API

AbstractAbiotic{H <: AbstractHabitat, B <: AbstractBudget} <: AbstractPartition

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

AbstractBudget

Abstract supertype for all budget types

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.

AbstractHabitat

Abstract supertype for all habitat types

AbstractMovement

Abstract supertype of movements

AbstractParams

Abstract supertype for all simulation parameter types

Abstract1Requirement{Energy}

Abstract supertype for all species energy requirement types, parameterised by the type(s) of energy required Energy.

AbstractScenario

Abstract supertype for all whole ecosystem change scenarios

AbstractTraitRelationship{TR}

The abstract supertype of relationships between a trait and its environment, parameterised on any TR.

AbstractTraits{T}

Abstract supertype for all trait types, parameterised by traits of any type T.

AlwaysMovement{K <: AbstractKernel, B <: BoundaryCondition} <: AbstractMovement

Movement can happen to any individual ("animal-like").

BirthOnlyMovement{K <: AbstractKernel, B <: BoundaryCondition} <: AbstractMovement

Movement can only happen to individuals that have just been born ("plant-like").

BoundaryCondition

An abstract type for what should happen at the boundaries of an ecosystem.

Cache

Cache houses an integer array of moves made by all species in a timestep for the update! function, netmigration.

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.

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.

CachedGridLandscape

Ecosystem abundances housed in the cached landscape. These are either stored in the matrix or output to a cache.

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.

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.

ContinuousTrait{C <: Number} <: AbstractTraits{T}

Abstract trait type that holds information on a single continuous trait for each species, of any Number type C.

Cylinder <: BoundaryCondition

A cylindrical boundary where species can cross the x boundary but not the y.

DiscreteHab <: AbstractHabitat{String}

This habitat subtype has a matrix of strings and a float grid square size

BasicTrait{T} <: AbstractTraits{T}

Basic trait type that holds information on a single trait for each species, of any type T.

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.

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.

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.

FluctScenario <: AbstractScenario

This scenario type holds a function that acts to fluctuate the environment.

Gauss{TR} <: AbstractTraitRelationship{TR}

The Gaussian relationship between a continuous trait and its environment, paramaterised on any TR.

GaussTrait{C <: Number} <: ContinuousTrait{C}

Trait type that holds Gaussian mean and variance trait information for each species, of any number type C.

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.

GridAbioticEnv{H, B} <: AbstractAbiotic{H, B}

This abiotic environment type holds a habitat and budget, as well as a string of subcommunity names.

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).

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.

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.

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.

MultiScenario{S1 <: AbstractScenario, S2 <: AbstractScenario} <: AbstractScenario

This scenario type holds multiple different scenario types.

NoBoundary <: BoundaryCondition

A hard boundary where no species can cross.

NoMovement{K <: AbstractKernel, B <: BoundaryCondition} <: AbstractMovement

No movement can take place.

NoRelContinuous{TR} <: AbstractTraitRelationship{TR}

The absense of a relationship between a continuous trait and its environment, paramaterised on any TR. Returns the value 1.

NoRelDiscrete{TR} <: AbstractTraitRelationship{TR}

The absense of a relationship between a discrete trait and its environment, paramaterised on any TR. Returns the value 1.

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.

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).

SimpleBudget <: AbstractBudget{Float64}

This budget type has a matrix of floats, representing the energy budget of each subcommunity in the abiotic environment.

SimpleRequirement <: Abstract1Requirement{Float64}

A simple energy requirement is a single float for each species.

SimpleScenario <: AbstractScenario

This scenario type holds a function that acts to change the entire ecosystem.

SizeRequirement <: Abstract1Requirement{Float64}

A simple energy requirement is a single float for each species.

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.

SolarRequirement <: Abstract1Requirement{typeof(1.0*kJ)}

A vector of solar energy requirements (kJ) for each species.

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.

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.

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.

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.

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).

Torus <: BoundaryCondition

A toroidal boundary where species can cross both boundaries.

