diff --git a/previews/PR116/africa/index.html b/previews/PR116/africa/index.html index 2c97bd90..f50ead10 100644 --- a/previews/PR116/africa/index.html +++ b/previews/PR116/africa/index.html @@ -323,4 +323,4 @@ grid = false, color = :algae, aspect_ratio = 1, subplot = 4, right_margin = 2.0 * Plots.mm, - title = "D", titleloc = :left, clim = (0, 1))

Figure 2: 100 year simulations of Africa with 50,000 species. (A) Species richness after 100 years of simulation with all species equal. (B) Species richness after 50 years, with one specialist introduced. (C) Species richness after 100 years, with one specialist introduced. (D) Representativeness after 50 years with one specialist introduced (0 is completely unrepresentative of the ecosystem as a whole, 1 is completely representative).

+ title = "D", titleloc = :left, clim = (0, 1))

Figure 2: 100 year simulations of Africa with 50,000 species. (A) Species richness after 100 years of simulation with all species equal. (B) Species richness after 50 years, with one specialist introduced. (C) Species richness after 100 years, with one specialist introduced. (D) Representativeness after 50 years with one specialist introduced (0 is completely unrepresentative of the ecosystem as a whole, 1 is completely representative).

diff --git a/previews/PR116/api/index.html b/previews/PR116/api/index.html index 99bfa4a9..9083c51f 100644 --- a/previews/PR116/api/index.html +++ b/previews/PR116/api/index.html @@ -1,45 +1,45 @@ -API · EcoSISTEM.jl
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API

EcoSISTEM.AbstractAbiotic — Type
AbstractAbiotic{H <: AbstractHabitat, B <: AbstractBudget} <: AbstractPartition

Abstract supertype for all abiotic environment types and a subtype of AbstractPartition

