female. Source: El Moustaid et al (2019).

Data for μ_temperature_response. Species: AedesAegypti, LifeStage: Male, Female. Source: Rossi et al (2014).

struct AedesAegypti <: Species end

Data for Aedes Aegypti mosquito. Disease vector.

struct AedesAlbopictus <: Species end

Data for Aedes Albopictus mosquito. Disease vector.

struct AnophelesArabiensis <: Species end

Data for Anopheles Arabiensis mosquito. Disease vector.

struct AnophelesGambiae <: Species end

Data for Anopheles Gambiae mosquito. Disease vector.

mutable struct ConstantTemperature <: Temperature end

Data for simulation that features a single constant temperature in °C. Generated internally.

Arguments

• value::Float64: Temperature value in °C; re-used by model at every time step.

mutable struct Density{D <: DensityDependence}
    model::Type{D}
    param::Float64
end

Data for density dependence model.

Arguments

• model::Type{D}: User-selected density dependence formulation. Includes LogisticDensity, LinearDensity, and NoDensity.
• param::Float64: Calculated internally by init function.

mutable struct Drive{G <: Genotype}
    genotype::Type{G}
    likelihood_slice::Array{Float64,2}
    s::Float64
    τ::Array{Float64,2}
    ϕ::Float64
    ξ_m::Float64
    ξ_f::Float64
    ω::Float64
    β::Float64
    η::Float64
    wildtype::Int64
    modified::Int64
end

Data for individual genotypes.

Fields

• genotype::Type{G}: Single genotype.
• likelihood_slice::Array{Float64,2}: Offspring likelihoods for this genotype.
• s::Float64: Multiplicative fertility modifier.
• τ::Array{Float64,2}: Offspring viability.
• ϕ::Float64: Male to female emergence ratio.
• ξ_m::Float64: Male pupatory success.
• ξ_f::Float64: Female pupatory success.
• ω::Float64: Multiplicative adult mortality modifier.
• β::Float64: Female fecundity.
• η::Float64: Male mating fitness.
• wildtype::Int64: Boolean demarcates homozygous recessive.
• modified::Int64: Boolean demarcates homozygous modified.

struct Egg <: LifeStage end

Egg life stage. Applicable to holometabolous (complete) or hemimetabolous (partial) metamorphosing insect species.

Data for q_temperature_response. Species: AnophelesGambiae, LifeStage: Egg. Source: Abiodun et al (2016).

Data for q_temperature_response. Species: AedesAegypti, LifeStage: Egg. Source: El Moustaid et al (2019).

mutable struct EggDurationRossi <: TemperatureResponse
    a::Float64
    b::Float64
    c::Float64
    d::Float64
    e::Float64
    f::Float64
end

Data for q_temperature_response. Species: AedesAegypti, LifeStage:, egg stage. Source: Rossi et al (2014).

Data for μ_temperature_response. Species: AnophelesGambiae, LifeStage: Egg. Source: Abiodun et al (2016).

Data for μ_temperature_response. Species: AedesAegypti, LifeStage: Egg. Source: El Moustaid et al (2019).

mutable struct EggMortalityRossi <: TemperatureResponse
    a::Float64
    b::Float64
end

Data for μ_temperature_response. Species: AedesAegypti, LifeStage: Egg. Source: Rossi et al (2014).

Arguments

• a::Float64: Death rate at low temperatures, validation range: (0, nothing)
• b::Float64: Influence factor of temperature, validation range: (0, nothing)

struct ExogenousInputs
    intervention::Dict{Symbol, Dict}
    temperature::Dict{Symbol, Float64}
    function ExogenousInputs(;
        intervention = Dict{Symbol, Dict}(),
        temperature = Dict{Symbol, Float64}())
        new(intervention,
        temperature)
    end
end

Data for perturbations to the simulated system, including (1) biological control interventions and (2) externally defined temperature series/shocks.

ExogenousInputs(network::Network)

Return allocated space for exogenous inputs to a Network.

ExogenousInputs(node::Node)

Return allocated space for exogenous inputs to Node.

struct Female <: LifeStage end

Female life stage. Applicable to holometabolous (complete) or hemimetabolous (partial) metamorphosing insect species.

mutable struct Genetics

    all_genotypes::Array{Drive{<:Genotype}}
    likelihood::Array{Float64, 3}
    S::Vector{Float64}
    Τ::Array{Float64,3}
    Φ::Vector{Float64}
    Ξ_m::Vector{Float64}
    Ξ_f::Vector{Float64}
    Ω::Vector{Float64}
    Β::Vector{Float64}
    Η::Vector{Float64}
    all_wildtypes::Vector{Int64}
    all_modified::Vector{Int64}

        function Genetics(all_genotypes::Array{Drive{<:Genotype}})

            gN = length(all_genotypes)
            likelihood = Array{Float64, 3}(undef, gN, gN, gN)
            S = Vector{Float64}(undef, gN)
            Τ = Array{Float64,3}(undef, gN, gN, gN)
            Φ = Vector{Float64}(undef, gN)
            Ξ_m = Vector{Float64}(undef, gN)
            Ξ_f = Vector{Float64}(undef, gN)
            Ω = Vector{Float64}(undef, gN)
            Β = Vector{Float64}(undef, gN)
            Η = Vector{Float64}(undef, gN)
            all_wildtypes = Vector{Int64}(undef, gN)
            all_modified = Vector{Int64}(undef, gN)

            for (index, g) in enumerate(all_genotypes)
                likelihood[:,:,index] = g.likelihood_slice
                S[index] = g.s
                Τ[:,:,index] = g.τ
                Φ[index] = g.ϕ
                Ξ_m[index] = g.ξ_m
                Ξ_f[index] = g.ξ_f
                Ω[index] = g.ω
                Β[index] = g.β
                Η[index] = g.η
                all_wildtypes[index] = g.wildtype
                all_modified[index] = g.modified
            end

            new(all_genotypes, likelihood, S, Τ, Φ, Ξ_m, Ξ_f, Ω, Β, Η,
            all_wildtypes, all_modified)

        end

end

Data for all genotypes in a population.

