From 74d43c052b5f85d0beaad2a1ada4163b2559ee37 Mon Sep 17 00:00:00 2001
From: Daniel Vedder <daniel.vedder@idiv.de>
Date: Wed, 17 Jul 2024 10:49:23 +0200
Subject: [PATCH] Moved some functions from populations.jl to new file
individuals.jl
---
src/Persefone.jl | 1 +
src/nature/individuals.jl | 194 +++++++++++++++++++++++++++++++++++++
src/nature/populations.jl | 195 +-------------------------------------
3 files changed, 197 insertions(+), 193 deletions(-)
create mode 100644 src/nature/individuals.jl
diff --git a/src/Persefone.jl b/src/Persefone.jl
index 6c4df60..2c4e0b6 100644
--- a/src/Persefone.jl
+++ b/src/Persefone.jl
@@ -141,6 +141,7 @@ include("nature/energy.jl")
include("nature/nature.jl")
include("nature/macros.jl")
include("nature/populations.jl")
+include("nature/individuals.jl")
include("nature/ecologicaldata.jl")
include("nature/species/skylark.jl")
include("nature/species/wolpertinger.jl")
diff --git a/src/nature/individuals.jl b/src/nature/individuals.jl
new file mode 100644
index 0000000..863bb8f
--- /dev/null
+++ b/src/nature/individuals.jl
@@ -0,0 +1,194 @@
+### Persefone.jl - a model of agricultural landscapes and ecosystems in Europe.
+###
+### This file contains life-history and other ecological functions that apply to
+### all animal individuals, such reproduction, death, and movement.
+###
+
+"""
+ reproduce!(animal, model, mate, n=1)
+
+Produce one or more offspring for the given animal at its current location.
+The `mate` argument gives the ID of the reproductive partner.
+"""
+function reproduce!(animal::Animal, model::SimulationModel,
+ n::Int64=1, mate::Int64=-1)
+ (animal.sex == male) && @warn "Male $(animalid(animal)) is reproducing."
+ for i in 1:n
+ if animal.sex == hermaphrodite
+ sex = hermaphrodite
+ else
+ sex = @rand([male, female])
+ end
+ bphase = populationparameters(typeof(animal)).birthphase
+ #TODO add DEB?
+ child = typeof(animal)(length(model.animals)+1, sex, (animal.id, mate), animal.pos, bphase)
+ push!(model.animals, child)
+ push!(animal.offspring, child.id)
+ mate > 0 && push!(model.animals[mate].offspring, child.id)
+ push!(model.landscape[child.pos...].animals, child.id)
+ create!(child, model)
+ end
+ @debug "$(animalid(animal)) has reproduced."
+end
+
+"""
+ kill!(animal, model, probability=1.0, cause="")
+
+Kill this animal, optionally with a given percentage probability.
+Returns true if the animal dies, false if not.
+"""
+function kill!(animal::Animal, model::SimulationModel,
+ probability::Float64=1.0, cause::String="")
+ if @rand() < probability
+ # remove the animal's location and territory pointers from the landscape
+ filter!(x -> x!=animal.id, model.landscape[animal.pos...].animals)
+ for pos in animal.territory
+ filter!(x -> x!=animal.id, model.landscape[pos...].territories)
+ end
+ # print the epitaph and remove the animal from the model
+ postfix = isempty(cause) ? "." : " from $cause."
+ @debug "$(animalid(animal)) has died$(postfix)"
+ model.animals[animal.id] = nothing
+ return true
+ end
+ return false
+end
+
+"""
+ migrate!(animal, model, arrival)
+
+Remove this animal from the map and add it to the migrant species pool.
+It will be returned to its current location at the specified `arrival` date.
+"""
+function migrate!(animal::Animal, model::SimulationModel, arrival::Date)
+ # keep model.migrants sorted by inserting the new migrant after migrants
+ # that will return earlier than it
+ i = findfirst(m -> m.second >= arrival, model.migrants)
+ if isnothing(i)
+ push!(model.migrants, Pair(animal, arrival))
+ else
+ insert!(model.migrants, i, Pair(animal, arrival))
+ end
+ filter!(x -> x!=animal.id, model.landscape[animal.pos...].animals)
+ model.animals[animal.id] = nothing
+ @debug "$(animalid(animal)) has migrated."