source
EcoSISTEM.AbstractEcosystem — Type
AbstractEcosystem{Part <: AbstractAbiotic, SL <: SpeciesList,
+API · EcoSISTEM.jl
Edit on GitHub
API
EcoSISTEM.AbstractAbiotic — Type
AbstractAbiotic{H <: AbstractHabitat, B <: AbstractBudget} <: AbstractPartition
Abstract supertype for all abiotic environment types and a subtype of AbstractPartition
source
EcoSISTEM.AbstractEcosystem — Type
AbstractEcosystem{Part <: AbstractAbiotic, SL <: SpeciesList,
     TR <: AbstractTraitRelationship} <: AbstractMetacommunity{Float64,
-        Matrix{Int64}, Matrix{Float64}, SL, Part}
Abstract supertype for all ecosystem types and a subtype of AbstractMetacommunity.
source
EcoSISTEM.AbstractRequirement — Type
Abstract1Requirement{Energy}
Abstract supertype for all species energy requirement types, parameterised by the type(s) of energy required Energy.
source
EcoSISTEM.AlwaysMovement — Type
AlwaysMovement{K <: AbstractKernel, B <: BoundaryCondition} <: AbstractMovement
Movement can happen to any individual ("animal-like").
source
EcoSISTEM.BirthOnlyMovement — Type
BirthOnlyMovement{K <: AbstractKernel, B <: BoundaryCondition} <: AbstractMovement
Movement can only happen to individuals that have just been born ("plant-like").
source
EcoSISTEM.Cache — Type
Cache
Cache houses an integer array of moves made by all species in a timestep for the update! function, netmigration.
source
EcoSISTEM.CachedEcosystem — Type
CachedEcosystem{Part <: AbstractAbiotic, SL <: SpeciesList,
-    TR <: AbstractTraitRelationship} <: AbstractEcosystem{Part, SL, TR}
CachedEcosystem houses the same information as Ecosystem (see ?Ecosystem), but holds the time period abundances as a CachedGridLandscape, so that they may be present or missing.
source
EcoSISTEM.CachedEcosystem — Method
CachedEcosystem(eco::Ecosystem, outputfile::String, rng::StepRangeLen)
Function to create a CachedEcosystem given an existing ecosystem, eco, output folder to which the simulations are saved, outputfile, and a range of times over which to simulate, rng.
source
EcoSISTEM.CachedGridLandscape — Type
CachedGridLandscape
Ecosystem abundances housed in the cached landscape. These are either stored in the matrix or output to a cache.
source
EcoSISTEM.ContinuousHab — Type
ContinuousHab{C <: Number} <: AbstractHabitat{C}
This habitat subtype houses a habitat matrix matrix of any units, a grid square size size and HabitatUpdate type change.
source
EcoSISTEM.ContinuousTimeHab — Type
ContinuousTimeHab{C <: Number, M <: AbstractArray{C, 3}} <: AbstractHabitat{C}
This habitat subtype houses a habitat matrix matrix of any units, the time slice of the habitat matrix currently being operated on time, a grid square size size and HabitatUpdate type change.
source
EcoSISTEM.ContinuousTrait — Type
ContinuousTrait{C <: Number} <: AbstractTraits{T}
Abstract trait type that holds information on a single continuous trait for each species, of any Number type C.
source
EcoSISTEM.Cylinder — Type
Cylinder <: BoundaryCondition
A cylindrical boundary where species can cross the x boundary but not the y.
source
EcoSISTEM.DiscreteHab — Type
DiscreteHab <: AbstractHabitat{String}
This habitat subtype has a matrix of strings and a float grid square size
source
EcoSISTEM.DiscreteTrait — Type
BasicTrait{T} <: AbstractTraits{T}
Basic trait type that holds information on a single trait for each species, of any type T.
source
EcoSISTEM.Ecosystem — Type
Ecosystem{Part <: AbstractAbiotic} <:
-   AbstractEcosystem{Part, SL, TR}
Ecosystem houses information on species and their interaction with their environment. For species, it holds abundances and locations, abundances, as well as properties such as trait information, spplist, and movement types, lookup. For environments, it provides information on environmental conditions and available resources,abenv. Finally, there is a slot for the relationship between the environment and the characteristics of the species, relationship.
source
EcoSISTEM.Ecosystem — Method
Ecosystem(spplist::SpeciesList, abenv::GridAbioticEnv,
-    rel::AbstractTraitRelationship)
Function to create an Ecosystem given a species list, an abiotic environment and trait relationship. An optional population function can be added, popfun, which defaults to generic random filling of the ecosystem.
source
EcoSISTEM.EqualPop — Type
EqualPop <: AbstractParams
Parameter type that holds information on a population's birth and death rates, birth and death, specifically populations where all species have the same information. l represents the longevity of species based on their energy requirements and s is the survival of species dependent on how well their traits reflect the environment. Finally boost is used to manipulate how much of a boost the species get from being in an environment with lots of available energy.
source
EcoSISTEM.FluctScenario — Type
FluctScenario <: AbstractScenario
This scenario type holds a function that acts to fluctuate the environment.
source
EcoSISTEM.Gauss — Type
Gauss{TR} <: AbstractTraitRelationship{TR}
The Gaussian relationship between a continuous trait and its environment, paramaterised on any TR.
source
EcoSISTEM.GaussTrait — Type
GaussTrait{C <: Number} <: ContinuousTrait{C}
Trait type that holds Gaussian mean and variance trait information for each species, of any number type C.
source
EcoSISTEM.GaussianKernel — Type
GaussianKernel <: AbstractKernel
GaussianMovement holds parameters for a gaussian movement kernel; a dispersal variance for a species, var, and a threshold, thresh, beyond which dispersal cannot take place.
source
EcoSISTEM.GridAbioticEnv — Type
GridAbioticEnv{H, B} <: AbstractAbiotic{H, B}
This abiotic environment type holds a habitat and budget, as well as a string of subcommunity names.
source
EcoSISTEM.GridLandscape — Type
GridLandscape
Ecosystem abundances housed in the landscape. These are represented in both 2 dimensions (for computational efficiency in simulations) and 3 dimensions (to represent species, their abundances and position in the grid).
source
EcoSISTEM.LongTailKernel — Type
LongTailKernel <: AbstractKernel
LongTailKernel holds parameters for a movement kernel; a dispersal variance for a species, var, and a threshold, thresh, beyond which dispersal cannot take place.
source
EcoSISTEM.Lookup — Type
Lookup
Lookup houses information on x, y grid locations and the probability of occurrence at the location for the species in question p. pnew and moves are initially empty storage and written over by the movement step in update!(). pnew is the recalculated probability based on which directions are available and moves is the number of moves to that grid location in that step.
source
EcoSISTEM.Match — Type
Match{TR} <: AbstractTraitRelationship{TR}
The relationship between a discrete trait and its environment, paramaterised on any TR. Current conditions are matched to a trait preference and checked for a match.
source
EcoSISTEM.MultiScenario — Type
MultiScenario{S1 <: AbstractScenario, S2 <: AbstractScenario} <: AbstractScenario
This scenario type holds multiple different scenario types.
source
EcoSISTEM.NoMovement — Type
NoMovement{K <: AbstractKernel, B <: BoundaryCondition} <: AbstractMovement
No movement can take place.
source
EcoSISTEM.NoRelContinuous — Type
NoRelContinuous{TR} <: AbstractTraitRelationship{TR}
The absense of a relationship between a continuous trait and its environment, paramaterised on any TR. Returns the value 1.
source
EcoSISTEM.NoRelDiscrete — Type
NoRelDiscrete{TR} <: AbstractTraitRelationship{TR}
The absense of a relationship between a discrete trait and its environment, paramaterised on any TR. Returns the value 1.
source
EcoSISTEM.PopGrowth — Type
PopGrowth <: AbstractParams
Basic parameter type that holds information on a population's birth and death rates, birth and death, as well as how these are altered by energy availability. l represents the longevity of species based on their energy requirements and s is the survival of species dependent on how well their traits reflect the environment.
source
EcoSISTEM.RainBin — Type
RainBin{C <: Int} <: ContinuousTrait{C}
Trait type that holds binned rainfall preference information created through ClimatePref. Holds an array of counts per rainfall band (mm).
source
EcoSISTEM.SimpleBudget — Type
SimpleBudget <: AbstractBudget{Float64}
This budget type has a matrix of floats, representing the energy budget of each subcommunity in the abiotic environment.
source
EcoSISTEM.SimpleScenario — Type
SimpleScenario <: AbstractScenario
This scenario type holds a function that acts to change the entire ecosystem.
source
EcoSISTEM.SolarBudget — Type
SolarBudget <: AbstractBudget{typeof(1.0*kJ)}
This budget type has a matrix of solar energy units, representing the energy budget of each subcommunity in the abiotic environment at a fixed point in time.
source
EcoSISTEM.SolarTimeBudget — Type
SolarTimeBudget <: AbstractBudget{typeof(1.0*kJ)}
This budget type has a matrix of solar energy units, representing the energy budget of each subcommunity in the abiotic environment along with which time dimension we are interested in.
source
EcoSISTEM.SpeciesList — Type
SpeciesList{TR <: AbstractTraits, R <: AbstractRequirement,
+        Matrix{Int64}, Matrix{Float64}, SL, Part}
Abstract supertype for all ecosystem types and a subtype of AbstractMetacommunity.
source
EcoSISTEM.AbstractRequirement — Type
Abstract1Requirement{Energy}
Abstract supertype for all species energy requirement types, parameterised by the type(s) of energy required Energy.
source
EcoSISTEM.AlwaysMovement — Type
AlwaysMovement{K <: AbstractKernel, B <: BoundaryCondition} <: AbstractMovement
Movement can happen to any individual ("animal-like").
source
EcoSISTEM.BirthOnlyMovement — Type
BirthOnlyMovement{K <: AbstractKernel, B <: BoundaryCondition} <: AbstractMovement
Movement can only happen to individuals that have just been born ("plant-like").
source
EcoSISTEM.Cache — Type
Cache
Cache houses an integer array of moves made by all species in a timestep for the update! function, netmigration.
source
EcoSISTEM.CachedEcosystem — Type
CachedEcosystem{Part <: AbstractAbiotic, SL <: SpeciesList,
+    TR <: AbstractTraitRelationship} <: AbstractEcosystem{Part, SL, TR}
CachedEcosystem houses the same information as Ecosystem (see ?Ecosystem), but holds the time period abundances as a CachedGridLandscape, so that they may be present or missing.
source
EcoSISTEM.CachedEcosystem — Method
CachedEcosystem(eco::Ecosystem, outputfile::String, rng::StepRangeLen)
Function to create a CachedEcosystem given an existing ecosystem, eco, output folder to which the simulations are saved, outputfile, and a range of times over which to simulate, rng.
source
EcoSISTEM.CachedGridLandscape — Type
CachedGridLandscape
Ecosystem abundances housed in the cached landscape. These are either stored in the matrix or output to a cache.
source
EcoSISTEM.ContinuousHab — Type
ContinuousHab{C <: Number} <: AbstractHabitat{C}
This habitat subtype houses a habitat matrix matrix of any units, a grid square size size and HabitatUpdate type change.
source
EcoSISTEM.ContinuousTimeHab — Type
ContinuousTimeHab{C <: Number, M <: AbstractArray{C, 3}} <: AbstractHabitat{C}
This habitat subtype houses a habitat matrix matrix of any units, the time slice of the habitat matrix currently being operated on time, a grid square size size and HabitatUpdate type change.
source
EcoSISTEM.ContinuousTrait — Type
ContinuousTrait{C <: Number} <: AbstractTraits{T}
Abstract trait type that holds information on a single continuous trait for each species, of any Number type C.
source
EcoSISTEM.Cylinder — Type
Cylinder <: BoundaryCondition
A cylindrical boundary where species can cross the x boundary but not the y.
source
EcoSISTEM.DiscreteHab — Type
DiscreteHab <: AbstractHabitat{String}
This habitat subtype has a matrix of strings and a float grid square size
source
EcoSISTEM.DiscreteTrait — Type
BasicTrait{T} <: AbstractTraits{T}
Basic trait type that holds information on a single trait for each species, of any type T.
source
EcoSISTEM.Ecosystem — Type
Ecosystem{Part <: AbstractAbiotic} <:
+   AbstractEcosystem{Part, SL, TR}