Fields

• all_genotypes::Array{Drive{<:Genotype}}: All genotypes in a population.
• likelihood::Array{Float64, 3}: Offspring likelihoods per genotype.
• S::Vector{Float64}: Multiplicative fertility modifier genedata_splitdriveper genotype, applied to oviposition.
• Τ::Array{Float64,3}: Offspring viability per genotype, applied to oviposition.
• Φ::Vector{Float64}: Male to female emergence ratio per genotype.
• Ξ_m::Vector{Float64}: Male pupatory success per genotype.
• Ξ_f::Vector{Float64}: Female pupatory success per genotype.
• Ω::Vector{Float64}: Multiplicative adult mortality modifier per genotype.
• Β::Vector{Float64}: Female fecundity per genotype (count of eggs laid).
• Η::Vector{Float64}: Male mating fitness per genotype.
• all_wildtypes::Vector{Int64}: Collect homozygous wildtype booleans.
• all_modified::Vector{Int64}: Collect homozygous modified booleans.

struct Larva <: LifeStage end

Larva life stage. Also referred to as "nymph" life stage. Applicable to holometabolous (complete) or hemimetabolous (partial) metamorphosing insect species.

Data for q_temperature_response. Species: AnophelesGambiae, LifeStage: Larva. Source: Abiodun et al (2016).

Data for q_temperature_response. Species: AedesAegypti, LifeStage: Larva. Source: El Moustaid et al (2019).

Data for q_temperature_response. Species: AedesAegypti, LifeStage: Larva. Source: Rossi et al (2014).

Data for μ_temperature_response. Species: AnophelesGambiae, LifeStage: Larva. Source: Abiodun et al (2016).

Data for μ_temperature_response. Species: AedesAegypti, LifeStage: Larva. Source: El Moustaid et al (2019).

Data for μ_temperature_response. Species: AedesAegypti, LifeStage: Larva. Source: Rossi et al (2014).

struct LinearDensity <: DensityDependence end

Density dependence model of type LinearDensity.

struct LogisticDensity <: DensityDependence end

Density dependence model of type LogisticDensity.

struct Male <: LifeStage end

Male life stage. Applicable to holometabolous (complete) or hemimetabolous (partial) metamorphosing insect species.

struct Network
    name::Symbol
    nodes::DataStructures.OrderedDict{Symbol,Node}
    migration::DataStructures.OrderedDict{DataType},Array{Matrix{Float64},2}}
    locations_key_map
end

Data for multiple interconnected spatial nodes.

Arguments

• name::Symbol: Name of network, usually location-relevant.
• nodes::DataStructures.OrderedDict{Symbol,Node}: Dictionary of data for nodes included in network (metapopulation).
• migration::DataStructures.OrderedDict{DataType}, Array{Matrix{Float64},2}}: Data defining species, genotype, and stage-specific transition rates. Entries default to zero.
• locations_key_map: Mapping of node location information. Used to assign transition rates.

Network(name::Symbol, nodes::DataStructures.OrderedDict{Symbol,Node}...)

Return Network instance containing specified metapopulation information.

struct NoDensity <: DensityDependence end

Density dependence model of type NoDensity.

mutable struct NoResponse <: TemperatureResponse
    baseline_value::Float64
end

Data for model without temperature response.

Arguments:

• baseline_value::Float64: Literature-sourced (rather than dynamically calculated) vital rate parameter.

mutable struct Node
    name::Symbol
    organisms::DataStructures.OrderedDict{Type{<:Species}, Organism}
    temperature::Temperature
    location::Tuple{Float64,Float64}
end

Data for a single spatial node.

Arguments

• name::Symbol: Name of node, usually location-relevant.
• organisms::DataStructures.OrderedDict{Type{<:Species}, Organism}: Dictionary containing data for all species inhabiting node.
• temperature::Temperature: Climatic specification for temperature.
• location::Tuple{Float64,Float64}: Geographic location denoted by coordinates.

mutable struct Organism{S <: Species}
    gene_data::Genetics
    all_stages::DataStructures.OrderedDict{Type{<:LifeStage}, Stage}
end

Generic data container for species-specific genetic and life stage information.

Arguments

• gene_data::Genetics: Species and modification-specific genetic data.
• all_stages::DataStructures.OrderedDict{Type{<:LifeStage}, Stage}: Dictionary of wildtype species-specific life stage data.

mutable struct ProportionalRelease <: Intervention
    node::Symbol
    organism::Type{<:Species}
    stage::Type{<:LifeStage}
    gene_index::Int64
    times::Vector{Float64}
    proportion::Float64
    callbacks::Vector
    adults_counting::String
end

Data for biological control interventions predicated on releasing modified organisms.

