From 0e3c37c58cfc22a0d7c24a2493569ff2108ac407 Mon Sep 17 00:00:00 2001
From: Daniel Vedder <daniel.vedder@idiv.de>
Date: Sat, 17 Dec 2022 14:15:31 +0100
Subject: [PATCH] Rewrote the wyvern
---
src/Persephone.jl | 2 +-
src/nature/lifehistory.jl | 6 +-
src/nature/nature.jl | 22 +++--
src/nature/species/wolpertinger.jl | 7 +-
src/nature/species/wyvern.jl | 128 +++++++++++++++--------------
src/parameters.toml | 7 +-
6 files changed, 91 insertions(+), 81 deletions(-)
diff --git a/src/Persephone.jl b/src/Persephone.jl
index 3a978d7..2470a0c 100644
--- a/src/Persephone.jl
+++ b/src/Persephone.jl
@@ -47,7 +47,7 @@ include("nature/lifehistory.jl")
include("nature/ecologicaldata.jl")
#include("nature/species/skylark.jl")
include("nature/species/wolpertinger.jl")
-#include("nature/species/wyvern.jl")
+include("nature/species/wyvern.jl")
include("core/simulation.jl")
end
diff --git a/src/nature/lifehistory.jl b/src/nature/lifehistory.jl
index e80a1d9..c15f759 100644
--- a/src/nature/lifehistory.jl
+++ b/src/nature/lifehistory.jl
@@ -10,7 +10,7 @@ A simplified version of `initpopulation()`. Creates a function that initialises
`popsize` individuals, spread at random across the landscape. If `popsize` is less
than 1, it is interpreted as a population density (i.e. 1 animal per `popsize` pixels).
"""
-function initrandompopulation(popsize::Float64, asexual::Bool=true)
+function initrandompopulation(popsize::Union{Int64,Float64}, asexual::Bool=true)
initfunc = function(species::Dict{String,Any}, model::AgentBasedModel)
if popsize < 1.0
x, y = size(model.landscape)
@@ -39,7 +39,7 @@ function reproduce!(animal::Animal, model::AgentBasedModel, n::Int64=1)
sex = animal.sex == hermaphrodite ? hermaphrodite : rand([male, female])
add_agent!(animal.pos, Animal, model, animal.traits, sex, 0)
end
- @debug "$(animal.traits["name"]) $(animal.id) has reproduced."
+ @debug "$(animalid(animal)) has reproduced."
end
"""
@@ -51,7 +51,7 @@ Returns true if the animal dies, false if not.
function kill!(animal::Animal, model::AgentBasedModel, probability::Float64=1.0, cause::String="")
if rand() < probability
postfix = isempty(cause) ? "." : " from $cause."
- @debug "$(animal.traits["name"]) $(animal.id) has died$(postfix)"
+ @debug "$(animalid(animal)) has died$(postfix)"
kill_agent!(animal, model)
return true
end
diff --git a/src/nature/nature.jl b/src/nature/nature.jl
index 71dad40..abc2043 100644
--- a/src/nature/nature.jl
+++ b/src/nature/nature.jl
@@ -6,9 +6,6 @@
## An enum used to assign a sex to each animal
@enum Sex hermaphrodite male female
-## This will be prepended to the names of the functions created by @species
-const SPECIESPREFIX = "speciesfunction_"
-
"""
Animal
@@ -25,6 +22,15 @@ by trait dictionaries passed by them during initialisation.
#XXX keep track of parents and/or offspring?
end
+"""
+ animalid(animal)
+
+A small utility function to return a string with the species name and ID of an animal.
+"""
+function animalid(a::Animal)
+ return "$(a.traits["name"]) $(a.id)"
+end
+
### MACROS IMPLEMENTING THE DOMAIN-SPECIFIC LANGUAGE FOR DEFINING SPECIES
@@ -64,9 +70,8 @@ Access to the rest of the model is given by the `model` variable (an object
of type `AgentBasedModel`).
