From 7ab4db8b7552294e17dda793fc293aa49a1ca78a Mon Sep 17 00:00:00 2001
From: Daniel Vedder <daniel.vedder@idiv.de>
Date: Thu, 16 May 2024 12:43:41 +0200
Subject: [PATCH] Fixed output functions
---
src/core/simulation.jl | 2 +-
src/nature/ecologicaldata.jl | 7 +++----
src/nature/macros.jl | 14 +-------------
src/nature/nature.jl | 13 ++++++++-----
src/nature/populations.jl | 15 ++-------------
src/nature/species/wolpertinger.jl | 3 +--
6 files changed, 16 insertions(+), 38 deletions(-)
diff --git a/src/core/simulation.jl b/src/core/simulation.jl
index d6552a6..7ec91bc 100644
--- a/src/core/simulation.jl
+++ b/src/core/simulation.jl
@@ -173,7 +173,7 @@ function stepsimulation!(model::SimulationModel)
end
updatenature!(model)
updateevents!(model)
- #outputdata(model) #FIXME
+ outputdata(model)
model.date += Day(1)
model
end
diff --git a/src/nature/ecologicaldata.jl b/src/nature/ecologicaldata.jl
index 449895f..78e85b7 100644
--- a/src/nature/ecologicaldata.jl
+++ b/src/nature/ecologicaldata.jl
@@ -24,14 +24,13 @@ daily, monthly, yearly, or at the end of a simulation, depending on the paramete
`nature.popoutfreq`.
"""
function savepopulationdata(model::SimulationModel)
- #FIXME
pops = Dict{String,Int}(s=>0 for s = @param(nature.targetspecies))
for a in model.animals
isnothing(a) && continue
- pops[string(typeof(a))] += 1
+ pops[speciesof(a)] += 1
end
for m in model.migrants
- pops[string(typeof(m.first))] += 1
+ pops[speciesof(m.first)] += 1
end
data = []
for p in keys(pops)
@@ -53,7 +52,7 @@ function saveindividualdata(model::SimulationModel)
data = []
for a in model.animals
isnothing(a) && continue
- push!(data, [model.date,a.id,a.pos[1],a.pos[2],a.traits["name"],a.sex,a.age])
+ push!(data, [model.date,a.id,a.pos[1],a.pos[2],speciesof(a),a.sex,a.age])
end
data
end
diff --git a/src/nature/macros.jl b/src/nature/macros.jl
index 5d6dcd6..fd8242f 100644
--- a/src/nature/macros.jl
+++ b/src/nature/macros.jl
@@ -350,19 +350,7 @@ Return an iterator over all conspecific animals in the given radius around this
excluding itself. This can only be used nested within [`@phase`](@ref).
"""
macro neighbours(args...)
- :(neighbours($(esc(:self)), $(esc(:model)); $(map(esc, args)...)))
-end
-
-"""
- @countanimals(radius=0, species="")
-
-Count the number of animals of the given species in this location.
-This is a utility wrapper that can only be used nested within
-[`@phase`](@ref) or [`@habitat`](@ref).
-"""
-macro countanimals(args...)
- #XXX do I want/need this?
- :(countanimals($(esc(:pos)), $(esc(:model)); $(map(esc, args)...)))
+ :(neighbours($(esc(:self)), $(esc(:model)), $(map(esc, args)...)))
end
##TODO test movement macros
diff --git a/src/nature/nature.jl b/src/nature/nature.jl
index 11975b6..2742a8d 100644
--- a/src/nature/nature.jl
+++ b/src/nature/nature.jl
@@ -39,17 +39,20 @@ function speciesof(a::Animal)
end
"""
- speciestype(animal)
+ speciestype(name)
Return the Type of this species.
"""
-function speciestype(species::String)
+function speciestype(name::String)
# get the species Type from its namestring by looking in the module namespace
speciestype = nothing
- for name in names(Persefone, all=true)
- string(name) == species && (speciestype = getfield(Persefone, name))
+ for var in names(Persefone, all=true)
+ if string(var) == name && getfield(Persefone, var) isa Type
+ speciestype = getfield(Persefone, var)
+ break
+ end
end
- isnothing(speciestype) && @error("Species $species is not defined.")
+ isnothing(speciestype) && @error("Species $name is not defined.")
speciestype
end
diff --git a/src/nature/populations.jl b/src/nature/populations.jl
index e7a8818..98cece6 100644
--- a/src/nature/populations.jl
+++ b/src/nature/populations.jl
@@ -214,26 +214,15 @@ function nearby_animals(pos::Tuple{Int64,Int64}, model::SimulationModel;
end
"""
- neighbours(animal, model; radius=0)
+ neighbours(animal, model, radius=0)
Return a list of conspecific animals in the given radius around this animal, excluding itself.
"""
-function neighbours(animal::Animal, model::SimulationModel; radius::Int64=0)
+function neighbours(animal::Animal, model::SimulationModel, radius::Int64=0)
filter(a -> a.id != animal.id,
nearby_animals(animal.pos, model, radius=radius, species=speciesof(animal)))
end
-"""
- countanimals(pos, model; radius= 0, species="")
-
-Count the number of animals in this location (optionally supplying a species name and radius).
-"""
-function countanimals(pos::Tuple{Int64,Int64}, model::SimulationModel;
- radius::Int64=0, species="")
- #XXX do I want/need this?
- length(nearby_animals(pos, model, radius=radius, species=species))
-end
-
"""
followanimal!(follower, leader, model, distance=0)
diff --git a/src/nature/species/wolpertinger.jl b/src/nature/species/wolpertinger.jl
index 02ea9c4..cee2c3b 100644
--- a/src/nature/species/wolpertinger.jl
+++ b/src/nature/species/wolpertinger.jl
@@ -27,8 +27,7 @@ and occasionally reproduce by spontaneous parthenogenesis...
#walk!(animal, direction, model; ifempty=false)
end
- if @rand() < self.fecundity &&
- @countanimals(species="Wolpertinger") < self.crowding
+ if @rand() < self.fecundity && length(@neighbours(10)) < self.crowding
@reproduce()
end
--
GitLab