Feature stochastic equations

Project.toml

@@ -4,13 +4,17 @@ authors = ["Eva Delmas <[email protected]>"]
 version = "0.1.0"
 
 [deps]
+DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Decimals = "abce61dc-4473-55a0-ba07-351d65e31d42"
 DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
 DiffEqCallbacks = "459566f4-90b8-5000-8ac3-15dfb0a30def"
 DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 EcologicalNetworks = "f03a62fe-f8ab-5b77-a061-bb599b765229"
+FiniteDiff = "6a86dc24-6348-571c-b903-95158fe2bd41"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Mangal = "b8b640a6-63d9-51e6-b784-5033db27bef2"
 OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"

src/BEFWM2.jl

@@ -1,30 +1,38 @@
 module BEFWM2
 
 # Dependencies
+import DifferentialEquations.CorrelatedWienerProcess
 import DifferentialEquations.Rodas4
 import DifferentialEquations.SSRootfind
 import DifferentialEquations.Tsit5
+using DataFrames
 using DiffEqBase
 using DiffEqCallbacks
 using EcologicalNetworks
+using FiniteDiff
+using LinearAlgebra
 using Mangal
 using OrderedCollections
 using SparseArrays
 using Statistics
 using Decimals
-
+using StatsBase
 
 # Include scripts
 include(joinpath(".", "macros.jl"))
 include(joinpath(".", "inputs/foodwebs.jl"))
 include(joinpath(".", "inputs/nontrophic_interactions.jl"))
 include(joinpath(".", "inputs/functional_response.jl"))
 include(joinpath(".", "inputs/biological_rates.jl"))
+include(joinpath(".", "inputs/stochasticity.jl"))
+include(joinpath(".", "inputs/stressor.jl"))
+include(joinpath(".", "inputs/allee_effect.jl"))
 include(joinpath(".", "inputs/environment.jl"))
 include(joinpath(".", "inputs/producer_competition.jl"))
 include(joinpath(".", "model/model_parameters.jl"))
 include(joinpath(".", "model/productivity.jl"))
 include(joinpath(".", "model/consumption.jl"))
+include(joinpath(".", "model/covariance_matrix.jl"))
 include(joinpath(".", "model/metabolic_loss.jl"))
 include(joinpath(".", "model/dbdt.jl"))
 include(joinpath(".", "model/generate_dbdt.jl"))
@@ -47,6 +55,8 @@ export A_competition_full
 export A_facilitation_full
 export A_interference_full
 export A_refuge_full
+export AddStochasticity
+export AlleeEffect
 export allometric_rate
 export AllometricParams
 export attack_rate
@@ -99,6 +109,7 @@ export potential_competition_links
 export potential_facilitation_links
 export potential_interference_links
 export potential_refuge_links
+export predators
 export predators_of
 export preys_of
 export producer_growth
@@ -108,6 +119,8 @@ export richness
 export simulate
 export species_persistence
 export species_richness
+export Stressor
+export tidy_output
 export total_biomass
 export trophic_levels
 

src/inputs/allee_effect.jl

@@ -0,0 +1,62 @@
+#=
+AlleeEffect
+=#
+
+#### Type definiton ####
+mutable struct AlleeEffect
+    addallee::Bool
+    target::Symbol
+    μ::Real
+    β::Real
+    exponent::Real
+end
+#### end ####
+
+#### Type display ####
+"""
+One line [`AlleeEffect`](@ref) display.
+"""
+function Base.show(io::IO, allee_effect::AlleeEffect)
+    if allee_effect.addallee == true
+        print(io, "AlleeEffect(addallee, target, μ, β, exponent)")
+    else
+        print(io, "Allee effects not added")
+    end
+end
+
+"""
+Multiline [`AlleeEffect`](@ref) display.
+"""
+function Base.show(io::IO, ::MIME"text/plain", allee_effect::AlleeEffect)
+    if allee_effect.addallee == true
+        addallee = allee_effect.addallee
+        target = allee_effect.target
+        mu = allee_effect.μ
+        beta = allee_effect.β
+        exponent = allee_effect.exponent
+
+        println(io, "AlleeEffect:")
+        println(io, "  addallee: $addallee")
+        println(io, "  target: $target")
+        println(io, "  μ: $mu")
+        println(io, "  β: $beta")
+        println(io, "  exponent: $exponent")
+
+    else
+        println(io, "AlleeEffect:")
+        print(io, "  Allee effects not added")
+    end
+end
+#### end ####
+
+"""
+Literally all I need here is a switch and some values:
+"""
+
+function AlleeEffect(fw::EcologicalNetwork; addallee::Bool = false, target = :x, μ::Real = 0, β::Real = 0, exponent::Real = 0)
+
+    target ∈ [:x, :e] ||
+        throw(ArgumentError("Invalid 'target': should be :x or :e."))
+    AlleeEffect(addallee, target, μ, β, exponent)
+
+end

src/inputs/biological_rates.jl

@@ -194,7 +194,7 @@ BioRates:
 """
 function BioRates(
     network::EcologicalNetwork;
-    d::Union{Vector{<:Real},<:Real} = allometric_rate(network, DefaultMortalityParams()),
+    d::Union{Vector{<:Real},<:Real} = zeros(richness(network)),
     r::Union{Vector{<:Real},<:Real} = allometric_rate(network, DefaultGrowthParams()),
     x::Union{Vector{<:Real},<:Real} = allometric_rate(network, DefaultMetabolismParams()),
     y::Union{Vector{<:Real},<:Real} = allometric_rate(