diff --git a/src/nature/lifehistory.jl b/src/nature/lifehistory.jl
index a8e70c00fe8c0b54563a7ca41f2008e6ae6d9c22..e80a1d9252aee85c2f5f6ddfb180264ef11157b2 100644
--- a/src/nature/lifehistory.jl
+++ b/src/nature/lifehistory.jl
@@ -1,12 +1,59 @@
### Persephone - a socio-economic-ecological model of European agricultural landscapes.
###
-### This file contains a set of utility functions needed by species.
+### This file contains a set of life-history related utility functions needed by species.
###
-#TODO initrandompopulation
+"""
+ initrandompopulation(popsize, asexual=true)
-#TODO killanimal!
+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)
+ initfunc = function(species::Dict{String,Any}, model::AgentBasedModel)
+ if popsize < 1.0
+ x, y = size(model.landscape)
+ popsize = Int(round(x*y*popsize))
+ end
+ for i in 1:popsize
+ sex = asexual ? hermaphrodite : rand([male, female])
+ add_agent!(Animal, model, species, sex, 0)
+ end
+ @debug "Initialised $(popsize) $(species["name"])s."
+ end
+ return initfunc
+end
-#TODO reproduce!
+#TODO initpopulation
-#TODO parentsalive?
+"""
+ reproduce!(animal, model, n=1)
+
+Produce one or more offspring for the given animal at its current location.
+"""
+function reproduce!(animal::Animal, model::AgentBasedModel, n::Int64=1)
+ # XXX at the moment we don't have intra-specific variation, so currently we
+ # don't need sexual recombination here
+ for i in 1:n
+ sex = animal.sex == hermaphrodite ? hermaphrodite : rand([male, female])
+ add_agent!(animal.pos, Animal, model, animal.traits, sex, 0)
+ end
+ @debug "$(animal.traits["name"]) $(animal.id) has reproduced."
+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::AgentBasedModel, probability::Float64=1.0, cause::String="")
+ if rand() < probability
+ postfix = isempty(cause) ? "." : " from $cause."
+ @debug "$(animal.traits["name"]) $(animal.id) has died$(postfix)"
+ kill_agent!(animal, model)
+ return true
+ end
+ return false
+end
diff --git a/src/nature/nature.jl b/src/nature/nature.jl
index 70c13b3f77827918fe2ba521b432760645c3d695..71dad4008376f919443ea08195a26725fae6a019 100644
--- a/src/nature/nature.jl
+++ b/src/nature/nature.jl
@@ -6,6 +6,9 @@
## 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
@@ -19,6 +22,7 @@ by trait dictionaries passed by them during initialisation.
traits::Dict{String,Any}
sex::Sex
age::Int32
+ #XXX keep track of parents and/or offspring?
end
@@ -33,7 +37,7 @@ custom syntax to describe species' biology:
```julia
@species name begin
- initialise! = initrandompopulation()
+ initialise! = initpopulation()
phase = "phase1"
...
@phase phase1 begin
@@ -51,14 +55,18 @@ life cycle (see the documentation to `@phase` for details).
There are two parameters that all species must define:
- `initialise!` should specify a function that will be used to create
the starting population for this species. This function must take
- exactly one argument (an `AgentBasedModel` object).
+ two arguments, a species dict and an `AgentBasedModel` object.
+ The easiest way to create this function is by using `initpopultion()`.
- `phase` should be a string specifying the name of the first phase
that individuals of this species will be assigned to on birth.
+
+Access to the rest of the model is given by the `model` variable (an object
+of type `AgentBasedModel`).
"""
macro species(name, body)
- funcname = "speciesfunction_"*name
+ funcname = Symbol(SPECIESPREFIX*string(name))
quote
- Core.@__doc__ function $(esc(funcname))()
+ Core.@__doc__ function $(esc(funcname))(model::AgentBasedModel)
$(esc(:name)) = string($(QuoteNode(name)))
$(esc(body))
vardict = Base.@locals
@@ -91,13 +99,14 @@ variables:
`model.landscape` (a two-dimensional array of pixels containing geographic
information).
-The utility macros `@respond`, `@trait`, and `@here` can be used within the body of
-`@phase` as short-hand for common expressions.
+Several utility macros can be used within the body of `@phase` as a short-hand for
+common expressions: `@respond`, `@trait`, `@here`, `@kill`, `@reproduce`
To transition an individual to another phase, simply redefine its phase variable:
`@trait(phase) = "newphase"`.
"""
macro phase(name, body)
+ #XXX Using an undeclared variable in the body doesn't throw an error?
:($(esc(name)) = function(animal::Animal, model::AgentBasedModel) $body end)
end
@@ -122,7 +131,11 @@ A utility macro to quickly access an animal's trait value.
This can only be used nested within `@phase`.
"""
macro trait(traitname)
- :(animal.traits[string($(QuoteNode(name)))])
+ if traitname in fieldnames(Animal)
+ :(animal.$(traitname))
+ else
+ :(animal.traits[string($(QuoteNode(traitname)))])
+ end
end
"""
@@ -135,6 +148,26 @@ macro here(property)
:(model.landscape[animal.pos...].$(property))
end
+"""
+ @kill
+
+Kill this animal. This is a thin wrapper around `kill!()`, and passes on any arguments.
+This can only be used nested within `@phase`.
+"""
+macro kill(args...)
+ :(kill!(animal, model, $(args...)))
+end
+
+"""
+ @reproduce
+
+Let this animal reproduce. This is a thin wrapper around `reproduce!()`, and passes on
+any arguments. This can only be used nested within `@phase`.
+"""
+macro reproduce(args...)
+ :(reproduce!(animal, model, $(args...)))
+end
+
### FUNCTIONS INTEGRATING THE NATURE MODEL WITH THE REST OF PERSEPHONE
@@ -156,9 +189,9 @@ 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("speciesfunction_"*s)
- species = @eval $funcname()
- species["initialise!"](model)
+ funcname = Symbol(SPECIESPREFIX*s)
+ species = @eval $funcname($model)
+ species["initialise!"](species, model)
end
# Initialise the data output
initecologicaldata()
diff --git a/src/nature/species/skylark.jl b/src/nature/species/skylark.jl
index 53a045382a40e1529bc0de5d3cd4362d08b74d49..4843816234b5afa6f9720df61a2a98d6303b7bea 100644
--- a/src/nature/species/skylark.jl
+++ b/src/nature/species/skylark.jl
@@ -8,18 +8,21 @@
@species Skylark begin
- initialise! = initrandompopulation()
- phase = "egg"
-
+ popdensity = 1/10000
lifeexpectancy = 365*5
+
eggharvestmortality = 0.9
+ eggpredationmortality = 0.1
+
+ initialise! = initrandompopulation(popsize)
+ phase = "egg"
@phase egg begin
- if !parentsalive(animal)
- killanimal(animal)
- end
+ @kill(@trait(eggpredationmortality), "predation")
- @respond harvest killanimal(animal, eggharvestmortality)
+ #TODO dies if parents die
+
+ @respond harvest @kill(@trait(eggharvestmortality), "harvest")
if animal.age == 14
@trait(phase) = "nestling"