Ecosystem houses information on species and their interaction with their environment. For species, it holds abundances and locations, abundances, as well as properties such as trait information, spplist, and movement types, lookup. For environments, it provides information on environmental conditions and available resources,abenv. Finally, there is a slot for the relationship between the environment and the characteristics of the species, relationship.
source
EcoSISTEM.Ecosystem — Method
Ecosystem(spplist::SpeciesList, abenv::GridAbioticEnv,
+    rel::AbstractTraitRelationship)
Function to create an Ecosystem given a species list, an abiotic environment and trait relationship. An optional population function can be added, popfun, which defaults to generic random filling of the ecosystem.
source
EcoSISTEM.EqualPop — Type
EqualPop <: AbstractParams
Parameter type that holds information on a population's birth and death rates, birth and death, specifically populations where all species have the same information. l represents the longevity of species based on their energy requirements and s is the survival of species dependent on how well their traits reflect the environment. Finally boost is used to manipulate how much of a boost the species get from being in an environment with lots of available energy.
source
EcoSISTEM.FluctScenario — Type
FluctScenario <: AbstractScenario
This scenario type holds a function that acts to fluctuate the environment.
source
EcoSISTEM.Gauss — Type
Gauss{TR} <: AbstractTraitRelationship{TR}
The Gaussian relationship between a continuous trait and its environment, paramaterised on any TR.
source
EcoSISTEM.GaussTrait — Type
GaussTrait{C <: Number} <: ContinuousTrait{C}
Trait type that holds Gaussian mean and variance trait information for each species, of any number type C.
source
EcoSISTEM.GaussianKernel — Type
GaussianKernel <: AbstractKernel
GaussianMovement holds parameters for a gaussian movement kernel; a dispersal variance for a species, var, and a threshold, thresh, beyond which dispersal cannot take place.
source
EcoSISTEM.GridAbioticEnv — Type
GridAbioticEnv{H, B} <: AbstractAbiotic{H, B}
This abiotic environment type holds a habitat and budget, as well as a string of subcommunity names.
source
EcoSISTEM.GridLandscape — Type
GridLandscape
Ecosystem abundances housed in the landscape. These are represented in both 2 dimensions (for computational efficiency in simulations) and 3 dimensions (to represent species, their abundances and position in the grid).
source
EcoSISTEM.LongTailKernel — Type
LongTailKernel <: AbstractKernel
LongTailKernel holds parameters for a movement kernel; a dispersal variance for a species, var, and a threshold, thresh, beyond which dispersal cannot take place.
source
EcoSISTEM.Lookup — Type
Lookup
Lookup houses information on x, y grid locations and the probability of occurrence at the location for the species in question p. pnew and moves are initially empty storage and written over by the movement step in update!(). pnew is the recalculated probability based on which directions are available and moves is the number of moves to that grid location in that step.
source
EcoSISTEM.Match — Type
Match{TR} <: AbstractTraitRelationship{TR}
The relationship between a discrete trait and its environment, paramaterised on any TR. Current conditions are matched to a trait preference and checked for a match.
source
EcoSISTEM.MultiScenario — Type
MultiScenario{S1 <: AbstractScenario, S2 <: AbstractScenario} <: AbstractScenario
This scenario type holds multiple different scenario types.
source
EcoSISTEM.NoMovement — Type
NoMovement{K <: AbstractKernel, B <: BoundaryCondition} <: AbstractMovement
No movement can take place.
source
EcoSISTEM.NoRelContinuous — Type
NoRelContinuous{TR} <: AbstractTraitRelationship{TR}
The absense of a relationship between a continuous trait and its environment, paramaterised on any TR. Returns the value 1.
source
EcoSISTEM.NoRelDiscrete — Type
NoRelDiscrete{TR} <: AbstractTraitRelationship{TR}
The absense of a relationship between a discrete trait and its environment, paramaterised on any TR. Returns the value 1.
source
EcoSISTEM.PopGrowth — Type
PopGrowth <: AbstractParams
Basic parameter type that holds information on a population's birth and death rates, birth and death, as well as how these are altered by energy availability. l represents the longevity of species based on their energy requirements and s is the survival of species dependent on how well their traits reflect the environment.
source
EcoSISTEM.RainBin — Type
RainBin{C <: Int} <: ContinuousTrait{C}
Trait type that holds binned rainfall preference information created through ClimatePref. Holds an array of counts per rainfall band (mm).
source
EcoSISTEM.SimpleBudget — Type
SimpleBudget <: AbstractBudget{Float64}
This budget type has a matrix of floats, representing the energy budget of each subcommunity in the abiotic environment.
source
EcoSISTEM.SimpleScenario — Type
SimpleScenario <: AbstractScenario
This scenario type holds a function that acts to change the entire ecosystem.
source
EcoSISTEM.SolarBudget — Type
SolarBudget <: AbstractBudget{typeof(1.0*kJ)}
This budget type has a matrix of solar energy units, representing the energy budget of each subcommunity in the abiotic environment at a fixed point in time.
source
EcoSISTEM.SolarTimeBudget — Type
SolarTimeBudget <: AbstractBudget{typeof(1.0*kJ)}
This budget type has a matrix of solar energy units, representing the energy budget of each subcommunity in the abiotic environment along with which time dimension we are interested in.
source
EcoSISTEM.SpeciesList — Type
SpeciesList{TR <: AbstractTraits, R <: AbstractRequirement,
             MO <: AbstractMovement, T <: AbstractTypes,
-            P <: AbstractParams} <: AbstractTypes
Species list houses all species-specific information including trait information, phylogenetic relationships, requirement for energy and movement types.
source
EcoSISTEM.SpeciesList — Method
SpeciesList{R <: AbstractRequirement,
+            P <: AbstractParams} <: AbstractTypes
Species list houses all species-specific information including trait information, phylogenetic relationships, requirement for energy and movement types.
source
EcoSISTEM.SpeciesList — Method
SpeciesList{R <: AbstractRequirement,
   MO <: AbstractMovement, P <: AbstractParams}(numspecies::Int64,
   numtraits::Int64, abun_dist::Distribution, req::R,
-  movement::MO, params::P)
Function to create a SpeciesList given a number of species, the number of traits they possess, their abundances, requirement from the environment and their movement kernel.
source
EcoSISTEM.SpeciesList — Method
SpeciesList{R <: AbstractRequirement, MO <: AbstractMovement,
+  movement::MO, params::P)
Function to create a SpeciesList given a number of species, the number of traits they possess, their abundances, requirement from the environment and their movement kernel.
source
EcoSISTEM.SpeciesList — Method
SpeciesList{R <: AbstractRequirement, MO <: AbstractMovement,
   T <: AbstractTypes, P <: AbstractParams}(numspecies::Int64,
   numtraits::Int64, abun_dist::Distribution, req::R,
-  movement::MO, phy::T, params::P)
Function to create a SpeciesList given a number of species, the number of traits they possess, their abundances, requirement from the environment and their movement kernel and any type of AbstractTypes.
source
EcoSISTEM.TempBin — Type
TempBin{C <: Int} <: ContinuousTrait{C}
Trait type that holds binned temperature preference information created through ClimatePref. Holds an array of counts per temperature band (°C).
source
EcoSISTEM.Torus — Type
Torus <: BoundaryCondition
A toroidal boundary where species can cross both boundaries.
source
EcoSISTEM.TraitCollection3 — Type
TraitCollection3{T1, T2, T3} <: AbstractTraits{Tuple{T1, T2, T3}}
Trait collection that holds three trait types, TR1, TR2 and TR3.
source
EcoSISTEM.Trapeze — Type
Trapeze{TR} <: AbstractTraitRelationship{TR}
The relationship between a continuous trait and its environment, paramaterised on any TR.
source
EcoSISTEM.Trapezoid — Type
Trapezoid{T<:Real} <: ContinuousUnivariateDistribution
Trapezoidal distribution as described at https://en.wikipedia.org/wiki/Trapezoidal_distribution.
source
EcoSISTEM.Unif — Type
Trapeze{TR} <: AbstractTraitRelationship{TR}
The relationship between a continuous trait and its environment, paramaterised on any TR.
source
EcoSISTEM.VolWaterBudget — Type
VolWaterBudget <: AbstractBudget{typeof(1.0*mm)}
This budget type has a matrix of water volumes, representing the energy budget of each subcommunity in the abiotic environment at a fixed point in time.
source
EcoSISTEM.VolWaterTimeBudget — Type
VolWaterTimeBudget <: AbstractBudget{typeof(1.0*mm)}
This budget type has a matrix of volumetric soil water units, representing the water budget of each subcommunity in the abiotic environment along with which time dimension we are interested in.
source
EcoSISTEM.WaterBudget — Type
WaterBudget <: AbstractBudget{typeof(1.0*mm)}
This budget type has a matrix of rainfall energy units, representing the energy budget of each subcommunity in the abiotic environment at a fixed point in time.
source
EcoSISTEM.WaterTimeBudget — Type
WaterTimeBudget <: AbstractBudget{typeof(1.0*mm)}
This budget type has a matrix of rainfall units, representing the water budget of each subcommunity in the abiotic environment along with which time dimension we are interested in.
source
EcoSISTEM.additiveTR2 — Type
additiveTR2{TR1, TR2} <: AbstractTraitRelationship{Tuple{TR1, TR2}}
Type that houses multiple AbstractTraitRelationships for two trait and habitat levels.
source
EcoSISTEM.additiveTR3 — Type
multiplicativeTR3{TR1, TR2, TR3} <: AbstractTraitRelationship{Tuple{TR1, TR2, TR3}}
Type that houses multiple AbstractTraitRelationships for three trait and habitat levels.
source
EcoSISTEM.multiplicativeTR2 — Type
multiplicativeTR2{TR1, TR2} <: AbstractTraitRelationship{Tuple{TR1, TR2}}
Type that houses multiple AbstractTraitRelationships for two trait and habitat levels.
source
EcoSISTEM.multiplicativeTR3 — Type
multiplicativeTR3{TR1, TR2, TR3} <: AbstractTraitRelationship{Tuple{TR1, TR2, TR3}}
Type that houses multiple AbstractTraitRelationships for three trait and habitat levels.
source
EcoSISTEM.BM — Function
BM(T::Real, σ²::Float64, start::Float64, lab::String="")
Function to evolve a Real value through Brownian motion, with a starting value,  start, and rate, σ².
source
EcoSISTEM.ContinuousEvolve — Method
ContinuousEvolve(val::Union{Float64, Unitful.Quantity{Float64}}, var::Union{Float64, Unitful.Quantity{Float64}}, tree::BinaryTree)
Function to evolve a continuous trait along a BinaryTree, tree via Brownian motion. Takes in a starting value, val and a variance, var.
source
EcoSISTEM.DiscreteEvolve — Function
DiscreteEvolve(numTraits::Int64, tree::BinaryTree)
Function to evolve a discrete switching trait along a BinaryTree, tree. Takes in a number of traits, numTraits to be switched between and rate to switch between traits, switch_rate with default value of 0.5.
source
EcoSISTEM.HabitatLoss — Method
HabitatLoss(eco::AbstractEcosystem, hab::ContinuousHab, timestep::Unitful.Time)
Function to destroy habitat for one timestep of the ecosystem using HabitatUpdate information.
source
EcoSISTEM.NoChange — Method
NoChange(eco::AbstractEcosystem, hab::ContinuousHab, timestep::Unitful.Time)
Function to keep the habitat the same for one timestep of the model.
source
EcoSISTEM.RainfallChange — Method
RainfallChange(eco::AbstractEcosystem, hab::ContinuousHab, timestep::Unitful.Time)
Function to change the rainfall for one timestep of the ecosystem using HabitatUpdate information.
source
EcoSISTEM.TempChange — Method
TempChange(eco::AbstractEcosystem, hab::ContinuousHab, timestep::Unitful.Time)
Function to increase the temperature for one timestep of the ecosystem using HabitatUpdate information.
source
EcoSISTEM.TempFluct — Method
TempFluct(eco::AbstractEcosystem, hab::ContinuousHab, timestep::Unitful.Time)
Function to fluctuate the temperature for one timestep of the ecosystem using HabitatUpdate information.
source