TraitCollection2{T1, T2} <: AbstractTraits{Tuple{T1, T2}}

Trait collection that holds two trait types, TR1 and TR2.

TraitCollection3{T1, T2, T3} <: AbstractTraits{Tuple{T1, T2, T3}}

Trait collection that holds three trait types, TR1, TR2 and TR3.

Trapeze{TR} <: AbstractTraitRelationship{TR}

The relationship between a continuous trait and its environment, paramaterised on any TR.

Trapezoid{T<:Real} <: ContinuousUnivariateDistribution

Trapezoidal distribution as described at https://en.wikipedia.org/wiki/Trapezoidal_distribution.

Trapeze{TR} <: AbstractTraitRelationship{TR}

The relationship between a continuous trait and its environment, paramaterised on any TR.

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.

VolWaterRequirement <: Abstract1Requirement{typeof(1.0*mm)}

A vector of soil water volume requirements (m^3) for each species.

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.

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.

WaterRequirement <: Abstract1Requirement{typeof(1.0*mm)}

A vector of water requirements (mm) for each species.

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.

additiveTR2{TR1, TR2} <: AbstractTraitRelationship{Tuple{TR1, TR2}}

Type that houses multiple AbstractTraitRelationships for two trait and habitat levels.

multiplicativeTR3{TR1, TR2, TR3} <: AbstractTraitRelationship{Tuple{TR1, TR2, TR3}}

Type that houses multiple AbstractTraitRelationships for three trait and habitat levels.

multiplicativeTR2{TR1, TR2} <: AbstractTraitRelationship{Tuple{TR1, TR2}}

Type that houses multiple AbstractTraitRelationships for two trait and habitat levels.

multiplicativeTR3{TR1, TR2, TR3} <: AbstractTraitRelationship{Tuple{TR1, TR2, TR3}}

Type that houses multiple AbstractTraitRelationships for three trait and habitat levels.

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.

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.

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.

HabitatLoss(eco::AbstractEcosystem, hab::ContinuousHab, timestep::Unitful.Time)

Function to destroy habitat for one timestep of the ecosystem using HabitatUpdate information.

NoChange(eco::AbstractEcosystem, hab::ContinuousHab, timestep::Unitful.Time)

Function to keep the habitat the same for one timestep of the model.

RainfallChange(eco::AbstractEcosystem, hab::ContinuousHab, timestep::Unitful.Time)

Function to change the rainfall for one timestep of the ecosystem using HabitatUpdate information.

TempChange(eco::AbstractEcosystem, hab::ContinuousHab, timestep::Unitful.Time)

Function to increase the temperature for one timestep of the ecosystem using HabitatUpdate information.

TempFluct(eco::AbstractEcosystem, hab::ContinuousHab, timestep::Unitful.Time)

Function to fluctuate the temperature for one timestep of the ecosystem using HabitatUpdate information.

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.

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.

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.

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.

budgetupdate!(eco::AbstractEcosystem, timestep::Unitful.Time)

Function to update the budget of an ecosystem for one timestep.

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.

combineTR

Function that combines the output of multiple trait relationships, which varies depending on whether multiplicative, additive etc.

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.

emptygridlandscape(gae::GridAbioticEnv, spplist::SpeciesList)

Function to create an empty GridLandscape given a GridAbioticEnv and a SpeciesList.

emptypopulate!(ml::GridLandscape, spplist::SpeciesList,
               abenv::AB, rel::R) where {AB <: EcoSISTEM.AbstractAbiotic, R <: EcoSISTEM.AbstractTraitRelationship}

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.

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).

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.

eraChange(eco::AbstractEcosystem, hab::ContinuousHab, timestep::Unitful.Time)

Function to step the ERA climate forward by one timestep.

genlookups(hab::AbstractHabitat, mov::GaussianMovement)

Function to generate lookup tables, which hold information on the probability of moving to neighbouring squares.

geom_mean_abun(eco::Ecosystem, qs::Vector{Float64})

Function to calculate the geometric mean abundance for the entire ecosystem.