Arguments

• node::Symbol: Node where releases occur.
• organism::Type{<:Species}: Species of organism being released.
• stage::Type{<:LifeStage}: LifeStage of organism being released.
• gene_index::Int64: Genotype being released to implement the intervention.
• times::Vector{Float64}: Release time points.
• proportion::Float64: Proportion of modified organisms released during each time period.
• callbacks::Vector
• adults_to_count::String: The LifeStage of the standing population against which to measure proportional release size. Choices include Male, Female, or All.

ProportionalRelease(node::Node, organism, stage::Type{T}, gene_index, times::Vector, proportion::Float64, adult_counting::String) where T <: LifeStage

Return ProportionalRelease object specifying details of biological control intervention where release size is predicated on real-time wild population level.

struct Pupa <: LifeStage end

Pupa life stage. Applicable to holometabolous (complete) metamorphosing insect species.

Data for q_temperature_response. Species: AnophelesGambiae, LifeStage: Pupa. Source: Abiodun et al (2016).

Data for q_temperature_response. Species: AedesAegypti, LifeStage: Pupa. Source: El Moustaid et al (2019).

Data for q_temperature_response. Species: AedesAegypti, LifeStage: Pupa. Source: Rossi et al (2014) and Poletti et al (2011) Table 1.

Data for μ_temperature_response. Species: AnophelesGambiae, LifeStage: Pupa. Source: Abiodun et al (2016).

Data for μ_temperature_response. Species: AedesAegypti, LifeStage: Pupa. Source: El Moustaid et al (2019).

Data for μ_temperature_response. Species: AedesAegypti, LifeStage: Pupa. Source: Rossi et al (2014).

mutable struct Release <: Intervention
    node::Symbol
    organism::Type{<:Species}
    stage::Type{<:LifeStage}
    gene_index::Int64
    times::Vector{Float64}
    values::Vector{Float64}
    callbacks::Vector
end

Data for biological control interventions predicated on releasing modified organisms. Applicable to both suppression and replacement techniques.

Arguments

• node::Symbol: Node where releases occur.
• organism::Type{<:Species}: Species of organism being released.
• stage::Type{<:LifeStage}: Life stage of organism being released.
• gene_index::Int64: Genotype being released to implement the intervention.
• times::Vector{Float64}: Release time points.
• values::Union{Float64, Vector{Float64}}: Number of modified organisms released during each time period. Variably sized releases permitted.
• callbacks::Vector

Release(node::Node, organism, stage, gene, times::Vector, fixed_release::Float64)

Return Release object specifying details of biological control intervention where release size is fixed over time.

Release(node::Node, organism, stage::Type{T}, gene, times::Vector, variable_release::Vector{Float64}) where T <: LifeStage

Return Release object specifying details of biological control intervention where release size is variable over time.

mutable struct ReleaseStrategy
    release_this_gene_index::Union{Nothing, Int64}=nothing
    release_this_life_stage=nothing
    release_location_force::Union{Nothing, Bool}=nothing
    release_start_time::Union{Nothing,Int64}=nothing
    release_end_time::Union{Nothing,Int64}=nothing
    release_time_interval::Int64=1
    release_size_min_per_timestep::Union{Int64, Float64}=0.0
    release_size_max_per_timestep::Union{Int64,Float64}=9e9
    release_max_over_timehorizon::Union{Int64,Float64}=9e9

end

Data defining the operational constraints for each organism.

Arguments

• release_this_gene_index: Gene index to be released. Generally defined by get_homozygous_modified.
• release_this_life_stage: Lifestage to be released. Varies according to genetic technology.
• release_location_force: Specify locations where releases are obligatory; only applicable when decision model is being run as an MINLP.
• release_start_time: Timestep (day) that releases are permitted to start.
• release_end_time: Timestep (day) that releases are required to end.
• release_time_interval: Minimum timestep interval (in days) permitted for releases.
• release_size_min_per_timestep: Minimum number of organisms that may be released on a single day.
• release_size_max_per_timestep: Maximum number of organisms that may be released on a single day.
• release_max_over_timehorizon: Maximum number of organisms that may be released over the problem horizon.

mutable struct ScenarioTemperature <: Temperature end

Data for simulation that uses ensembles of temperature time series in °C.

Arguments

• data::Matrix{Float64}: Array of ensemble members, each column of which is a time series of temperature values in °C.
• probability::Vector{Float64}: Vector of probabilities with which given scenarios are expected to occur (one probability applicable per ensemble member).
• selected_scenario::Int: Index to run dynamic model over selected scenarios; Int argument required. For decision model, use nothing.

mutable struct SinusoidalTemperature <: Temperature
    a::Float64
    b::Int64
    c::Int64
    d::Float64
end

Data for simulation that features sinusoidal temperature fluctuation in °C. Uses cosine implementation applicable to the Southern Hemisphere. Generated internally.

Arguments

• a::Float64: Amplitude.
• b::Float64: Periodicity coefficient.
• c::Float64: Time period (days).
• d::Float64: Mean.

mutable struct Stage{L <: LifeStage}
    μ_temperature_response::TemperatureResponse
    q_temperature_response::TemperatureResponse
    n::Union{Nothing, Int64}
    density::Density{<: DensityDependence}
    dependency::Union{Nothing, Type{<:LifeStage}}
    N0::Int64
end

Data for life stages. Applies to any organism represented by stage-structured population equations.