"""
macro species(name, body)
- funcname = Symbol(SPECIESPREFIX*string(name))
quote
- Core.@__doc__ function $(esc(funcname))(model::AgentBasedModel)
+ Core.@__doc__ function $(esc(name))(model::AgentBasedModel)
$(esc(:name)) = string($(QuoteNode(name)))
$(esc(body))
vardict = Base.@locals
@@ -174,7 +179,7 @@ end
"""
stepagent!(animal, model)
-Update an animal by one day.
+Update an animal by one day, executing it's currently active phase function.
"""
function stepagent!(animal::Animal, model::AgentBasedModel)
animal.age += 1
@@ -188,9 +193,8 @@ Initialise the model with all simulated animal populations.
"""
function initnature!(model::AgentBasedModel)
# The config file determines which species are simulated in this run
- for s in param("nature.targetspecies")
- funcname = Symbol(SPECIESPREFIX*s)
- species = @eval $funcname($model)
+ for speciesname in param("nature.targetspecies")
+ species = @eval $(Symbol(speciesname))($model)
species["initialise!"](species, model)
end
# Initialise the data output
diff --git a/src/nature/species/wolpertinger.jl b/src/nature/species/wolpertinger.jl
index a8956f2..67a4914 100644
--- a/src/nature/species/wolpertinger.jl
+++ b/src/nature/species/wolpertinger.jl
@@ -13,8 +13,9 @@ of a deer.
@species Wolpertinger begin
popdensity = 1/100000
fecundity = 0.02
- mortality = 0.01
+ mortality = 0.015
maxspeed = 5
+ crowdingfactor = maxspeed*2
initialise! = initrandompopulation(popdensity)
phase = "lifephase"
@@ -29,7 +30,9 @@ of a deer.
walk!(animal, direction, model; ifempty=false)
end
- if rand() < @trait(fecundity)
+ #TODO density-dependent reproduction
+ #neighbours = length((n.id for n in nearby_agents(animal, model, @trait(maxspeed))))
+ if rand() < @trait(fecundity) # && neighbours < @trait(crowdingfactor)
@reproduce
end
diff --git a/src/nature/species/wyvern.jl b/src/nature/species/wyvern.jl
index 2c96df9..c852d69 100644
--- a/src/nature/species/wyvern.jl
+++ b/src/nature/species/wyvern.jl
@@ -5,75 +5,77 @@
### Thankfully, wyverns are not a species we have to manage for...
###
-##TODO convert to @species syntax
-
"""
- initwyvern!(model)
-
-Initialise a population of Wyverns in pairs locations around the landscape.
+Beware the wyvern! This evolutionary cousin of the dragon may only have two
+legs, but that doesn't make it any less dangerous...
"""
-function initwyvern!(model::AgentBasedModel)
- species = getspecies("Wyvern")
- x, y = size(model.landscape)
- for i in 1:species.traits["initpop"]
- add_agent!(Animal, model, species, hermaphrodite, 0, species.traits["birthenergy"])
- end
- @debug "$(species.traits["initpop"]) wyverns are now lying in wait in the landscape."
-end
+@species Wyvern begin
+ popsize = 10
+ fecundity = 0.02
+ maxage = 365
+ speed = 20
+ vision = 50
+ aggression = 0.2
+ huntsuccess = 0.8
-"""
- updatewyvern!(animal, model)
+ initialise! = initrandompopulation(popsize)
+ phase = "winter"
-Wyverns are ferocious hunters, scouring the landscape for their favourite
-prey: wolpertingers...
-"""
-function updatewyvern!(w::Animal, model::AgentBasedModel)
- # check if the wyvern has reached its end-of-life
- if w.age == trait(w, "maxage")
- kill_agent!(w, model)
- return
- end
- # check if a wolpertinger is in pouncing distance
- for a in nearby_agents(w, model, trait(w, "speed"))
- (a.species.name != "Wolpertinger") && continue
- move_agent!(w, a.pos, model)
- w.energy -= trait(w, "pounceenergy")
- if rand() < trait(w, "huntsuccess")
- @debug "Wyvern $(w.id) killed wolpertinger $(a.id)."
- w.energy += Int(round(a.energy/2))
- kill_agent!(a, model)
- @goto reproduce
+ """
+ Wyverns are ferocious hunters, scouring the landscape for their favourite
+ prey: wolpertingers...
