diff --git a/src/core/simulation.jl b/src/core/simulation.jl
index b77917b4cdd8d83f36e456938e27c5d1edaa94e2..1a6f390390e63f92fbae0cd8bd8272d962ee5559 100644
--- a/src/core/simulation.jl
+++ b/src/core/simulation.jl
@@ -59,6 +59,7 @@ Initialise a model object using a ready-made settings dict. This is
a helper function for `initialise()`.
"""
function initmodel(settings::Dict{String, Any})
+ #TODO catch exceptions and print them to the log file
#TODO remove Agents.jl-related code, reimplement this more cleanly (#72)
@debug "Initialising model object."
createdatadir(settings["core.outdir"], settings["core.overwrite"])
@@ -127,6 +128,7 @@ end
Execute one update of the model.
"""
function stepsimulation!(model::AgentBasedModel)
+ #TODO catch exceptions and print them to the log file
with_logger(model.logger) do
@info "Simulating day $(model.date)."
#TODO remove Agents.jl-related code, reimplement this more cleanly (#72)
@@ -135,6 +137,8 @@ function stepsimulation!(model::AgentBasedModel)
stepagent!(model[a], model)
catch exc
# check if the KeyError comes from the `model[a]` or the function call
+ #FIXME this also silences KeyErrors caused in the species code (e.g.
+ # by accessing dead mates) - will be fixed once I reorganise the code
isa(exc, KeyError) && isa(exc.key, Int) ? continue : throw(exc)
end
end
diff --git a/src/nature/macros.jl b/src/nature/macros.jl
index 6ca2086d267e72c429db3d6e5af3c66bc2109316..ccf9386f24e055cbd4e32a10df00b25aee6074a1 100644
--- a/src/nature/macros.jl
+++ b/src/nature/macros.jl
@@ -113,7 +113,8 @@ macro phase(name, body)
#TODO the docstrings give a lot of warnings in the log - can I fix that?
quote
Core.@__doc__ function $(esc(name))($(esc(:animal))::Animal, $(esc(:model))::AgentBasedModel)
- $(esc(:pos)) = $(esc(:animal)).pos
+ #TODO add `self` as a synonym for `animal`
+ $(esc(:pos)) = $(esc(:animal)).pos #XXX does this make sense?
#$(esc(:date)) = $(esc(:model)).date #XXX does this make sense?
$(esc(body))
end
@@ -128,8 +129,7 @@ A utility macro to quickly access an animal's trait value.
This can only be used nested within [`@phase`](@ref).
"""
macro trait(traitname)
- #TODO provide a version that can access another animal's traits
- #XXX replace with an @v macro? (shorter, and not all variables are "traits")
+ #FIXME actually, we can get rid of this altogether if we add a Python-style `self`
#XXX This would error if called in the first part of a species definition block
# (i.e. outside of a @phase block). Although this is specified in the documentation,
# it is unexpected and liable to be overlooked. Can we add a third clause to
@@ -145,7 +145,7 @@ This can only be used in a context where the `model` object is available
(e.g. nested within [`@phase`](@ref)).
"""
macro animal(id)
- :($(esc(:model))[$(id)])
+ :($(esc(:model))[$(esc(id))])
end
"""
@@ -156,7 +156,7 @@ This can only be used in a context where the `model` object is available
(e.g. nested within [`@phase`](@ref)).
"""
macro isalive(id)
- :(isalive($(id), $(esc(:model))))
+ :(isalive($(esc(id)), $(esc(:model))))
end
"""
diff --git a/src/nature/nature.jl b/src/nature/nature.jl
index 4cd5599ec034e1f7140555702cdcc472f0cd2ccd..2edc9fa9617e7e0c216ed361c6d5d061d5a933ae 100644
--- a/src/nature/nature.jl
+++ b/src/nature/nature.jl
@@ -73,7 +73,7 @@ Update an animal by one day, executing it's currently active phase function.
"""
function stepagent!(animal::Animal, model::AgentBasedModel)
animal.age += 1
- animal.traits[animal.phase](animal,model) #FIXME -> note to self: why?
+ animal.traits[animal.phase](animal,model) #FIXME -> note to self: why, what's wrong?
end
"""
@@ -106,5 +106,3 @@ function updatenature!(model::AgentBasedModel)
end
#XXX what else needs to go here?
end
-
-#TODO test migration
diff --git a/src/nature/populations.jl b/src/nature/populations.jl
index d7680ecf6f71c15cfece0be16bf03c8c09437ebf..2288ecde68081e7b59a248b60d1bdccee09ee907 100644
--- a/src/nature/populations.jl
+++ b/src/nature/populations.jl
@@ -39,7 +39,7 @@ This can be used to create the `initialise!` variable in a species definition bl
function initpopulation(habitatdescriptor::Function; phase::Union{String,Nothing}=nothing,
popsize::Int64=-1, popdensity::Int64=-1, pairs::Bool=false,
asexual::Bool=false, initfunction::Function=(a,m)->nothing)
- #TODO add a constructor function for the individual?