Arguments

• μ_temperature_response::TemperatureResponse: Mortality rate. Responsive to temperature.
• q_temperature_response::TemperatureResponse: Developmental rate. 1/total time (days or portion thereof) spent in stage. Responsive to temperature.
• n::Union{Nothing, Int64}: Number of bins allocated to stage (parameter, Erlang distribution).
• density::Density: Specify density dependence model.
• dependency::Union{Nothing, Type{<:LifeStage}}: Organism internal reference, do not modify.
• N0::Int64: Initial stage-specific population count per node. Specify "0" for all stages except Female life stage.

Stage{Female}(μ::Float64, n::Int64, density, dependency, N0::Int64)

Return Female life stage populated with input data. Not dynamically responsive to temperature. Applicable to holometabolous (complete) or hemimetabolous (partial) metamorphosing insect species.

Stage{Female}(μ::TemperatureResponse, n::Int64, density, dependency, N0::Int64)

Return Female life stage populated with input data. Dynamically responsive to temperature. Applicable to holometabolous (complete) or hemimetabolous (partial) metamorphosing insect species.

Stage{L}(μ::Float64, n::Int64, density, dependency, N0::Int64) where {L <: LifeStage}

Return juvenile life stage populated with input data. Applicable to holometabolous (complete) or hemimetabolous (partial) metamorphosing insect species.

Stage{Male}(μ::Float64, n::Int64, density, dependency, N0::Int64)

Return Male life stage populated with input data. Not dynamically responsive to temperature. Applicable to holometabolous (complete) or hemimetabolous (partial) metamorphosing insect species.

Stage{Male}(μ::TemperatureResponse, n::Int64, density, dependency, N0::Int64)

Return Male life stage populated with input data. Dynamically responsive to temperature. Applicable to holometabolous (complete) or hemimetabolous (partial) metamorphosing insect species.

mutable struct TemperatureSeriesData <: ExogenousChange
    node::Symbol
    times::Vector{Float64}
    values::Vector{Float64}
    set::diffeq.CallbackSet
end

Data for time series of temperature.

Arguments

• node::Symbol: Node where temperature is realized.
• times::Vector{Float64}: Time step (day) of realized temperature value.
• values::Vector{Float64}: Temperature in °C.
• set::diffeq.CallbackSet

mutable struct TemperatureShockData <: ExogenousChange
    node::Symbol
    times::Vector{Tuple{Float64, Float64}}
    values::Union{Float64, Vector{Float64}}
    set::diffeq.CallbackSet
end

Data for temperature shocks.

Arguments

• node::Symbol: Node where temperature shock occurs.
• times::Vector{Tuple{Float64,Float64}}: Vector of tuples defining shock start/stop time points. Multiple discrete shock periods may be included.
• values::Union{Float64, Vector{Float64}}: Single fixed temperature value in °C or vector of variable temperature values in °C added to the baseline temperature during the specified time period. Multiple discrete temperature changes may be included; values may be positive or negative.
• set::diffeq.CallbackSet

function TemperatureShockData(node::Node, times::Vector{Tuple{Float64,Float64}}, fixed_shock::Float64)

Return TemperatureShockData instance specifying data for fixed (all the same) shock values.

TemperatureShockData(node::Node, times::Vector{Tuple{Float64,Float64}}, variable_shock::Vector{Float64})

Return TemperatureShockData instance specifying data for variable shock values.

mutable struct TimeSeriesTemperature <: Temperature end

Data for simulation that uses temperature time series in °C.

Arguments

• value::Float64: Time series of temperature values in °C.
• probability::Float64: Probability with which timeseries expected to be observed.
• selected_scenario::Int

NodeStrategy(node_number, strategy_vector::Vector)

Return dictionary containing constraint data (ReleaseStrategy) per organism for each node.

assign_migration!(network::Network, migration_data::Dict, species::Type{<:Species})

Return Network instance with migration field populated by user-specified transition rates.

Note to user:

• Input data must be formatted as a nested dictionary. First level denotes relevant life stage and gene, second level includes to/from nodes and transition rate.
• Stage and gene combinations not specified by input data retain a default transition rate of zero.

compute_density(data::Density{LinearDensity}, stage)

Return the effect of LinearDensity on life stage instance. Calculated each time step.

compute_density(data::Density{LogisticDensity}, stage)

Return the effect of LogisticDensity on life stage instance. Calculated each time step.

compute_density(data::Density{NoDensity}, stage)

Return the effect of NoDensity on life stage instance. Calculated each time step.

count_genotypes(genetics::Genetics)

Return the total count of genotypes in the Genetics object.

count_genotypes(network::Network, node::Symbol, species::Type{<:Species})

Return the total count of genotypes from Genetics for Species in Node of Network.

count_genotypes(node::Node, species::Type{<:Species})

Return the total count of genotypes from Genetics for Species in Node.

count_nodes(network::Network)

Return a count of the nodes contained in the Network object.

count_nodes(node::Node)

Return 1 (the count of the nodes contained in the Node object).

count_organisms(network::Network, node::Symbol)

Count the species populating the specified Node of Network.

count_organisms(node::Node)

Count the species populating Node.

count_substages(network::Network, node::Symbol, species::Type{<:Species})

Return count of the total substages for Species in the specified Node of Network.