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

get_traits(tree::AbstractTree, tips::Bool=true)

Function to retrieve functional traits assigned to a phylogenetic tree, either just tips or all nodes.

getbudget(eco::Ecosystem)

Function to extract budget from Ecosystem object.

getdimension(eco::Ecosystem)

Function to extract dimension of habitat from Ecosystem object.

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.

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.

getgridsize(eco::Ecosystem)

Function to extract grid cell size of habitat from Ecosystem object.

gethabitat(eco::Ecosystem)

Function to extract habitat from Ecosystem object.

getlookup(eco::Ecosystem)

Function to extract movement lookup table of species from Ecosystem object.

getpref(traits::T, field::Symbol) where T <: AbstractTraits

Function to extract trait preferences for all species in the ecosystem.

getpref(traits::T, field::Symbol) where T <: AbstractTraits

Function to extract the trait relationship of all species in the ecosystem.

getsize(eco::Ecosystem)

Function to extract size of habitat from Ecosystem object.

gettraitrel(eco::Ecosystem)

Function to extract trait relationships.

habitatupdate!(eco::AbstractEcosystem, timestep::Unitful.Time)

Function to update the habitat of an ecosystem for one timestep.

makeunique(eco::Ecosystem)

Function to convert type of similarity in SpeciesList to UniqueTypes, i.e. an identity matrix.

mean_abun(eco::Ecosystem, qs::Vector{Float64})

Function to calculate the mean arithmetic abundance for the entire ecosystem.

meta_shannon(eco::Ecosystem, qs::Vector{Float64})

Function to calculate the Shannon entropy for the entire ecosystem.

meta_simpson(eco::Ecosystem, qs::Vector{Float64})

Function to calculate the Simpson diversity for the entire ecosystem.

meta_speciesrichness(eco::Ecosystem, qs::Vector{Float64})

Function to calculate the species richness for the entire ecosystem.

move!(eco::Ecosystem, ::AbstractMovement, i::Int64, sp::Int64, grd::Matrix{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

pd(eco::Ecosystem, qs::Vector{Float64})

Function to calculate Faith's phylogenetic diversity (PD) for the entire ecosystem.

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::Matrix{Bool})

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.

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.

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::Matrix{Bool})

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.

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.

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.

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.

resetrate!(eco::Ecosystem, rate::Quantity{Float64, typeof(𝐓^-1)})

Function to reset the rate of habitat change for a species.

runscenario!(eco::Ecosystem, timestep::Unitful.Time, scenario::S, currentstep::Unitful.Time) where S <: AbstractScenario

This function runs any scenario type for one timestep.

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.

simplehabitatAE(val::Union{Float64, Unitful.Quantity{Float64}},
    dimension::Tuple{Int64, Int64}, maxbud::Float64, area::Unitful.Area{Float64},
    active::Matrix{Bool})

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.

simplenicheAE(numniches::Int64, dimension::Tuple,
                    maxBud::Float64, area::Unitful.Area{Float64},
                    active::Matrix{Bool})

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.

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'.

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'.

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.

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.

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.

sorenson(eco::Ecosystem, qs::Vector{Float64})

Function to calculate the Sorenson similarity for the entire ecosystem.

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).

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.

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::Matrix{Bool})

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.

traitfun(eco::AbstractEcosystem, pos::Int64, sp::Int64)

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

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.

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.

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).

EcoSISTEM.unziptemp(path::String)

Helper function for the FAIR Data Pipeline to unzip files that are stored as zips to a temporary folder.

update!(eco::Ecosystem, time::Unitful.Time)

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

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.

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.

worldclimChange(eco::AbstractEcosystem, hab::ContinuousHab, timestep::Unitful.Time)

Function to step the Worldclim climate forward by one timestep.

AbstractClimate

Abstract supertype of all climate data.

CERA <: AbstractClimate

Type that houses data extracted from CERA-20C raster files.