+ """
+ @phase summer begin
+ for a in nearby_agents(animal, model, @trait(speed))
+ # check if a wolpertinger is in pouncing distance
+ if a.traits["name"] == "Wolpertinger"
+ move_agent!(animal, a.pos, model)
+ if rand() < @trait(huntsuccess)
+ @debug "$(animalid(animal)) killed $(animalid(a))."
+ kill_agent!(a, model)
+ @goto reproduce
+ end
+ elseif a.traits["name"] == "Wyvern" && rand() < @trait(aggression)
+ # wyverns also fight against each other if they get too close
+ move_agent!(animal, a.pos, model)
+ outcome = rand()
+ if outcome < 0.4
+ @debug "$(animalid(animal)) killed $(animalid(a)) in a fight."
+ kill_agent!(a, model)
+ elseif outcome < 0.8
+ @kill 1.0 "wounds sustained in a fight"
+ end
+ @goto reproduce
+ end
end
- end
- # check if a wolpertinger is in seeing distance, or walk in a random direction
- direction = Tuple(rand([-1,1], 2))
- for a in nearby_agents(w, model, trait(w, "vision"))
- if a.species.name == "Wolpertinger"
- direction = get_direction(w.pos, a.pos, model)
- break
+ # check if a wolpertinger is in seeing distance, or walk in a random direction
+ direction = Tuple(rand([-1,1], 2))
+ for a in nearby_agents(animal, model, @trait(vision))
+ if a.traits["name"] == "Wolpertinger"
+ direction = get_direction(animal.pos, a.pos, model)
+ break
+ end
+ end
+ for i in 1:@trait(speed)
+ walk!(animal, direction, model; ifempty=false)
+ end
+ # reproduce every once in a blue moon
+ @label reproduce
+ (rand() < @trait(fecundity)) && @reproduce
+ # hibernate from November to March
+ if monthday(model.date) == (11,1)
+ @trait(phase) = "winter"
end
- end
- for i in 1:trait(w, "speed")
- walk!(w, direction, model; ifempty=false)
- w.energy -= 1
+ (@trait(age) == maxage) && @kill(1.0, "old age")
end
- # reproduce every once in a blue moon
- @label reproduce
- if rand() < trait(w, "fecundity")
- @debug "Wyvern $(w.id) has reproduced."
- add_agent!(w.pos, Animal, model, getspecies("Wyvern"),
- hermaphrodite, 0, trait(w, "birthenergy"))
+
+ """
+ Fortunately, wyverns hibernate in winter.
+ """
+ @phase winter begin
+ # hibernate from November to March
+ if monthday(model.date) == (3,1)
+ @trait(phase) = "summer"
+ end
end
end
-
-newspecies("Wyvern",
- initwyvern!,
- updatewyvern!,
- Dict("initpop"=>100,
- "birthenergy"=>1000,
- "fecundity"=>0.01,
- "maxage"=>365,
- "speed"=>10,
- "vision"=>50,
- "pounceenergy"=>20,
- "huntsuccess"=>0.3))
diff --git a/src/parameters.toml b/src/parameters.toml
index b24fe1e..69677aa 100644
--- a/src/parameters.toml
+++ b/src/parameters.toml
@@ -15,13 +15,14 @@ loglevel = "debug" # verbosity level: "debug", "info", "quiet"
seed = 0 # seed value for the RNG (0 -> random value)
# dates to start and end the simulation
startdate = 2020-01-01
-enddate = 2020-12-31
+#enddate = 2020-01-01
+enddate = 2021-12-31
[farm]
-farmmodel = "FieldManager" # which version of the farm model to use
+farmmodel = "FieldManager" # which version of the farm model to use (not yet implemented)
[nature]
-targetspecies = ["Wolpertinger"] # list of target species to simulate
+targetspecies = ["Wolpertinger", "Wyvern"] # list of target species to simulate
popoutfreq = "daily" # output frequency population-level data, daily/monthly/yearly/end/never
indoutfreq = "end" # output frequency individual-level data, daily/monthly/yearly/end/never
--
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