count_substages(node::Node, species::Type{<:Species}, stage::Type{<:LifeStage})

Return count of the substages in LifeStage for Species in Node.

count_substages(node::Node, species::Type{<:Species}, stage::Type{Female})

Return count of the substages for Species in Node. Specific to the Female lifestage.

count_substages(node::Node, species::Type{<:Species})

Return count of the total substages for Species in Node.

count_temperature_scenarios(temperature_model::ScenarioTemperature)

Return the total count of temperature scenarios in ScenarioTemperature or TimeSeriesTemperature object.

create_decision_model(network::Network, tspan; node_strategy::DataStructures.OrderedDict, species::Type{<:Species}=AedesAegypti,do_binary::Bool=false, optimizer=nothing)

Build mathematical program. Problem created as an NLP (dobinary=false) or MINLP (dobinary=true).

Arguments

• network: Data for one or more interconnected spatial nodes.
• tspan: Time horizon of the problem, defined in days.
• node_strategy: Operational constraints specific to organism types within each node.
• node_species: Species present in the node, defined as a vector.
• do_binary: Boolean indicating whether the problem is formulated as a MINLP (true) or NLP (false); defaults to false.
• optimizer: Optimization solver to be used.
• slack_small: Boolean flag to enable small slack variables within selected constraints. These introduce minor constraint relaxations with corresponding penalties in the objective function. Defaults to false.
• slack_large: Boolean flag to enable large slack variables for constraints where greater flexibility may be required to preserve model feasibility. Defaults to false.

create_decision_model(node::Node, tspan; node_strategy::DataStructures.OrderedDict, species::Type{<:Species}=AedesAegypti,do_binary::Bool=false, optimizer=nothing)

Build mathematical program. Problem created as an NLP (dobinary=false) or MINLP (dobinary=true). NB: Node is recreated as a Network object internally; this does not change the problem but is relevant for data exploration as it adds one index layer to the formatted results.

dens_lin()

Return linear density dependence.

dens_log()

Return logarithmic density dependence.

dens_none()

Return no density dependence.

format_decision_model_results(sol)

Return dictionary containing optimization model results. Indexed per node, organism, life stage, and genotype.

format_dynamic_model_results(network::Network, sol)

Return dictionary containing ODE model results. Indexed per node, organism, life stage, and genotype.

format_dynamic_model_results(node::Node, sol)

Return dictionary containing ODE model results. Indexed per organism, life stage, and genotype.

genetics_mcr()

Return Mutagenic Chain Reaction (MCR) inheritance.

genetics_mendelian()

Return Mendelian inheritance.

genetics_ridl()

Return Release of Insects carrying a Dominant Lethal gene (RIDL) inheritance.

genetics_wolbachia()

Return Wolbachia inheritance.

get_density(node::Node, species::Type{<:Species}, life_stage::Type{<:LifeStage})

Return the density dependence model and parameterization for LifeStage of Species in Node.

get_duration(node::Node, species::Type{<:Species}, life_stage::Type{<:LifeStage})

Return the temperature-sensitive duration (q_temperature_response) for the LifeStage of Species in Node.

    function get_exogenous_intervention(inputs::ExogenousInputs, node::Node, organism, stage, gene)

Returns biological control intervention relevant to specified `Node`, `Organism`, `LifeStage`, and `Genotype`.

get_exogenous_intervention(inputs::ExogenousInputs, node::Node, organism, stage::Type{Female}, gene, female_index)

Return biological control intervention relevant to Female.

get_exogenous_temperature(inputs::ExogenousInputs, node)

Return temperature relevant to Node.

get_genetics(network::Network, node::Symbol, species::Type{<:Species})

Return Genetics data for Species in Node of Network.

get_genetics(node::Node, species::Type{<:Species})

Return Genetics data for Species in Node.

get_genotypes(node::Node, species::Type{<:Species})

Return genotype data from Genetics for Species in Node.

get_homozygous_modified(network::Network, node::Node, species::Type{<:Species})

Return the index of the homozygous modified genotype in Genetics for Species in Node of Network.

get_homozygous_modified(node::Node, species::Type{<:Species})

Return the index of the homozygous modified genotype in Genetics for Species in Node.

get_initial_temperature(node::Node)

Return entry for the first index of values in Temperature of Node.

get_lifestage(node::Node, species::Type{<:Species}, life_stage::Type{<:LifeStage})

Return data for specified LifeStage of Species in Node.

get_lifestages(node::Node, species::Type{<:Species})

Return all data for all LifeStages of Species in Node.

get_location(network::Network)

Return the coordinates of Network.

get_location(node::Node)

Return the coordinates of Node.

get_migration(network::Network, species::Type{<:Species})

Return the migration characterizing each genotype and Lifestage for Species in Network.

get_mortality(node::Node, species::Type{<:Species}, life_stage::Type{<:LifeStage})

Return the temperature-sensitive mortality (μ_temperature_response) for the LifeStage of Species in Node.

get_name(network::Network)

Return the name (symbol) of the Network object.

get_name(node::Node)

Return the name (symbol) of the Node object.

get_names(network::Network)

Return the names (symbols) of the nodes within the Network object.

get_nodes(network::Network)

Return the Node object(s) contained in the Network object.

get_organisms(network::Network, node::Symbol)

Return vector of species populating the specified Node of Network.

get_organisms(node::Node)

Return vector of species populating Node.