EcoSISTEM.abundances — Method
abundances(cache::CachedEcosystem, tm::Unitful.Time)
Function to extract abundances for an ecosystem, cache, at a certain point in time, tm. If the abundances for that time are missing from the ecosystem, then the function checks on disk for the last saved version and simulates forward.
source
EcoSISTEM.assign_traits! — Method
assign_traits!(tree::AbstractTree, start::Vector{Float64},
-  σ²::Vector{Float64})
Function to evolve continuous functional traits through a phylogenetic tree through Brownian motion, with a starting value, start, and rate, σ².
source
EcoSISTEM.assign_traits! — Method
assign_traits!(tree::AbstractTree, switch_rate::Vector{Float64},
-traits::Vector{Vector{String}})
Function to evolve categorical functional traits through a phylogenetic tree with a specific switching rate.
source
EcoSISTEM.bioclimAE — Method
bioclimAE(bc::Worldclim_bioclim, maxbud::Unitful.Quantity{Float64}, area::Unitful.Area{Float64})
Function to create a ContinuousHab, SimpleBudget type abiotic environment from an Wordclim type climate.  It either creates a SimpleBudget type filled with the maximum budget value maxbud or uses a provided budget of type SolarBudget.  If a Bool matrix of active grid squares is included, active, this is used, else one is created with all grid cells active.
source
EcoSISTEM.budgetupdate! — Method
budgetupdate!(eco::AbstractEcosystem, timestep::Unitful.Time)
Function to update the budget of an ecosystem for one timestep.
source
EcoSISTEM.calc_lookup_moves! — Method
calc_lookup_moves!(bound, x::Int64, y::Int64, sp::Int64, eco::Ecosystem, abun::Int64)
Function to calculate the number of moves taken by a species, sp, from a specific grid square location (x, y). There is a boundary condition, bound, which determines how the species can move across space (see AbstractBoundary). The total abundance of individuals is given in abun, which may be the number of births in the timestep, or total indiviuals.
source
EcoSISTEM.combineTR — Method
combineTR
Function that combines the output of multiple trait relationships, which varies depending on whether multiplicative, additive etc.
source
EcoSISTEM.convert_coords — Function
convert_coords(eco, i::Int64, width::Int64)
-convert_coords(eco, x::Int64, y::Int64, width::Int64)
Function to convert coordinates from two-dimensional (x,y) format to one dimension (i), or vice versa, using the width of the grid. This function can also be applied to arrays of coordinates.
source
EcoSISTEM.emptygridlandscape — Method
emptygridlandscape(gae::GridAbioticEnv, spplist::SpeciesList)
Function to create an empty GridLandscape given a GridAbioticEnv and a SpeciesList.
source
EcoSISTEM.emptypopulate! — Method
emptypopulate!(ml::GridLandscape, spplist::SpeciesList,
-               abenv::AB, rel::R) where {AB <: EcoSISTEM.AbstractAbiotic, R <: EcoSISTEM.AbstractTraitRelationship}
source
EcoSISTEM.energy_adjustment — Method
energy_adjustment(eco::Ecosystem, bud::AbstractBudget, i::Int64, sp::Int64)
Function to calculate how much birth and death rates should be adjusted by, according to how much energy is available, bud, in the grid square, i, and how much energy the species, sp, requires.
source
EcoSISTEM.equalpop — Method
equalpop(params::EqualPop, numspp)
Function that takes demographic parameters from type EqualPop and converts them into type PopGrowth based on the number of species (numspp).
source
EcoSISTEM.eraAE — Method
eraAE(era::ERA, maxbud::Unitful.Quantity{Float64})
Function to create a ContinuousHab, SimpleBudget type abiotic environment from an ERA type climate. It either creates a SimpleBudget type filled with the maximum budget value maxbud or uses a provided budget of type SolarTimeBudget. If a Bool matrix of active grid squares is included, active, this is used, else one is created with all grid cells active.
source
EcoSISTEM.eraChange — Method
eraChange(eco::AbstractEcosystem, hab::ContinuousHab, timestep::Unitful.Time)
Function to step the ERA climate forward by one timestep.
source
EcoSISTEM.genlookups — Method
genlookups(hab::AbstractHabitat, mov::GaussianMovement)
Function to generate lookup tables, which hold information on the probability of moving to neighbouring squares.
source
EcoSISTEM.geom_mean_abun — Method
geom_mean_abun(eco::Ecosystem, qs::Vector{Float64})
Function to calculate the geometric mean abundance for the entire ecosystem.
source
EcoSISTEM.get_neighbours — Function
get_neighbours(mat::Matrix, x_coord::Int64, y_coord::Int64, chess::Int64=4)
Function to get the neighbours of a grid square in a matrix in 4 or 8 directions
source
EcoSISTEM.get_traits — Function
get_traits(tree::AbstractTree, tips::Bool=true)
Function to retrieve functional traits assigned to a phylogenetic tree, either just tips or all nodes.
source
EcoSISTEM.getdispersaldist — Method
getdispersaldist(eco::Ecosystem)
Function to extract average dispersal distance of species from Ecosystem object. Returns a vector of distances, unless a specific species is provided as a String or Integer.
source
EcoSISTEM.getdispersalvar — Method
getdispersalvar(eco::Ecosystem)
Function to extract dispersal varaince of species from Ecosystem object. Returns a vector of distances, unless a specific species is provided as a String or Integer.
source
EcoSISTEM.getlookup — Method
getlookup(eco::Ecosystem)
Function to extract movement lookup table of species from Ecosystem object.
source
EcoSISTEM.getpref — Method
getpref(traits::T, field::Symbol) where T <: AbstractTraits
Function to extract trait preferences for all species in the ecosystem.
source
EcoSISTEM.getrelationship — Method
getpref(traits::T, field::Symbol) where T <: AbstractTraits
Function to extract the trait relationship of all species in the ecosystem.
source
EcoSISTEM.getsize — Method
getsize(eco::Ecosystem)
Function to extract size of habitat from Ecosystem object.
source
EcoSISTEM.habitatupdate! — Method
habitatupdate!(eco::AbstractEcosystem, timestep::Unitful.Time)
Function to update the habitat of an ecosystem for one timestep.
source
EcoSISTEM.makeunique — Method
makeunique(eco::Ecosystem)
Function to convert type of similarity in SpeciesList to UniqueTypes, i.e. an identity matrix.
source
EcoSISTEM.mean_abun — Method
mean_abun(eco::Ecosystem, qs::Vector{Float64})
Function to calculate the mean arithmetic abundance for the entire ecosystem.
source
EcoSISTEM.meta_shannon — Method
meta_shannon(eco::Ecosystem, qs::Vector{Float64})
Function to calculate the Shannon entropy for the entire ecosystem.
source
EcoSISTEM.meta_simpson — Method
meta_simpson(eco::Ecosystem, qs::Vector{Float64})
Function to calculate the Simpson diversity for the entire ecosystem.
source
EcoSISTEM.move! — Method
move!(eco::Ecosystem, ::AbstractMovement, i::Int64, sp::Int64, grd::Array{Int64, 2}, abun::Int64)
Function to calculate the movement of species sp from a given position in the landscape i, using the lookup table found in the Ecosystem and updating the movement patterns on a cached grid, grd. Optionally, a number of births can be provided, so that movement only takes place as part of the birth process, instead of the entire population
source
EcoSISTEM.pd — Method
pd(eco::Ecosystem, qs::Vector{Float64})
Function to calculate Faith's phylogenetic diversity (PD) for the entire ecosystem.
source
EcoSISTEM.peakedgradAE — Method
peakedgradAE(minT::Unitful.Temperature{Float64},
+  movement::MO, phy::T, params::P)
Function to create a SpeciesList given a number of species, the number of traits they possess, their abundances, requirement from the environment and their movement kernel and any type of AbstractTypes.
source
EcoSISTEM.TempBin — Type
TempBin{C <: Int} <: ContinuousTrait{C}
Trait type that holds binned temperature preference information created through ClimatePref. Holds an array of counts per temperature band (°C).
source
EcoSISTEM.Torus — Type
Torus <: BoundaryCondition
A toroidal boundary where species can cross both boundaries.
source
EcoSISTEM.TraitCollection3 — Type
TraitCollection3{T1, T2, T3} <: AbstractTraits{Tuple{T1, T2, T3}}
Trait collection that holds three trait types, TR1, TR2 and TR3.
source
EcoSISTEM.Trapeze — Type
Trapeze{TR} <: AbstractTraitRelationship{TR}
The relationship between a continuous trait and its environment, paramaterised on any TR.
source
EcoSISTEM.Trapezoid — Type
Trapezoid{T<:Real} <: ContinuousUnivariateDistribution
Trapezoidal distribution as described at https://en.wikipedia.org/wiki/Trapezoidal_distribution.
source
EcoSISTEM.Unif — Type
Trapeze{TR} <: AbstractTraitRelationship{TR}
The relationship between a continuous trait and its environment, paramaterised on any TR.
source
EcoSISTEM.VolWaterBudget — Type
VolWaterBudget <: AbstractBudget{typeof(1.0*mm)}
This budget type has a matrix of water volumes, representing the energy budget of each subcommunity in the abiotic environment at a fixed point in time.
source
EcoSISTEM.VolWaterTimeBudget — Type
VolWaterTimeBudget <: AbstractBudget{typeof(1.0*mm)}
This budget type has a matrix of volumetric soil water units, representing the water budget of each subcommunity in the abiotic environment along with which time dimension we are interested in.
source
EcoSISTEM.WaterBudget — Type
WaterBudget <: AbstractBudget{typeof(1.0*mm)}
This budget type has a matrix of rainfall energy units, representing the energy budget of each subcommunity in the abiotic environment at a fixed point in time.
source
EcoSISTEM.WaterTimeBudget — Type
WaterTimeBudget <: AbstractBudget{typeof(1.0*mm)}
This budget type has a matrix of rainfall units, representing the water budget of each subcommunity in the abiotic environment along with which time dimension we are interested in.
source
EcoSISTEM.additiveTR2 — Type
additiveTR2{TR1, TR2} <: AbstractTraitRelationship{Tuple{TR1, TR2}}
Type that houses multiple AbstractTraitRelationships for two trait and habitat levels.
source
EcoSISTEM.additiveTR3 — Type
multiplicativeTR3{TR1, TR2, TR3} <: AbstractTraitRelationship{Tuple{TR1, TR2, TR3}}
Type that houses multiple AbstractTraitRelationships for three trait and habitat levels.
source
EcoSISTEM.multiplicativeTR2 — Type
multiplicativeTR2{TR1, TR2} <: AbstractTraitRelationship{Tuple{TR1, TR2}}
Type that houses multiple AbstractTraitRelationships for two trait and habitat levels.
source
EcoSISTEM.multiplicativeTR3 — Type
multiplicativeTR3{TR1, TR2, TR3} <: AbstractTraitRelationship{Tuple{TR1, TR2, TR3}}
Type that houses multiple AbstractTraitRelationships for three trait and habitat levels.
source
EcoSISTEM.BM — Function
BM(T::Real, σ²::Float64, start::Float64, lab::String="")
Function to evolve a Real value through Brownian motion, with a starting value,  start, and rate, σ².
source
EcoSISTEM.ContinuousEvolve — Method
ContinuousEvolve(val::Union{Float64, Unitful.Quantity{Float64}}, var::Union{Float64, Unitful.Quantity{Float64}}, tree::BinaryTree)
Function to evolve a continuous trait along a BinaryTree, tree via Brownian motion. Takes in a starting value, val and a variance, var.
source
EcoSISTEM.DiscreteEvolve — Function
DiscreteEvolve(numTraits::Int64, tree::BinaryTree)
Function to evolve a discrete switching trait along a BinaryTree, tree. Takes in a number of traits, numTraits to be switched between and rate to switch between traits, switch_rate with default value of 0.5.
source
EcoSISTEM.HabitatLoss — Method
HabitatLoss(eco::AbstractEcosystem, hab::ContinuousHab, timestep::Unitful.Time)
Function to destroy habitat for one timestep of the ecosystem using HabitatUpdate information.
source
EcoSISTEM.NoChange — Method
NoChange(eco::AbstractEcosystem, hab::ContinuousHab, timestep::Unitful.Time)
Function to keep the habitat the same for one timestep of the model.
source
EcoSISTEM.RainfallChange — Method
RainfallChange(eco::AbstractEcosystem, hab::ContinuousHab, timestep::Unitful.Time)
Function to change the rainfall for one timestep of the ecosystem using HabitatUpdate information.
source
EcoSISTEM.TempChange — Method
TempChange(eco::AbstractEcosystem, hab::ContinuousHab, timestep::Unitful.Time)
Function to increase the temperature for one timestep of the ecosystem using HabitatUpdate information.
source