+end
+
+"""
+ occupy!(animal, model, position)
+
+Add the given location to the animal's territory.
+"""
+function occupy!(animal::Animal, model::SimulationModel, position::Tuple{Int64,Int64})
+ if isoccupied(model, speciesof(animal), position) #XXX should this be an error?
+ @warn "Position $position is already occupied by a $(speciesof(animal))."
+ end
+ push!(animal.territories, position)
+ push!(model.landscape[position...], animal.id)
+end
+
+"""
+ vacate!(animal, model, position)
+
+Remove this position from the animal's territory.
+"""
+function vacate!(animal::Animal, model::SimulationModel, position::Tuple{Int64,Int64})
+ filter!(x -> x!=position, animal.territory)
+ filter!(x -> x!=animal.id, model.landscape[position...].territories)
+end
+
+"""
+ vacate!(animal, model)
+
+Remove the animal's complete territory.
+"""
+function vacate!(animal::Animal, model::SimulationModel)
+ for pos in animal.territory
+ filter!(x -> x!=animal.id, model.landscape[pos...].territories)
+ end
+ animal.territory = Vector{Tuple{Int64,Int64}}()
+end
+
+"""
+ followanimal!(follower, leader, model, distance=0)
+
+Move the follower animal to a location near the leading animal.
+"""
+function followanimal!(follower::Animal, leader::Animal, model::SimulationModel,
+ distance::Length=0m)
+ #TODO test function
+ dist = Int(floor(distance / @param(world.mapresolution)))
+ spacing = Tuple(@rand(-dist:dist, 2))
+ targetposition = safebounds(spacing .+ leader.pos, model)
+ move!(follower, model, targetposition)
+end
+
+"""
+ move!(animal, model, position)
+
+Move the animal to the given position, making sure that this is in-bounds.
+If the position is out of bounds, the animal stops at the map edge.
+"""
+function move!(animal::Animal, model::SimulationModel, position::Tuple{Int64,Int64})
+ #XXX should this function give some sort of warning (e.g. return false)
+ # if the original position is not reachable?
+ filter!(x -> x != animal.id, model.landscape[animal.pos...].animals)
+ animal.pos = safebounds(position, model)
+ push!(model.landscape[animal.pos...].animals, animal.id)
+end
+
+"""
+ walk!(animal, model, direction, distance=1pixel)
+
+Let the animal move a given number of steps in the given direction ("north", "northeast",
+"east", "southeast", "south", "southwest", "west", "northwest", "random").
+"""
+function walk!(animal::Animal, model::SimulationModel, direction::String, distance::Length=-1m)
+ distance < 0m ? steps = 1 : steps = Int(floor(distance/@param(world.mapresolution)))
+ if direction == "north"
+ shift = (0,-steps)
+ elseif direction == "northeast"
+ shift = (steps,-steps)
+ elseif direction == "east"
+ shift = (steps,0)
+ elseif direction == "southeast"
+ shift = (steps,steps)
+ elseif direction == "south"
+ shift = (0,steps)
+ elseif direction == "southwest"
+ shift = (-steps,steps)
+ elseif direction == "west"
+ shift = (-steps,0)
+ elseif direction == "northwest"
+ shift = (-steps,-steps)
+ elseif direction == "random"
+ shift = Tuple(@rand([-steps,0,steps], 2))
+ else
+ @error "Invalid direction in @walk: "*direction
+ end
+ walk!(animal, model, shift)
+end
+
+"""
+ walk!(animal, model, direction, distance=-1)
+
+Let the animal move in the given direction, where the direction is
+defined by an (x, y) tuple to specify the shift in coordinates.
+If maxdist >= 0, move no further than the specified distance.