get_previous_lifestage(node::Node, species::Type{<:Species}, ::Stage{T}) where T <: LifeStage

Show LifeStage dependency: return data for the LifeStage previous to the specified LifeStage of Species in Node.

get_probability(temperature_model::ScenarioTemperature)

Return the probability with which each temperature scenario occurs from ScenarioTemperature or TimeSeriesTemperature object.

get_release_data(optimized_schedule::Vector{Float64})

Return re-formatted schedule of optimal release times and values produced by decision model, for simplified application in dynamic model.

get_temperature(node::Node)

Return Temperature for Node. Object contains type and values.

get_temperature_response(ctemp::Float64, response::AdultMortalityAbiodun, ::Float64)

Return q_temperature_response. Species: AnophelesGambiae, LifeStage: Male, Female. Source: Abiodun et al (2016).

get_temperature_response(ctemp::Float64, response::AdultMortalityMoustaid, ::Float64)

Return μ_temperature_response. Species: AedesAegypti, LifeStage: Male, Female. Source: El Moustaid et al (2019).

get_temperature_response(ctemp::Float64, response::AdultMortalityRossi, ::Float64)

Return μ_temperature_response. Species: AedesAegypti, LifeStage: Male, Female. Source: Rossi et al (2014).

get_temperature_response(ctemp::Float64, response::EggDurationAbiodun, ::Float64)

Return q_temperature_response. Species: AnophelesGambiae, LifeStage: Egg. Source: Abiodun et al (2016).

get_temperature_response(ctemp::Float64, response::EggDurationMoustaid, ::Float64)

Return q_temperature_response. Species: AedesAegypti, LifeStage: Egg. Source: El Moustaid et al (2019).

get_temperature_response(ctemp::Float64, response::EggDurationRossi, ::Float64)

Return q_temperature_response. Species: AedesAegypti, LifeStage: Egg. Source: Rossi et al (2014).

get_temperature_response(ctemp::Float64, response::EggMortalityAbiodun, ::Float64)

Return q_temperature_response. Species: AnophelesGambiae, LifeStage: Egg. Source: Abiodun et al (2016).

get_temperature_response(ctemp::Float64, response::EggMortalityMoustaid, duration::Float64)

Return μ_temperature_response. Species: AedesAegypti, LifeStage: Egg. Source: El Moustaid et al (2019).

get_temperature_response(ctemp::Float64, response::EggMortalityRossi, ::Float64)

Return μ_temperature_response. Species: AedesAegypti, LifeStage: Egg. Source: Rossi et al (2014).

get_temperature_response(ctemp::Float64, response::LarvaDurationAbiodun, ::Float64)

Return q_temperature_response. Species: AnophelesGambiae, LifeStage: Larva. Source: Abiodun et al (2016).

get_temperature_response(ctemp::Float64, response::LarvaDurationMoustaid, ::Float64)

Return q_temperature_response. Species: AedesAegypti, LifeStage: Larva. Source: El Moustaid et al (2019).

get_temperature_response(ctemp::Float64, response::LarvaDurationRossi, ::Float64)

Return q_temperature_response. Species: AedesAegypti, LifeStage: Larva. Source: Rossi et al (2014).

get_temperature_response(ctemp::Float64, response::LarvaMortalityAbiodun, ::Float64)

Return q_temperature_response. Species: AnophelesGambiae, LifeStage: Larva. Source: Abiodun et al (2016).

get_temperature_response(ctemp::Float64, response::LarvaMortalityMoustaid, duration::Float64)

Return μ_temperature_response. Species: AedesAegypti, LifeStage: Larva. Source: El Moustaid et al (2019).

get_temperature_response(ctemp::Float64, response::LarvaMortalityRossi, ::Float64)

Return μ_temperature_response. Species: AedesAegypti, LifeStage:, larval stage. Source: Rossi et al (2014).

get_temperature_response(::Float64, response::NoResponse, ::Float64) = response.baseline_value

Return NoResponse data (model without temperature response).

get_temperature_response(ctemp::Float64, response::PupaDurationAbiodun, ::Float64)

Return q_temperature_response. Species: AnophelesGambiae, LifeStage: Pupa. Source: Abiodun et al (2016).

get_temperature_response(ctemp::Float64, response::PupaDurationMoustaid, ::Float64)

Return q_temperature_response. Species: AedesAegypti, LifeStage: Pupa. Source: El Moustaid et al (2019).

get_temperature_response(ctemp::Float64, response::PupaDurationRossi, ::Float64)

Return q_temperature_response. Species: AedesAegypti, LifeStage: Pupa. Source: Rossi et al (2014) and Poletti et al (2011) Table 1.

get_temperature_response(ctemp::Float64, response::PupaMortalityAbiodun, ::Float64)

Return q_temperature_response. Species: AnophelesGambiae, LifeStage: Pupa. Source: Abiodun et al (2016).

get_temperature_response(ctemp::Float64, response::PupaMortalityMoustaid, duration::Float64)

Return μ_temperature_response. Species: AedesAegypti, LifeStage: Pupa. Source: El Moustaid et al (2019).

get_temperature_response(ctemp::Float64, response::PupaMortalityRossi, ::Float64)

Return μ_temperature_response. Species: AedesAegypti, LifeStage: Pupa. Source: Rossi et al (2014).

get_temperature_response(ctemp::Float64, response::TemperatureResponse)