+ #TODO add a constructor function/macro for the individual
function(species::Dict{String,Any}, model::AgentBasedModel)
n = 0
lastn = 0
@@ -107,7 +107,7 @@ function reproduce!(animal::Animal, model::AgentBasedModel, mate::Int64, n::Int6
for i in 1:n
sex = (animal.sex == hermaphrodite) ? hermaphrodite : @rand([male, female])
# We need to generate a fresh species dict here
- species = @eval $(Symbol(animal.traits["name"]))($model)
+ species = @eval $(Symbol(animal.name))($model)
a = add_agent!(animal.pos, Animal, model, species, (animal.id, mate), sex, 0)
push!(offspring, a.id)
end
diff --git a/src/nature/species/skylark.jl b/src/nature/species/skylark.jl
index 50268688c19e2deee6d777b459d6cd514f3d697f..f79c9fea027acd6a125d0c42925af8cef7df0309 100644
--- a/src/nature/species/skylark.jl
+++ b/src/nature/species/skylark.jl
@@ -55,7 +55,8 @@ At the moment, this implementation is still in development.
# @distanceto(forest) > 5 && # at least 50m from forest edges
# @distanceto(builtup) > 5) # and from anthropogenic structures
- @initialise(habitats, popdensity=300, pairs=true, initfunction=initskylark)
+ @initialise(habitats, phase="mating", popdensity=300, pairs=true,
+ initfunction=initskylark)
"""
As an egg, simply check for mortality and hatching.
@@ -101,7 +102,7 @@ At the moment, this implementation is still in development.
@phase nonbreeding begin
# flocking behaviour - follow a random neighbour or move randomly
#TODO add feeding and mortality, respect habitat when moving
- neighbours = map(a->a.id, @neighbours(10))
+ neighbours = map(a->a.id, @neighbours(10)) #FIXME
#isempty(neighbours) ? @randomwalk(5) : @follow(@rand(neighbours), 2)
if isempty(neighbours)
@randomwalk(5)
@@ -133,17 +134,17 @@ At the moment, this implementation is still in development.
return
end
m, d = monthday(model.date)
- nest = ((m == @trait(nestingbegin)[1] && d > @trait(nestingbegin)[2]
+ nest = ((m == @trait(nestingbegin)[1] && d >= @trait(nestingbegin)[2]
&& @chance(0.05)) || (m > @trait(nestingbegin)[1]))
nest && @setphase(nestbuilding)
return
end
# look for a mate among the neighbouring birds, or move randomly
for n in @neighbours(50)
- if n.sex != @trait(sex) && n.mate == -1
+ if n.sex != @trait(sex) && n.phase == "mating" && n.mate == -1
@trait(mate) = n.id
n.mate = @trait(id)
- @debug "$(animalid(@trait(id))) and $(animalid(n.id)) have mated."
+ @debug "$(animalid(animal)) and $(animalid(n)) have mated."
return
end
end
@@ -154,26 +155,35 @@ At the moment, this implementation is still in development.
Females select a location and build a nest. Males do nothing. (Sound familiar?)
"""
@phase nestbuilding begin
+ if !@isalive(@trait(mate))
+ @setphase(nonbreeding)
+ return
+ end
if @trait(sex) == female
if isempty(@trait(nest))
# try to find a nest in the neighbourhood, or move on
- nest = @randompixel(10, @trait(habitats))
- if isnothing(nest)
- nest = ()
+ nestlocation = @randompixel(10, @trait(habitats))
+ if isnothing(nestlocation)
@randomwalk(20)
else
# if we've found a location, start the clock on the building time
# (building time doubles for the first nest of the year)
+ @trait(nest) = nestlocation
@trait(nestcompletion) = @rand(nestbuildingtime)
month(model.date) == 4 && (@trait(nestcompletion) *= 2)
+ @debug "$(animalid(animal)) is building a nest."
end
else
# wait while nest is being built, then lay eggs and go to next phase
if @trait(nestcompletion) > 0
@trait(nestcompletion) -= 1
else
+ #XXX more accurately, a female lays one egg per day, not all at once
@trait(clutch) = @reproduce(@trait(mate), @rand(eggsperclutch))
@animal(@trait(mate)).clutch = @trait(clutch)
+ for c in @trait(clutch) #FIXME find a cleaner solution for this
+ initskylark(@animal(c), model)
+ end
@setphase(breeding)
end
end
@@ -224,7 +234,7 @@ function initskylark(animal::Animal, model::AgentBasedModel)
@migrate(returndate)
end
# set individual life-history parameters that are defined as ranges for the species
- @trait(nestlingtime) = @rand(@trait(nestlingtime))
+ @trait(nestlingtime) = @rand(@trait(nestlingtime)) #FIXME no effect?
@trait(fledglingtime) = @rand(@trait(fledglingtime))
#TODO other stuff?
end
diff --git a/src/world/landscape.jl b/src/world/landscape.jl
index b324298db50e8da1f8b917e4f20cd70edf8f5ab0..220e51f8979b431d5786943845fe054759dd5040 100644
--- a/src/world/landscape.jl
+++ b/src/world/landscape.jl
@@ -184,8 +184,8 @@ habitatdescriptor (create this using [`@habitat`](@ref)).
"""
function randompixel(pos::Tuple{Int64,Int64}, model::AgentBasedModel, range::Int64=1,
habitatdescriptor::Function=(pos,model)->nothing)
- for x in @shuffle!((pos[1]-range):(pos[1]+range))
- for y in @shuffle!((pos[2]-range):(pos[2]+range))
+ for x in @shuffle!(collect((pos[1]-range):(pos[1]+range)))
+ for y in @shuffle!(collect((pos[2]-range):(pos[2]+range)))
!inbounds((x,y), model) && continue
habitatdescriptor((x,y), model) && return (x,y)
end