+"""
+function walk!(animal::Animal, model::SimulationModel, direction::Tuple{Int64,Int64},
+ maxdist::Length=-1m)
+ #TODO test
+ distance = Int(floor(maxdist/@param(world.mapresolution)))
+ if distance >= 0
+ direction[1] > distance && (direction[1] = distance)
+ direction[2] > distance && (direction[2] = distance)
+ direction[1] < -distance && (direction[1] = -distance)
+ direction[2] < -distance && (direction[2] = -distance)
+ end
+ newpos = animal.pos .+ direction
+ move!(animal, model, newpos)
+end
+
+#TODO add a walk function with a habitat descriptor
+##TODO add walktoward or similar function (incl. pathfinding?)
diff --git a/src/nature/populations.jl b/src/nature/populations.jl
index 1b2799a..e47bcd2 100644
--- a/src/nature/populations.jl
+++ b/src/nature/populations.jl
@@ -1,11 +1,9 @@
### Persefone.jl - a model of agricultural landscapes and ecosystems in Europe.
###
-### This file contains a set of utility functions for species, including initialisation,
-### reproduction, and mortality.
+### This file contains functions that apply to all animal populations, such as for
+### initialisation, or querying for neighbours.
###
-##TODO move the life-history functions into a new file `individuals.jl`
-
"""
PopInitParams
@@ -141,89 +139,6 @@ end
#XXX initpopulation with dispersal from an original source?
#XXX initpopulation based on known occurences in real-life?
-"""
- reproduce!(animal, model, mate, n=1)
-
-Produce one or more offspring for the given animal at its current location.
-The `mate` argument gives the ID of the reproductive partner.
-"""
-function reproduce!(animal::Animal, model::SimulationModel,
- n::Int64=1, mate::Int64=-1)
- (animal.sex == male) && @warn "Male $(animalid(animal)) is reproducing."
- for i in 1:n
- if animal.sex == hermaphrodite
- sex = hermaphrodite
- else
- sex = @rand([male, female])
- end
- bphase = populationparameters(typeof(animal)).birthphase
- #TODO add DEB?
- child = typeof(animal)(length(model.animals)+1, sex, (animal.id, mate), animal.pos, bphase)
- push!(model.animals, child)
- push!(animal.offspring, child.id)
- mate > 0 && push!(model.animals[mate].offspring, child.id)
- push!(model.landscape[child.pos...].animals, child.id)
- create!(child, model)
- end
- @debug "$(animalid(animal)) has reproduced."
-end
-
-"""
- kill!(animal, model, probability=1.0, cause="")
-
-Kill this animal, optionally with a given percentage probability.
-Returns true if the animal dies, false if not.
-"""
-function kill!(animal::Animal, model::SimulationModel,
- probability::Float64=1.0, cause::String="")
- if @rand() < probability
- # remove the animal's location and territory pointers from the landscape
- filter!(x -> x!=animal.id, model.landscape[animal.pos...].animals)
- for pos in animal.territory
- filter!(x -> x!=animal.id, model.landscape[pos...].territories)
- end
- # print the epitaph and remove the animal from the model
- postfix = isempty(cause) ? "." : " from $cause."
- @debug "$(animalid(animal)) has died$(postfix)"
- model.animals[animal.id] = nothing
- return true
- end
- return false
-end
-
-"""
- migrate!(animal, model, arrival)
-
-Remove this animal from the map and add it to the migrant species pool.
-It will be returned to its current location at the specified `arrival` date.
-"""
-function migrate!(animal::Animal, model::SimulationModel, arrival::Date)
- # keep model.migrants sorted by inserting the new migrant after migrants
- # that will return earlier than it
- i = findfirst(m -> m.second >= arrival, model.migrants)
- if isnothing(i)
- push!(model.migrants, Pair(animal, arrival))
- else
- insert!(model.migrants, i, Pair(animal, arrival))
- end
- filter!(x -> x!=animal.id, model.landscape[animal.pos...].animals)
- model.animals[animal.id] = nothing
- @debug "$(animalid(animal)) has migrated."
-end
-
-"""
- occupy!(animal, model, position)
-
-Add the given location to the animal's territory.
-"""
-function occupy!(animal::Animal, model::SimulationModel, position::Tuple{Int64,Int64})
- if isoccupied(model, speciesof(animal), position) #XXX should this be an error?
- @warn "Position $position is already occupied by a $(speciesof(animal))."
- end
- push!(animal.territories, position)
- push!(model.landscape[position...], animal.id)
-end
-
"""
isoccupied(model, position, species)
@@ -236,28 +151,6 @@ function isoccupied(model::SimulationModel, species::String, position::Tuple{Int
return false
end
-"""
- vacate!(animal, model, position)
-
-Remove this position from the animal's territory.