Return TemperatureResponse data (model with temperature response).

get_temperature_scenarios(temperature_model::ScenarioTemperature)

Return the values of all temperature scenarios in ScenarioTemperature or TimeSeriesTemperature object.

get_temperature_value(temperature_model::ConstantTemperature, temp_value_from_inputs::Float64, t)

Return value of temperature in °C for specifed time step. Accounts for perturbations to baseline temperature model where applicable.

get_temperature_value(temperature_model::ScenarioTemperature, temp_value_from_inputs::Float64, t)

Return value of temperature in °C for selected scenario and specifed time step. Perturbations to baseline temperature, where applicable, should be directly added to time series prior to running model.

get_temperature_value(temperature_model::SinusoidalTemperature, temp_value_from_inputs::Float64, t)

Return value of temperature in °C for specifed time step. Accounts for perturbations to baseline temperature model where applicable.

get_temperature_value(temperature_model::TimeSeriesTemperature, temp_value_from_inputs::Float64, t)

Return value of temperature in °C for specifed time step. Perturbations to baseline temperature, where applicable, should be directly added to time series prior to running model.

get_wildtype(network::Network, node::Node, species::Type{<:Species})

Return the index of the wildtype genotype in Genetics for Species in Node of Network.

get_wildtype(node::Node, species::Type{<:Species})

Return the index of the wildtype genotype in Genetics for Species in Node.

make_organisms(species::Type{<:Species},genetics::Genetics,stages::DataStructures.OrderedDict)

Return Organism object.

make_organisms(species::Vector,genetics::Vector,stages::Vector)

Return Organism object.

perturb_temperature_timeseries(current_temperature::TimeSeriesTemperature, perturbation)

Alter daily values across entire temperature timeseries by the size of perturbation input. Perturbation may be positive or negative.

plot_decision_mcr_females(sol)

Return visualization of adult female population dynamics across all genotypes.

plot_decision_mendelian_females(sol)

Return visualization of adult female population dynamics across all genotypes.

plot_decision_ridl_females(sol)

Return visualization of adult female population dynamics across all genotypes.

plot_decision_wolbachia_females(sol)

Return visualization of adult female population dynamics across all genotypes.

plot_dynamic_mcr_females(node::Node, sol)

Return visualization of adult female population dynamics across all genotypes.

plot_dynamic_mendelian_females(node::Node, sol)

Return visualization of adult female population dynamics across all genotypes.

plot_dynamic_ridl_females(node::Node, sol)

Return visualization of adult female population dynamics across all genotypes.

plot_dynamic_wolbachia_females(node::Node, sol)

Return visualization of adult female population dynamics across all genotypes.

population_model_network(du, u, (network, inputs), t)

Solve network implementation of dynamic population model.

population_model_node(du, u, (network, inputs), t)

Solve node implementation of dynamic population model.

set_scenario!(data::ScenarioTemperature, selected_scenario::Int)

Update the selected_scenario of Temperature for ScenarioTemperature in Node.

set_scenario!(data::ScenarioTemperature, selected_scenario::Int)

Update the selected_scenario of Temperature for ScenarioTemperature.

solve_decision_model(model::JuMP.Model, objective_function::Nothing=nothing; kwargs...)

Solve mathematical program using default objective function @objective(model, Min, 0). This permits comparison to dynamic population model output.

solve_dynamic_model(network::Network, algorithm, tspan)

Return ODE model solution for network problem with no releases.

solve_dynamic_model(network::Network, releases::Union{Vector{Release}, Vector{ProportionalRelease}}, algorithm, tspan)

Return ODE model solution for network problem with releases.

solve_dynamic_model(network::Network, releases::Union{Vector{Release},Vector{ProportionalRelease}}, shocks::Vector{TemperatureShockData}, algorithm, tspan)

Return ODE model solution for network problem with releases and temperature shocks.

solve_dynamic_model(network::Network, shocks::Vector{TemperatureShockData}, algorithm, tspan)

Return ODE model solution for network problem with temperature shocks.

solve_dynamic_model(node::Node, algorithm, tspan)

Return ODE model solution for single node problem with no releases.

solve_dynamic_model(node::Node, shocks::TemperatureShockData, algorithm, tspan)

Return ODE model solution for single node problem with temperature shocks.

solve_dynamic_model(node::Node, releases::Union{Vector{Release},Vector{ProportionalRelease}}, algorithm, tspan)

Return ODE model solution for single node problem with releases.

solve_dynamic_model(node::Node, releases::Union{Vector{Release},Vector{ProportionalRelease}}, shocks::TemperatureShockData, algorithm, tspan)

Return ODE model solution for single node problem with releases and temperature shocks.

solve_scenarios_dynamic_model(network::Network, algorithm, tspan, scenarios_of_interest::Vector{Int})

Return ODE model solution for network problem with scenarions and no releases.

solve_scenarios_dynamic_model(network::Network, releases, algorithm, tspan, scenarios_of_interest::Vector{Int})

Return ODE model solution for node problem with scenarios and releases.

solve_scenarios_dynamic_model(node::Node, algorithm, tspan, scenarios_of_interest::Vector{Int})

Return ODE model solution for node problem with scenarios and no releases.

solve_scenarios_dynamic_model(node::Node, releases, algorithm, tspan, scenarios_of_interest::Vector{Int})

Return ODE model solution for node problem with scenarios and releases.

stages_abiodun()