EcoSISTEM.TempFluct — Method
TempFluct(eco::AbstractEcosystem, hab::ContinuousHab, timestep::Unitful.Time)
Function to fluctuate the temperature for one timestep of the ecosystem using HabitatUpdate information.
source
EcoSISTEM.abundances — Method
abundances(cache::CachedEcosystem, tm::Unitful.Time)
Function to extract abundances for an ecosystem, cache, at a certain point in time, tm. If the abundances for that time are missing from the ecosystem, then the function checks on disk for the last saved version and simulates forward.
source
EcoSISTEM.assign_traits! — Method
assign_traits!(tree::AbstractTree, start::Vector{Float64},
+  σ²::Vector{Float64})
Function to evolve continuous functional traits through a phylogenetic tree through Brownian motion, with a starting value, start, and rate, σ².
source
EcoSISTEM.assign_traits! — Method
assign_traits!(tree::AbstractTree, switch_rate::Vector{Float64},
+traits::Vector{Vector{String}})
Function to evolve categorical functional traits through a phylogenetic tree with a specific switching rate.
source
EcoSISTEM.bioclimAE — Method
bioclimAE(bc::Worldclim_bioclim, maxbud::Unitful.Quantity{Float64}, area::Unitful.Area{Float64})
Function to create a ContinuousHab, SimpleBudget type abiotic environment from an Wordclim type climate.  It either creates a SimpleBudget type filled with the maximum budget value maxbud or uses a provided budget of type SolarBudget.  If a Bool matrix of active grid squares is included, active, this is used, else one is created with all grid cells active.
source
EcoSISTEM.budgetupdate! — Method
budgetupdate!(eco::AbstractEcosystem, timestep::Unitful.Time)
Function to update the budget of an ecosystem for one timestep.
source
EcoSISTEM.calc_lookup_moves! — Method
calc_lookup_moves!(bound, x::Int64, y::Int64, sp::Int64, eco::Ecosystem, abun::Int64)
Function to calculate the number of moves taken by a species, sp, from a specific grid square location (x, y). There is a boundary condition, bound, which determines how the species can move across space (see AbstractBoundary). The total abundance of individuals is given in abun, which may be the number of births in the timestep, or total indiviuals.
source
EcoSISTEM.combineTR — Method
combineTR
Function that combines the output of multiple trait relationships, which varies depending on whether multiplicative, additive etc.
source
EcoSISTEM.convert_coords — Function
convert_coords(eco, i::Int64, width::Int64)
+convert_coords(eco, x::Int64, y::Int64, width::Int64)
Function to convert coordinates from two-dimensional (x,y) format to one dimension (i), or vice versa, using the width of the grid. This function can also be applied to arrays of coordinates.
source
EcoSISTEM.emptygridlandscape — Method
emptygridlandscape(gae::GridAbioticEnv, spplist::SpeciesList)
Function to create an empty GridLandscape given a GridAbioticEnv and a SpeciesList.
source
EcoSISTEM.emptypopulate! — Method
emptypopulate!(ml::GridLandscape, spplist::SpeciesList,
+               abenv::AB, rel::R) where {AB <: EcoSISTEM.AbstractAbiotic, R <: EcoSISTEM.AbstractTraitRelationship}
source
EcoSISTEM.energy_adjustment — Method
energy_adjustment(eco::Ecosystem, bud::AbstractBudget, i::Int64, sp::Int64)
Function to calculate how much birth and death rates should be adjusted by, according to how much energy is available, bud, in the grid square, i, and how much energy the species, sp, requires.
source
EcoSISTEM.equalpop — Method
equalpop(params::EqualPop, numspp)
Function that takes demographic parameters from type EqualPop and converts them into type PopGrowth based on the number of species (numspp).
source
EcoSISTEM.eraAE — Method
eraAE(era::ERA, maxbud::Unitful.Quantity{Float64})
Function to create a ContinuousHab, SimpleBudget type abiotic environment from an ERA type climate. It either creates a SimpleBudget type filled with the maximum budget value maxbud or uses a provided budget of type SolarTimeBudget. If a Bool matrix of active grid squares is included, active, this is used, else one is created with all grid cells active.
source
EcoSISTEM.eraChange — Method
eraChange(eco::AbstractEcosystem, hab::ContinuousHab, timestep::Unitful.Time)
Function to step the ERA climate forward by one timestep.
source
EcoSISTEM.genlookups — Method
genlookups(hab::AbstractHabitat, mov::GaussianMovement)
Function to generate lookup tables, which hold information on the probability of moving to neighbouring squares.
source
EcoSISTEM.geom_mean_abun — Method
geom_mean_abun(eco::Ecosystem, qs::Vector{Float64})
Function to calculate the geometric mean abundance for the entire ecosystem.
source
EcoSISTEM.get_neighbours — Function
get_neighbours(mat::Matrix, x_coord::Int64, y_coord::Int64, chess::Int64=4)
Function to get the neighbours of a grid square in a matrix in 4 or 8 directions
source
EcoSISTEM.get_traits — Function
get_traits(tree::AbstractTree, tips::Bool=true)
Function to retrieve functional traits assigned to a phylogenetic tree, either just tips or all nodes.
source
EcoSISTEM.getdispersaldist — Method
getdispersaldist(eco::Ecosystem)
Function to extract average dispersal distance of species from Ecosystem object. Returns a vector of distances, unless a specific species is provided as a String or Integer.
source
EcoSISTEM.getdispersalvar — Method
getdispersalvar(eco::Ecosystem)
Function to extract dispersal varaince of species from Ecosystem object. Returns a vector of distances, unless a specific species is provided as a String or Integer.
source
EcoSISTEM.getlookup — Method
getlookup(eco::Ecosystem)
Function to extract movement lookup table of species from Ecosystem object.
source
EcoSISTEM.getpref — Method
getpref(traits::T, field::Symbol) where T <: AbstractTraits
Function to extract trait preferences for all species in the ecosystem.
source
EcoSISTEM.getrelationship — Method
getpref(traits::T, field::Symbol) where T <: AbstractTraits
Function to extract the trait relationship of all species in the ecosystem.
source
EcoSISTEM.getsize — Method
getsize(eco::Ecosystem)
Function to extract size of habitat from Ecosystem object.
source
EcoSISTEM.habitatupdate! — Method
habitatupdate!(eco::AbstractEcosystem, timestep::Unitful.Time)
Function to update the habitat of an ecosystem for one timestep.
source
EcoSISTEM.makeunique — Method
makeunique(eco::Ecosystem)
Function to convert type of similarity in SpeciesList to UniqueTypes, i.e. an identity matrix.
source
EcoSISTEM.mean_abun — Method
mean_abun(eco::Ecosystem, qs::Vector{Float64})
Function to calculate the mean arithmetic abundance for the entire ecosystem.
source
EcoSISTEM.meta_shannon — Method
meta_shannon(eco::Ecosystem, qs::Vector{Float64})
Function to calculate the Shannon entropy for the entire ecosystem.
source
EcoSISTEM.meta_simpson — Method
meta_simpson(eco::Ecosystem, qs::Vector{Float64})
Function to calculate the Simpson diversity for the entire ecosystem.
source
EcoSISTEM.move! — Method
move!(eco::Ecosystem, ::AbstractMovement, i::Int64, sp::Int64, grd::Array{Int64, 2}, abun::Int64)
Function to calculate the movement of species sp from a given position in the landscape i, using the lookup table found in the Ecosystem and updating the movement patterns on a cached grid, grd. Optionally, a number of births can be provided, so that movement only takes place as part of the birth process, instead of the entire population
source
EcoSISTEM.pd — Method
pd(eco::Ecosystem, qs::Vector{Float64})
Function to calculate Faith's phylogenetic diversity (PD) for the entire ecosystem.
source
EcoSISTEM.peakedgradAE — Method
peakedgradAE(minT::Unitful.Temperature{Float64},
    maxT::Unitful.Temperature{Float64},
    dimension::Tuple{Int64, Int64}, maxbud::Unitful.Quantity{Float64},
    area::Unitful.Area{Float64}, rate::Quantity{Float64, 𝚯*𝐓^-1},
-   active::Array{Bool, 2})
Function to create a temperature gradient ContinuousHab, SimpleBudget type abiotic environment. Given a min and max temperature, it generates a gradient from minima at the top and bottom peaking to maximum in the middle. It creates a ContinuousHab environment with dimensions dimension and a specified area area. It also creates a SimpleBudget type filled with the maximum budget value maxbud. The rate of temperature change is specified using the parameter rate. If a Bool matrix of active grid squares is included, active, this is used, else one is created with all grid cells active.
source
EcoSISTEM.raingrad — Method
raingrad(minT::Unitful.Temperature{Float64}, maxT::Unitful.Temperature{Float64},
+   active::Array{Bool, 2})
Function to create a temperature gradient ContinuousHab, SimpleBudget type abiotic environment. Given a min and max temperature, it generates a gradient from minima at the top and bottom peaking to maximum in the middle. It creates a ContinuousHab environment with dimensions dimension and a specified area area. It also creates a SimpleBudget type filled with the maximum budget value maxbud. The rate of temperature change is specified using the parameter rate. If a Bool matrix of active grid squares is included, active, this is used, else one is created with all grid cells active.
source
EcoSISTEM.raingrad — Method
raingrad(minT::Unitful.Temperature{Float64}, maxT::Unitful.Temperature{Float64},
   size::Unitful.Length{Float64},
-  dim::Tuple{Int64, Int64}, rate::Quantity{Float64, 𝚯*𝐓^-1})
Function to create a ContinuousHab habitat with a rainfall gradient.
source
EcoSISTEM.raingradAE — Method
raingradAE(min::Unitful.Temperature{Float64},
+  dim::Tuple{Int64, Int64}, rate::Quantity{Float64, 𝚯*𝐓^-1})
Function to create a ContinuousHab habitat with a rainfall gradient.
source
EcoSISTEM.raingradAE — Method
raingradAE(min::Unitful.Temperature{Float64},
   max::Unitful.Temperature{Float64},
   dimension::Tuple{Int64, Int64}, maxbud::Float64,
   area::Unitful.Area{Float64}, rate::Quantity{Float64, typeof(𝚯*𝐓^-1)},
-  active::Array{Bool, 2})
Function to create a rain gradient ContinuousHab, SimpleBudget type abiotic environment. Given a min and max rainfall, it generates a gradient from minimum at the bottom to maximum at the top. It creates a ContinuousHab environment with dimensions dimension and a specified area area. It also creates a SimpleBudget type filled with the maximum budget value maxbud. The rate of rainfall change is specified using the parameter rate. If a Bool matrix of active grid squares is included, active, this is used, else one is created with all grid cells active.
source
EcoSISTEM.randomniches — Method
randomniches(dimension::Tuple, types::Vector{String}, clumpiness::Float64, weights::Vector)
Function to create a DiscreteHab habitat of dimension dimension, made up of sampled string types, types, that have a weighting, weights and clumpiness parameter, clumpiness.
source
EcoSISTEM.reenergise! — Method
reenergise!(eco::Ecosystem, budget::Union{Float64, Unitful.Quantity{Float64}}, grid::Tuple{Int64, Int64})
Function to refill an ecosystem eco, with energy from a budget value, budget and a grid size.
source
EcoSISTEM.repopulate! — Method
repopulate!(eco::Ecosystem, abun::Int64)
Function to repopulate an ecosystem eco, with option for including trait preferences. An additional abun parameter can be included, in order to repopulate the ecosystem with a specified number of individuals.
source
EcoSISTEM.resetrate! — Method
resetrate!(eco::Ecosystem, rate::Quantity{Float64, typeof(𝐓^-1)})
Function to reset the rate of habitat change for a species.
source
EcoSISTEM.runscenario! — Method
runscenario!(eco::Ecosystem, timestep::Unitful.Time, scenario::S, currentstep::Unitful.Time) where S <: AbstractScenario
This function runs any scenario type for one timestep.
source
EcoSISTEM.simplehabitat — Method
simplehabitat(val::Unitful.Quantity, size::Unitful.Length,
-dim::Tuple{Int64, Int64})
Function to create a ContinuousHab habitat of dimension dim, with cell size and filled value, val.
source
EcoSISTEM.simplehabitatAE — Method
simplehabitatAE(val::Union{Float64, Unitful.Quantity{Float64}},
+  active::Array{Bool, 2})