-"""
-function vacate!(animal::Animal, model::SimulationModel, position::Tuple{Int64,Int64})
- filter!(x -> x!=position, animal.territory)
- filter!(x -> x!=animal.id, model.landscape[position...].territories)
-end
-
-"""
- vacate!(animal, model)
-
-Remove the animal's complete territory.
-"""
-function vacate!(animal::Animal, model::SimulationModel)
- for pos in animal.territory
- filter!(x -> x!=animal.id, model.landscape[pos...].territories)
- end
- animal.territory = Vector{Tuple{Int64,Int64}}()
-end
-
"""
isalive(id, model)
@@ -346,87 +239,3 @@ function distanceto(pos::Tuple{Int64,Int64}, model::SimulationModel, animal::Ani
#XXX this is very imprecise because diagonal distances are not calculated trigonometrically
maximum(abs.(animal.pos .- pos)) * @param(world.mapresolution)
end
-
-"""
- followanimal!(follower, leader, model, distance=0)
-
-Move the follower animal to a location near the leading animal.
-"""
-function followanimal!(follower::Animal, leader::Animal, model::SimulationModel,
- distance::Length=0m)
- #TODO test function
- dist = Int(floor(distance / @param(world.mapresolution)))
- spacing = Tuple(@rand(-dist:dist, 2))
- targetposition = safebounds(spacing .+ leader.pos, model)
- move!(follower, model, targetposition)
-end
-
-"""
- move!(animal, model, position)
-
-Move the animal to the given position, making sure that this is in-bounds.
-If the position is out of bounds, the animal stops at the map edge.
-"""
-function move!(animal::Animal, model::SimulationModel, position::Tuple{Int64,Int64})
- #XXX should this function give some sort of warning (e.g. return false)
- # if the original position is not reachable?
- filter!(x -> x != animal.id, model.landscape[animal.pos...].animals)
- animal.pos = safebounds(position, model)
- push!(model.landscape[animal.pos...].animals, animal.id)
-end
-
-"""
- walk!(animal, model, direction, distance=1pixel)
-
-Let the animal move a given number of steps in the given direction ("north", "northeast",
-"east", "southeast", "south", "southwest", "west", "northwest", "random").
-"""
-function walk!(animal::Animal, model::SimulationModel, direction::String, distance::Length=-1m)
- distance < 0m ? steps = 1 : steps = Int(floor(distance/@param(world.mapresolution)))
- if direction == "north"
- shift = (0,-steps)
- elseif direction == "northeast"
- shift = (steps,-steps)
- elseif direction == "east"
- shift = (steps,0)
- elseif direction == "southeast"
- shift = (steps,steps)
- elseif direction == "south"
- shift = (0,steps)
- elseif direction == "southwest"
- shift = (-steps,steps)
- elseif direction == "west"
- shift = (-steps,0)
- elseif direction == "northwest"
- shift = (-steps,-steps)
- elseif direction == "random"
- shift = Tuple(@rand([-steps,0,steps], 2))
- else
- @error "Invalid direction in @walk: "*direction
- end
- walk!(animal, model, shift)
-end
-
-"""
- walk!(animal, model, direction, distance=-1)
-
-Let the animal move in the given direction, where the direction is
-defined by an (x, y) tuple to specify the shift in coordinates.
-If maxdist >= 0, move no further than the specified distance.
-"""
-function walk!(animal::Animal, model::SimulationModel, direction::Tuple{Int64,Int64},
- maxdist::Length=-1m)
- #TODO test
- distance = Int(floor(maxdist/@param(world.mapresolution)))
- if distance >= 0
- direction[1] > distance && (direction[1] = distance)
- direction[2] > distance && (direction[2] = distance)
- direction[1] < -distance && (direction[1] = -distance)
- direction[2] < -distance && (direction[2] = -distance)
- end
- newpos = animal.pos .+ direction
- move!(animal, model, newpos)
-end
-
-#TODO add a walk function with a habitat descriptor
-##TODO add walktoward or similar function (incl. pathfinding?)
--
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