Return life stage-specific temperature response formulations derived from Abiodun et al 2016.

stages_moustaid()

Return life stage-specific temperature response formulations derived from El Moustaid et al 2019.

stages_noresponse()

Return life stage-specific formulations with no temperature response.

stages_rossi()

Return life stage-specific temperature response formulations derived from Rossi et al 2014.

temperature_effect(ctemp::Float64, stage)

Return effect of temperature on organism vital rates (mortality, duration = μ_temperature_response, q_temperature_response).

update_density!(node::Node, species::Type{<:Species}, ::Type{T}; new_density::Density) where T <: LifeStage

Update both the functional form and parameterization of the density dependence model for LifeStage of Species in Node.

update_density!(stages::DataStructures.OrderedDict,lifestage::Type{T},new_density::Density) where {T <: LifeStage}

Update both the functional form and parameterization of the density dependence model for LifeStage.

update_density_model!(node::Node, species::Type{<:Species}, ::Type{T}; new_density_model::Density) where T <: LifeStage

Update the functional form of the density dependence model for LifeStage of Species in Node.

update_density_parameter!(node::Node, species::Type{<:Species}, ::Type{T}; new_param_value::Float64) where T <: LifeStage

Update the parameterization of the density dependence model for LifeStage of Species in Node.

update_duration!(node::Node, species::Type{<:Species}, life_stage::Type{<:LifeStage}, new_q)

Update the temperature-sensitive duration (q_temperature_response) for the LifeStage of Species in Node.

update_egg_duration!(stages::DataStructures.OrderedDict, vital_rate::Float64)

Return updated duration for Egg stage. Note: Exclusively applicable to NoResponse temperature type.

update_egg_mortality!(stages::DataStructures.OrderedDict, vital_rate::Float64)

Return updated mortality for Egg stage. Note: Exclusively applicable to NoResponse temperature type.

update_female_mortality!(stages::DataStructures.OrderedDict, vital_rate::Float64)

Return updated mortality for Female stage. Note: Exclusively applicable to NoResponse temperature type.

update_genetics!(node::Node, species::Type{<:Species}, new_genetics)

Update Genetics data for Species in Node.

update_genetics_S!(node::Node, species::Type{<:Species}, new_sigma::Array{Float64,1})

Update S data in Genetics for Species in Node.

update_genetics_Β!(node::Node, species::Type{<:Species}, new_beta::Array{Float64,1})

Update Β data in Genetics for Species in Node.

update_genetics_Η!(gene_data, new_eta::Array{Float64,1})

Update Η data in Genetics. Helper function.

update_genetics_Η!(node::Node, species::Type{<:Species}, new_eta::Array{Float64,1})

Update Η data in Genetics for Species in Node.

update_genetics_Ω!(gene_data, new_omega::Array{Float64,1})

Update Ω data in Genetics. Helper function.

update_genetics_Ω!(node::Node, species::Type{<:Species}, new_omega::Array{Float64,1})

Update Ω data in Genetics for Species in Node.

update_larva_duration!(stages::DataStructures.OrderedDict, vital_rate::Float64)

Return updated duration for Larva stage. Note: Exclusively applicable to NoResponse temperature type.

update_larva_mortality!(stages::DataStructures.OrderedDict, vital_rate::Float64)

Return updated mortality for Larva stage. Note: Exclusively applicable to NoResponse temperature type.

update_male_mortality!(stages::DataStructures.OrderedDict, vital_rate::Float64)

Return updated mortality for Male stage. Note: Exclusively applicable to NoResponse temperature type.

update_migration!(network::Network, species::Type{<:Species}, new_migration)

Update the migration characterizing each genotype and Lifestage for Species in Network.

update_mortality!(node::Node, species::Type{<:Species}, life_stage::Type{<:LifeStage}, new_μ)

Update the temperature-sensitive mortality (μ_temperature_response) for the LifeStage of Species in Node.

update_organism!(network::Network, node::Symbol, new_species)

Update the species populating the specified Node of Network.

update_organism!(node::Node, new_species)

Update the species populating Node.

update_population_size!(stages::DataStructures, Stage}, new_popsize::Int64)

Return updated population size. Note: new_popsize argument refers specifically to the Female population; if e.g. new_popsize = 500, the full adult population (Females and Males) will be 500*2.

update_pupa_duration!(stages::DataStructures.OrderedDict, vital_rate::Float64)

Return updated duration for Pupa stage. Note: Exclusively applicable to NoResponse temperature type.

update_pupa_mortality!(stages::DataStructures.OrderedDict, vital_rate::Float64)

Return updated mortality for Pupa stage. Note: Exclusively applicable to NoResponse temperature type.

update_temperature!(node::Node, temp_type::Type{<:ConstantTemperature}, new_temperature::Float64)

Update the values of ConstantTemperature for Node.

update_temperature!(node::Node, temp_type::Type{<:ScenarioTemperature}, new_temperature::ScenarioTemperature)

Update the values of Temperature for ScenarioTemperature in Node.

update_temperature!(node::Node, temp_type::Type{<:SinusoidalTemperature}, new_temperature::Vector{Float64})

Update the values of Temperature for SinusoidalTemperature in Node.

update_temperature!(node::Node, temp_type::Type{<:TimeSeriesTemperature}, new_temperature::Vector{Float64})

Update the values of Temperature for TimeSeriesTemperature in Node.