Function to create a rain gradient ContinuousHab, SimpleBudget type abiotic environment. Given a min and max rainfall, it generates a gradient from minimum at the bottom to maximum at the top. It creates a ContinuousHab environment with dimensions dimension and a specified area area. It also creates a SimpleBudget type filled with the maximum budget value maxbud. The rate of rainfall change is specified using the parameter rate. If a Bool matrix of active grid squares is included, active, this is used, else one is created with all grid cells active.
source
EcoSISTEM.randomniches — Method
randomniches(dimension::Tuple, types::Vector{String}, clumpiness::Float64, weights::Vector)
Function to create a DiscreteHab habitat of dimension dimension, made up of sampled string types, types, that have a weighting, weights and clumpiness parameter, clumpiness.
source
EcoSISTEM.reenergise! — Method
reenergise!(eco::Ecosystem, budget::Union{Float64, Unitful.Quantity{Float64}}, grid::Tuple{Int64, Int64})
Function to refill an ecosystem eco, with energy from a budget value, budget and a grid size.
source
EcoSISTEM.repopulate! — Method
repopulate!(eco::Ecosystem, abun::Int64)
Function to repopulate an ecosystem eco, with option for including trait preferences. An additional abun parameter can be included, in order to repopulate the ecosystem with a specified number of individuals.
source
EcoSISTEM.resetrate! — Method
resetrate!(eco::Ecosystem, rate::Quantity{Float64, typeof(𝐓^-1)})
Function to reset the rate of habitat change for a species.
source
EcoSISTEM.runscenario! — Method
runscenario!(eco::Ecosystem, timestep::Unitful.Time, scenario::S, currentstep::Unitful.Time) where S <: AbstractScenario
This function runs any scenario type for one timestep.
source
EcoSISTEM.simplehabitat — Method
simplehabitat(val::Unitful.Quantity, size::Unitful.Length,
+dim::Tuple{Int64, Int64})
Function to create a ContinuousHab habitat of dimension dim, with cell size and filled value, val.
source
EcoSISTEM.simplehabitatAE — Method
simplehabitatAE(val::Union{Float64, Unitful.Quantity{Float64}},
     dimension::Tuple{Int64, Int64}, maxbud::Float64, area::Unitful.Area{Float64},
-    active::Array{Bool, 2})
Function to create a simple ContinuousHab, SimpleBudget type abiotic environment. It creates a ContinuousHab filled with a given value, val, dimensions (dimension) and a specified area (area). It also creates a SimpleBudget type filled with the maximum budget value (maxbud). The rate of temperature change is specified using the parameter rate. If a Bool matrix of active grid squares is included, active, this is used, else one is created with all grid cells active.
source
EcoSISTEM.simplenicheAE — Method
simplenicheAE(numniches::Int64, dimension::Tuple,
+    active::Array{Bool, 2})
Function to create a simple ContinuousHab, SimpleBudget type abiotic environment. It creates a ContinuousHab filled with a given value, val, dimensions (dimension) and a specified area (area). It also creates a SimpleBudget type filled with the maximum budget value (maxbud). The rate of temperature change is specified using the parameter rate. If a Bool matrix of active grid squares is included, active, this is used, else one is created with all grid cells active.
source
EcoSISTEM.simplenicheAE — Method
simplenicheAE(numniches::Int64, dimension::Tuple,
                     maxBud::Float64, area::Unitful.Area{Float64},
-                    active::Array{Bool, 2})
Function to create a simple DiscreteHab, SimpleBudget type abiotic environment. Given a number of niche types numniches, it creates a DiscreteHab environment with dimensions dimension and a specified area area. It also creates a SimpleBudget type filled with the maximum budget value maxbud. If a Bool matrix of active grid squares is included, active, this is used, else one is created with all grid cells active.
source
EcoSISTEM.simulate! — Method
simulate!(cache::CachedEcosystem,  srt::Unitful.Time, timestep::Unitful.Time)
Function to run a cached ecosystem, cache at a specified timepoint, srt, for a particular timestep, 'timestep'.
source
EcoSISTEM.simulate! — Method
simulate!(eco::Ecosystem, duration::Unitful.Time, interval::Unitful.Time,
-     timestep::Unitful.Time)
Function to run an ecosystem, eco for specified length of times, duration, for a particular timestep, 'timestep'.
source
EcoSISTEM.simulate! — Method
simulate!(eco::Ecosystem, times::Unitful.Time, timestep::Unitful.Time, cacheInterval::Unitful.Time,
cacheFolder::String, scenario_name::String)
Function to run an ecosystem, eco for specified length of times, duration, for a particular timestep, 'timestep'. A cache interval and folder/file name  are specified for saving output.
source
EcoSISTEM.simulate_record! — Method
simulate_record!(eco::Ecosystem, duration::Unitful.Time, interval::Unitful.Time,
-     timestep::Unitful.Time)
Function to run an ecosystem, eco for specified length of times, duration, for a particular timestep, 'timestep', and time interval for abundances to be recorded, interval. Optionally, there may also be a scenario by which the whole ecosystem is updated, such as removal of habitat patches.
source
EcoSISTEM.simulate_record_diversity! — Method
simulate_record_diversity!(storage::AbstractArray, eco::Ecosystem,
+                    active::Array{Bool, 2})
Function to create a simple DiscreteHab, SimpleBudget type abiotic environment. Given a number of niche types numniches, it creates a DiscreteHab environment with dimensions dimension and a specified area area. It also creates a SimpleBudget type filled with the maximum budget value maxbud. If a Bool matrix of active grid squares is included, active, this is used, else one is created with all grid cells active.
source
EcoSISTEM.simulate! — Method
simulate!(cache::CachedEcosystem,  srt::Unitful.Time, timestep::Unitful.Time)
Function to run a cached ecosystem, cache at a specified timepoint, srt, for a particular timestep, 'timestep'.
source
EcoSISTEM.simulate! — Method
simulate!(eco::Ecosystem, duration::Unitful.Time, interval::Unitful.Time,
+     timestep::Unitful.Time)
Function to run an ecosystem, eco for specified length of times, duration, for a particular timestep, 'timestep'.
source
EcoSISTEM.simulate! — Method
simulate!(eco::Ecosystem, times::Unitful.Time, timestep::Unitful.Time, cacheInterval::Unitful.Time,
cacheFolder::String, scenario_name::String)
Function to run an ecosystem, eco for specified length of times, duration, for a particular timestep, 'timestep'. A cache interval and folder/file name  are specified for saving output.
source
EcoSISTEM.simulate_record! — Method
simulate_record!(eco::Ecosystem, duration::Unitful.Time, interval::Unitful.Time,
+     timestep::Unitful.Time)
Function to run an ecosystem, eco for specified length of times, duration, for a particular timestep, 'timestep', and time interval for abundances to be recorded, interval. Optionally, there may also be a scenario by which the whole ecosystem is updated, such as removal of habitat patches.
source
EcoSISTEM.simulate_record_diversity! — Method
simulate_record_diversity!(storage::AbstractArray, eco::Ecosystem,
   times::Unitful.Time, interval::Unitful.Time,timestep::Unitful.Time,
-  scenario::SimpleScenario, divfun::Function, qs::Float64)
Function to run an ecosystem, eco for specified length of times, duration, for a particular timestep, 'timestep', and time interval for a diversity to be calculated and recorded, interval. Optionally, there may also be a scenario by which the whole ecosystem is updated, such as removal of habitat patches.
source
EcoSISTEM.sorenson — Method
sorenson(eco::Ecosystem, qs::Vector{Float64})
Function to calculate the Sorenson similarity for the entire ecosystem.
source
EcoSISTEM.tematch — Method
tematch(sppl::SpeciesList, abenv::AbstractAbiotic)
Function to check that the types of a trait list and habitat list are the same for a species list (sppl) and abiotic environment (abenv).
source
EcoSISTEM.tempgrad — Method
tempgrad(minT::Unitful.Temperature{Float64}, maxT::Unitful.Temperature{Float64},
+  scenario::SimpleScenario, divfun::Function, qs::Float64)
Function to run an ecosystem, eco for specified length of times, duration, for a particular timestep, 'timestep', and time interval for a diversity to be calculated and recorded, interval. Optionally, there may also be a scenario by which the whole ecosystem is updated, such as removal of habitat patches.
source
EcoSISTEM.sorenson — Method
sorenson(eco::Ecosystem, qs::Vector{Float64})
Function to calculate the Sorenson similarity for the entire ecosystem.
source
EcoSISTEM.tematch — Method
tematch(sppl::SpeciesList, abenv::AbstractAbiotic)
Function to check that the types of a trait list and habitat list are the same for a species list (sppl) and abiotic environment (abenv).
source
EcoSISTEM.tempgrad — Method
tempgrad(minT::Unitful.Temperature{Float64}, maxT::Unitful.Temperature{Float64},
   size::Unitful.Length{Float64},
-  dim::Tuple{Int64, Int64}, rate::Quantity{Float64, 𝚯*𝐓^-1})
Function to create a ContinuousHab habitat with a temperature gradient.
source
EcoSISTEM.tempgradAE — Method
tempgradAE(min::Unitful.Temperature{Float64},
+  dim::Tuple{Int64, Int64}, rate::Quantity{Float64, 𝚯*𝐓^-1})
Function to create a ContinuousHab habitat with a temperature gradient.
source
EcoSISTEM.tempgradAE — Method
tempgradAE(min::Unitful.Temperature{Float64},
   max::Unitful.Temperature{Float64},
   dimension::Tuple{Int64, Int64}, maxbud::Float64,
   area::Unitful.Area{Float64}, rate::Quantity{Float64, typeof(𝚯*𝐓^-1)},
-  active::Array{Bool, 2})
Function to create a temperature gradient ContinuousHab, SimpleBudget type abiotic environment. Given a min and max temperature, it generates a gradient from minimum at the bottom to maximum at the top. It creates a ContinuousHab environment with dimensions dimension and a specified area area. It also creates a SimpleBudget type filled with the maximum budget value maxbud. The rate of temperature change is specified using the parameter rate. If a Bool matrix of active grid squares is included, active, this is used, else one is created with all grid cells active.
source
EcoSISTEM.traitfun — Method
traitfun(eco::AbstractEcosystem, pos::Int64, sp::Int64)
Function to calculate relationship between the current environment and a species' particular trait.
source
EcoSISTEM.traitpopulate! — Method
traitpopulate!(ml::GridLandscape, spplist::SpeciesList,
-               abenv::AbstractAbiotic)
Function to populate a grid landscape given the abundances found in species list based upon how well the species traits match their environment.
source
EcoSISTEM.traitrepopulate! — Method
repopulate!(eco::Ecosystem, abun::Int64)
Function to repopulate an ecosystem eco, with option for including trait preferences. An additional abun parameter can be included, in order to repopulate the ecosystem with a specified number of individuals.
source
EcoSISTEM.trmatch — Method
trmatch(sppl::SpeciesList, traitrel::AbstractTraitRelationship)
Function to check that the types of a trait list and trait relationship list are the same for a species list (sppl) and trait relationship (traitrel).
source
EcoSISTEM.update! — Method
update!(eco::Ecosystem, time::Unitful.Time)
Function to update a ecosystem abundances and environment for one timestep.
source
EcoSISTEM.update_energy_usage! — Method
update_energy_usage!(eco::Ecosystem)
Function to calculate how much energy has been used up by the current species in each grid square in the ecosystem, eco. This function is parameterised on whether the species have one type of energy requirement or two.
source
EcoSISTEM.worldclimAE — Method
worldclimAE(wc::Worldclim_monthly, maxbud::Unitful.Quantity{Float64})
Function to create a ContinuousTimeHab, SimpleBudget type abiotic environment from a Wordclim type climate.  It either creates a SimpleBudget type filled with the maximum budget value maxbud or uses a provided budget of type SolarTimeBudget.  If a Bool matrix of active grid squares is included, active, this is used, otherwise one is all grid cells are considered active.
source
EcoSISTEM.worldclimChange — Method
worldclimChange(eco::AbstractEcosystem, hab::ContinuousHab, timestep::Unitful.Time)
Function to step the Worldclim climate forward by one timestep.
source