CHELSA_bioclim <: AbstractClimate

Type that houses data extracted from CHELSA raster files.

CHELSA_monthly <: AbstractClimate

Type that houses data extracted from CHELSA raster files.

CRUTS <: AbstractClimate

Type that houses data extracted from CRUTS raster files.

ERA <: AbstractClimate

Type that houses data extracted from ERA raster files.

Landcover <: AbstractClimate

Type that houses data extracted from EarthEnv Landcover raster files.

Reference <: AbstractClimate

Type that houses a reference data array.

Worldclim_bioclim <: AbstractClimate

Type that houses data extracted from Bioclim raster files.

Worldclim_monthly <: AbstractClimate

Type that houses data extracted from Worldclim raster files.

read(f, filename)

Function to read raster file into julia.

convert_coords(i::Int64, width::Int64)
convert_coords(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.

create_reference(gridsize::Float64)

Function to create a reference grid array of type Reference.

downresolution(data::Union{ERA, Worldclim_monthly, Worldclim_bioclim}, rescale::Int64; fn)

Function to decrease the resolution of a climate dataset, by a factor, rescale, and aggregation function, fn. The aggregation function has a default setting of taking the mean value.

downresolution!(resized_array::Matrix{T}, array::Matrix{T}, rescale::Int64, fn)
downresolution!(resized_array::Array{T, 3}, array::Matrix{T}, dim::Int64, rescale::Int64, fn)

Function to decrease the resolution of a climate dataset in place, by a factor, rescale, and aggregation function, fn. The aggregation function has a default setting of taking the mean value.

extractvalues(x::Vector{typeof(1.0°)},y::Vector{typeof(1.0°)},
    bc::Worldclim_bioclim, dim::Unitful.Time)

Function to extract values from a bioclim object, at specified x, y locations and time, dim.

extractvalues(x::Vector{typeof(1.0°)},y::Vector{typeof(1.0°)},
    bc::Worldclim_bioclim, dim::Unitful.Time)

Function to extract values from a bioclim object, at specified x, y locations and over a time period, dim.

extractvalues(x::Vector{typeof(1.0°)},y::Vector{typeof(1.0°)},
    wc::Worldclim_monthly, dim::Unitful.Time)

Function to extract values from a worldclim object, at specified x, y locations and over a range of times, dim.

extractvalues(x::Vector{typeof(1.0°)},y::Vector{typeof(1.0°)},
    wc::Worldclim_monthly, dim::Unitful.Time)

Function to extract values from a worldclim object, at specified x, y locations and time, dim.

readCERA(dir::String, file::String, params::String)

Function to extract a certain parameter, param, from an CERA-20C netcdf file, and convert into an axis array.

readCHELSA_monthly(dir::String)

Function to extract all raster files from a specified folder directory, and convert into an axis array.

readCRUTS(dir::String)

Function to extract all raster files from a specified folder directory, and convert into an axis array.

readERA(dir::String, file::String, param::String, dim::Vector{Vector{T}})
    where T<: Unitful.Time

Function to extract a certain parameter, param, from a directory, dir, containing ERA netcdf files, for a certain timerange, dim, and convert into an axis array.

readERA(dir::String, param::String, dim::StepRange(typeof(1month)))

Function to extract a certain parameter, param, from an ERA netcdf file, for a certain timerange, dim, and convert into an axis array.

readbioclim(dir::String)

Function to extract all raster files from a specified folder directory, and convert into an axis array.

readfile(file::String)

Function to import a selected file from a path string.

readlc(dir::String)

Function to extract all raster files from a specified folder directory, and convert into an axis array.

readworldclim(dir::String)

Function to extract all raster files from a specified folder directory, and convert into an axis array.

searchdir(path,key)

Function to search a directory path using a given key string.

upresolution(data::Union{ERA, Worldclim_monthly, Worldclim_bioclim}, rescale::Int64; fn)

Function to increase the resolution of a climate dataset, by a factor, rescale.