+  active::Array{Bool, 2})

Function to create a temperature gradient ContinuousHab, SimpleBudget type abiotic environment. Given a min and max temperature, it generates a gradient from minimum at the bottom to maximum at the top. It creates a ContinuousHab environment with dimensions dimension and a specified area area. It also creates a SimpleBudget type filled with the maximum budget value maxbud. The rate of temperature change is specified using the parameter rate. If a Bool matrix of active grid squares is included, active, this is used, else one is created with all grid cells active.

source
EcoSISTEM.traitfun — Method
traitfun(eco::AbstractEcosystem, pos::Int64, sp::Int64)

Function to calculate relationship between the current environment and a species' particular trait.

source
EcoSISTEM.traitpopulate! — Method
traitpopulate!(ml::GridLandscape, spplist::SpeciesList,
+               abenv::AbstractAbiotic)

Function to populate a grid landscape given the abundances found in species list based upon how well the species traits match their environment.

source
EcoSISTEM.traitrepopulate! — Method
repopulate!(eco::Ecosystem, abun::Int64)

Function to repopulate an ecosystem eco, with option for including trait preferences. An additional abun parameter can be included, in order to repopulate the ecosystem with a specified number of individuals.

source
EcoSISTEM.trmatch — Method
trmatch(sppl::SpeciesList, traitrel::AbstractTraitRelationship)

Function to check that the types of a trait list and trait relationship list are the same for a species list (sppl) and trait relationship (traitrel).

source
EcoSISTEM.update! — Method
update!(eco::Ecosystem, time::Unitful.Time)

Function to update a ecosystem abundances and environment for one timestep.

source
EcoSISTEM.update_energy_usage! — Method
update_energy_usage!(eco::Ecosystem)

Function to calculate how much energy has been used up by the current species in each grid square in the ecosystem, eco. This function is parameterised on whether the species have one type of energy requirement or two.

source
EcoSISTEM.worldclimAE — Method

worldclimAE(wc::Worldclim_monthly, maxbud::Unitful.Quantity{Float64})

Function to create a ContinuousTimeHab, SimpleBudget type abiotic environment from a Wordclim type climate. It either creates a SimpleBudget type filled with the maximum budget value maxbud or uses a provided budget of type SolarTimeBudget. If a Bool matrix of active grid squares is included, active, this is used, otherwise one is all grid cells are considered active.

source
EcoSISTEM.worldclimChange — Method
worldclimChange(eco::AbstractEcosystem, hab::ContinuousHab, timestep::Unitful.Time)

Function to step the Worldclim climate forward by one timestep.

source
diff --git a/previews/PR116/basics/index.html b/previews/PR116/basics/index.html index a2c39149..08858788 100644 --- a/previews/PR116/basics/index.html +++ b/previews/PR116/basics/index.html @@ -23,4 +23,4 @@ lensim = length(0years:record_interval:times) # Burnin @time simulate!(eco, burnin, timestep)

Plot using SpatialEcology

using SpatialEcology
-plot(eco)
+plot(eco) diff --git a/previews/PR116/diversity/index.html b/previews/PR116/diversity/index.html index f1d30be0..14106a46 100644 --- a/previews/PR116/diversity/index.html +++ b/previews/PR116/diversity/index.html @@ -5,4 +5,4 @@ # Or metacommunity measures norm_meta_alpha(eco, 1.0) # Or multiple values of q -norm_sub_beta(eco, 0.0:3.0) +norm_sub_beta(eco, 0.0:3.0) diff --git a/previews/PR116/examples/index.html b/previews/PR116/examples/index.html index bd1289c9..d262bab7 100644 --- a/previews/PR116/examples/index.html +++ b/previews/PR116/examples/index.html @@ -492,4 +492,4 @@ titlefontsize=24, title = titles[i], margin = 10.0*Plots.mm, label = "", subplot = i, titleloc = :left, clim = (0, 1.5e4), link = :both)) -end

Total abundance of two species in island ecosystems after 10 years of simulation, with species populated at opposite sides of the island. Those with higher dispersal distances moved further away from their starting populations at a faster rate. (A) Mean dispersal distance of 0.5km, (B) mean dispersal distance of 1km, (C) Mean dispersal distance of 2km, Mean dispersal distance of 4km.

+end

Total abundance of two species in island ecosystems after 10 years of simulation, with species populated at opposite sides of the island. Those with higher dispersal distances moved further away from their starting populations at a faster rate. (A) Mean dispersal distance of 0.5km, (B) mean dispersal distance of 1km, (C) Mean dispersal distance of 2km, Mean dispersal distance of 4km.

diff --git a/previews/PR116/index.html b/previews/PR116/index.html index 1873eb42..97e7c5b0 100644 --- a/previews/PR116/index.html +++ b/previews/PR116/index.html @@ -1,2 +1,2 @@ -Home · EcoSISTEM.jl
Edit on GitHub

EcoSISTEM.jl

EcoSISTEM is a Julia package that provides functionality for simulating species undergoing dynamic biological processes such as birth, death, competition and dispersal, as well as environmental changes in climate and habitat.

The package was primarily developed for global scale simulations of plant biodiversity. The underlying model for this is described in the arXiv paper arXiv:1911.12257 (q-bio.QM) Dynamic virtual ecosystems as a tool for detecting large-scale responses of biodiversity to environmental and land-use change.

There are substantial changes to the package introduced through the dev branch (docs), including epidemiological simulations and refactoring of the code base for further flexibility.

This package is in beta now, so please raise an issue if you find any problems. For more information on how to contribute, please read our contributing guidelines.

+Home · EcoSISTEM.jl
Edit on GitHub

EcoSISTEM.jl

EcoSISTEM is a Julia package that provides functionality for simulating species undergoing dynamic biological processes such as birth, death, competition and dispersal, as well as environmental changes in climate and habitat.

The package was primarily developed for global scale simulations of plant biodiversity. The underlying model for this is described in the arXiv paper arXiv:1911.12257 (q-bio.QM) Dynamic virtual ecosystems as a tool for detecting large-scale responses of biodiversity to environmental and land-use change.

There are substantial changes to the package introduced through the dev branch (docs), including epidemiological simulations and refactoring of the code base for further flexibility.

This package is in beta now, so please raise an issue if you find any problems. For more information on how to contribute, please read our contributing guidelines.

diff --git a/previews/PR116/pipeline/index.html b/previews/PR116/pipeline/index.html index 3ec34aef..7eae8ace 100644 --- a/previews/PR116/pipeline/index.html +++ b/previews/PR116/pipeline/index.html @@ -8,4 +8,4 @@ # Stage the code run using the unique identifier fair add <code-run> # Push the run and corresponding metadata back to the online registry -fair push +fair push diff --git a/previews/PR116/search/index.html b/previews/PR116/search/index.html index 15c62962..2beb636b 100644 --- a/previews/PR116/search/index.html +++ b/previews/PR116/search/index.html @@ -1,2 +1,2 @@ -Search · EcoSISTEM.jl

Loading search...

    +Search · EcoSISTEM.jl

    Loading search...

      diff --git a/previews/PR116/simulation-jl/index.html b/previews/PR116/simulation-jl/index.html index 0a9a06dc..cf90894d 100644 --- a/previews/PR116/simulation-jl/index.html +++ b/previews/PR116/simulation-jl/index.html @@ -1,2 +1,2 @@ -- · EcoSISTEM.jl
      Edit on GitHub

      Table of datasets currently in use by EcoSISTEM.jl

      Preliminary list of parameters/datasets.

      Name of parameter/ datasetDescriptionValueSourceOther info (e.g. stability)
      p_sProbability of developing symptoms0.96http://gabgoh.github.io/COVID/index.html (From Thibaud's original model)
      p_hProbability of hospitalisation0.2Guess
      cfr_homeCase fatality ratio (at home)0.1Guess
      cfr_hospitalCase fatality ratio (at hospital)0.1Guess
      T_latLatent period5 dayshttp://gabgoh.github.io/COVID/index.html (From Thibaud's original model)
      T_asymAsymptomatic period3 dayshttp://gabgoh.github.io/COVID/index.html (From Thibaud's original model)
      T_symSymptomatic period5 dayshttp://gabgoh.github.io/COVID/index.html (From Thibaud's original model)
      T_hospHospitalisation period5 dayshttps://www.icnarc.org/Our-Audit/Audits/Cmp/Reports (From Thibaud's original model)
      T_recRecovery period11 dayshttp://gabgoh.github.io/COVID/index.html (From Thibaud's original model)
      mu_1Probability of becoming Asymptomatic1/T_lat
      mu_2Probability of becoming Symptomaticps * 1/Tasym
      hospitalisationProbability of becoming Hospitalisedph * 1/Tsym
      sigma_1Probability of Recovery from Asymptomatic(1 - ps) * 1/Tasym
      sigma_2Probability of Recovery from Symptomatic(1 - ph) * (1 - cfrhome) * 1/T_rec
      sigma_hospitalProbability of Recovery from Hospital(1 - cfrhosp) * 1/Thosp
      death_homeProbability of Death at homecfrhome * 2/Thosp
      death_hospitalProbability of Death at hospitalcfrhosp * 1/Thosp
      ScotlandDensity2011Scottish population density at 1km gridUK census 2011 - A Reeves 'Covid19-ScottishCensusData' repo
      dispersal_distAverage dispersal distance of virus per disease category2.0km per infectious disease categoryGuessVaries depending on grid size
      mean_prefMean temperature preference of virus298KGuessCurrently tuned to fit environment perfectly
      var_prefTemperature niche width of virus0.1KGuessCurrently tuned to fit environment perfectly
      birthProbability of giving birth per individual1.3e-4/day (20-40 year olds), 0 otherwiseGuess
      deathProbability of giving natural mortality per individual2.7e-5/dayGuess
      virusgrowthasympRate of generating virus per asymptomatic individual0.1/dayGuess
      virusgrowthsympRate of generating virus per symptomatic individual0.1/dayGuess
      beta_forceForce of infection10.0/dayGuess
      beta_envEnvironmental transmission10.0/dayGuess
      +- · EcoSISTEM.jl
      Edit on GitHub

      Table of datasets currently in use by EcoSISTEM.jl

      Preliminary list of parameters/datasets.

      Name of parameter/ datasetDescriptionValueSourceOther info (e.g. stability)
      p_sProbability of developing symptoms0.96http://gabgoh.github.io/COVID/index.html (From Thibaud's original model)
      p_hProbability of hospitalisation0.2Guess
      cfr_homeCase fatality ratio (at home)0.1Guess
      cfr_hospitalCase fatality ratio (at hospital)0.1Guess
      T_latLatent period5 dayshttp://gabgoh.github.io/COVID/index.html (From Thibaud's original model)
      T_asymAsymptomatic period3 dayshttp://gabgoh.github.io/COVID/index.html (From Thibaud's original model)
      T_symSymptomatic period5 dayshttp://gabgoh.github.io/COVID/index.html (From Thibaud's original model)
      T_hospHospitalisation period5 dayshttps://www.icnarc.org/Our-Audit/Audits/Cmp/Reports (From Thibaud's original model)
      T_recRecovery period11 dayshttp://gabgoh.github.io/COVID/index.html (From Thibaud's original model)
      mu_1Probability of becoming Asymptomatic1/T_lat
      mu_2Probability of becoming Symptomaticps * 1/Tasym
      hospitalisationProbability of becoming Hospitalisedph * 1/Tsym
      sigma_1Probability of Recovery from Asymptomatic(1 - ps) * 1/Tasym
      sigma_2Probability of Recovery from Symptomatic(1 - ph) * (1 - cfrhome) * 1/T_rec
      sigma_hospitalProbability of Recovery from Hospital(1 - cfrhosp) * 1/Thosp
      death_homeProbability of Death at homecfrhome * 2/Thosp
      death_hospitalProbability of Death at hospitalcfrhosp * 1/Thosp
      ScotlandDensity2011Scottish population density at 1km gridUK census 2011 - A Reeves 'Covid19-ScottishCensusData' repo
      dispersal_distAverage dispersal distance of virus per disease category2.0km per infectious disease categoryGuessVaries depending on grid size
      mean_prefMean temperature preference of virus298KGuessCurrently tuned to fit environment perfectly
      var_prefTemperature niche width of virus0.1KGuessCurrently tuned to fit environment perfectly
      birthProbability of giving birth per individual1.3e-4/day (20-40 year olds), 0 otherwiseGuess
      deathProbability of giving natural mortality per individual2.7e-5/dayGuess
      virusgrowthasympRate of generating virus per asymptomatic individual0.1/dayGuess
      virusgrowthsympRate of generating virus per symptomatic individual0.1/dayGuess
      beta_forceForce of infection10.0/dayGuess
      beta_envEnvironmental transmission10.0/dayGuess