diff --git a/src/nature/nature.jl b/src/nature/nature.jl
index 4fca51f3ded4ee9dd79429a8dfea10d54dfe5739..92f3c6f199f9a74d496051e3278f708d9bb74c40 100644
--- a/src/nature/nature.jl
+++ b/src/nature/nature.jl
@@ -7,6 +7,7 @@
## An enum used to assign a sex to each animal
@enum Sex hermaphrodite male female
+#XXX hermaphrodite probably is not needed and its implementation is iffy
"""
Animal
@@ -24,13 +25,15 @@ i.e. the trait `phase` can be accessed and modified with `animal.phase`.)
#XXX add `phase` and `species` (rather than `name`) directly to the struct?
traits::Dict{String,Any}
energy::Union{EnergyBudget,Nothing} # DEB is optional
+ parents::Tuple{Int64,Int64} #XXX two parents for hermaphrodites?
sex::Sex
age::Int
end
# DEB is optional
Animal(id::Int64, pos::Tuple{Int64,Int64}, traits::Dict{String,Any},
- sex::Sex, age::Int) = Animal(id, pos, traits, nothing, sex, age)
+ parents::Tuple{Int64,Int64}, sex::Sex, age::Int) =
+ Animal(id, pos, traits, nothing, parents, sex, age)
# Overloading the `getproperty` and `setproperty!` methods for `Animal` allows
# us to write `animal.property` instead of `animal.traits["property"]`.
diff --git a/src/nature/populations.jl b/src/nature/populations.jl
index c0029a1c4562fa4116d0357137402f6a1381d7e1..e00d22f4e113bd0514a0a2cba72f9cce6a9d55f2 100644
--- a/src/nature/populations.jl
+++ b/src/nature/populations.jl
@@ -20,8 +20,10 @@ This can be used to create the `initialise!` variable in a species definition bl
- `popsize` determines the number of individuals that will be created. If this is zero or
negative, one individual will be created in every suitable location in the landscape.
If `popsize` is greater than the number of suitable locations, multiple individuals
- will be created in one place. (Maximum population density can be set in the habitat
- descriptor using the [`@countanimals`](@ref) macro.)
+ will be created in one place.
+
+- `popdensity`: if this is greater than zero, the chance of creating an individual (or
+ pair of individuals) at a suitable location is 1/popdensity.
- If `pairs` is true, a male and a female individual will be created in each selected
location, otherwise, only one individual will be created at a time.
@@ -35,8 +37,8 @@ This can be used to create the `initialise!` variable in a species definition bl
individual has been created and placed.
"""
function initpopulation(habitatdescriptor::Function; phase::Union{String,Nothing}=nothing,
- popsize::Int64=-1, pairs::Bool=false, asexual::Bool=false,
- initfunction::Function=(a,m)->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?
function(species::Dict{String,Any}, model::AgentBasedModel)
n = 0
@@ -47,18 +49,20 @@ function initpopulation(habitatdescriptor::Function; phase::Union{String,Nothing
while n == 0 || n < popsize
for x in @shuffle!(Vector(1:width))
for y in @shuffle!(Vector(1:height))
- if habitatdescriptor((x,y), model)
+ if habitatdescriptor((x,y), model) &&
+ (popdensity <= 0 || @chance(1/popdensity)) #XXX what if pd==0?
if pairs
- a1 = add_agent!((x,y), Animal, model,
- deepcopy(species), female, 0)
- a2 = add_agent!((x,y), Animal, model,
- deepcopy(species), male, 0)
+ a1 = add_agent!((x,y), Animal, model, deepcopy(species),
+ (-1,-1), female, 0)
+ a2 = add_agent!((x,y), Animal, model, deepcopy(species),
+ (-1, -1), male, 0)
initfunction(a1, model)
initfunction(a2, model)
n += 2
else
sex = asexual ? hermaphrodite : @rand([male, female])
- a = add_agent!((x,y),Animal,model,deepcopy(species),sex,0)
+ a = add_agent!((x,y), Animal, model, deepcopy(species),
+ (-1, -1), sex,0)
initfunction(a, model)
n += 1
end
@@ -92,16 +96,18 @@ end
#XXX initpopulation based on known occurences in real-life?
"""
- reproduce!(animal, model, n=1)
+ 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::AgentBasedModel, n::Int64=1)
+function reproduce!(animal::Animal, model::AgentBasedModel, mate::Int64, n::Int64=1)
+ (animal.sex == male) && @warn "Male $(animalid(animal)) is reproducing."
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)
- add_agent!(animal.pos, Animal, model, species, sex, 0)
+ add_agent!(animal.pos, Animal, model, species, (animal.id, mate), sex, 0)
end
@debug "$(animalid(animal)) has reproduced."
end
diff --git a/src/nature/species/wolpertinger.jl b/src/nature/species/wolpertinger.jl
index 482076348d87664e92bbc9f565fa205b014e5d5a..4f5c14ccaca850ced253110f5e9e9dea18d0fbb4 100644
--- a/src/nature/species/wolpertinger.jl
+++ b/src/nature/species/wolpertinger.jl
@@ -31,7 +31,7 @@ of a deer.
if @rand() < @trait(fecundity) &&
@countanimals(species="Wolpertinger") < @trait(crowding)
- @reproduce
+ @reproduce(-1)
end
@kill @trait(mortality)
diff --git a/src/nature/species/wyvern.jl b/src/nature/species/wyvern.jl
index eb1d9889fbe0abe7de221734bbf4d2b785301da7..7becb7120252485d245b03b9d449bcba0276fcba 100644
--- a/src/nature/species/wyvern.jl
+++ b/src/nature/species/wyvern.jl
@@ -61,7 +61,7 @@ legs, but that doesn't make it any less dangerous...
end
# reproduce every once in a blue moon
@label reproduce
- (@rand() < @trait(fecundity)) && @reproduce
+ (@rand() < @trait(fecundity)) && @reproduce(-1)
# hibernate from November to March
if monthday(model.date) == (11,1)
@trait(phase) = "winter"
diff --git a/src/parameters.toml b/src/parameters.toml
index 45a4519b968dd80730b1c485af187459b19d9624..b9539d390e8065de3bcdc6a1af40204da3239e67 100644
--- a/src/parameters.toml
+++ b/src/parameters.toml
@@ -21,9 +21,9 @@ startdate = 2022-01-01
enddate = 2022-12-31
[world]
-landcovermap = "data/regions/jena/landcover.tif" # location of the landcover map
-farmfieldsmap = "data/regions/jena/fields.tif" # location of the field geometry map
-weatherfile = "data/regions/jena/weather.csv" # location of the weather data file
+landcovermap = "data/regions/jena-small/landcover.tif" # location of the landcover map
+farmfieldsmap = "data/regions/jena-small/fields.tif" # location of the field geometry map
+weatherfile = "data/regions/jena-small/weather.csv" # location of the weather data file
[farm]
farmmodel = "FieldManager" # which version of the farm model to use (not yet implemented)
diff --git a/src/world/landscape.jl b/src/world/landscape.jl
index 4d8e28376da5e6d98eed1293dbba40920e3083e8..628781cfc84e3e3de1514536fd5c0e8fccc460b5 100644
--- a/src/world/landscape.jl
+++ b/src/world/landscape.jl
@@ -3,9 +3,9 @@
### This file manages the landscape maps that underlie the model.
###
+## IMPORTANT: do not change the order of this enum, or initlandscape() will break!
"The land cover classes encoded in the Mundialis Sentinel data."
@enum LandCover nodata forest grass water builtup soil agriculture
-## Do not change the order of this enum, or initlandscape() will break!
"The types of landscape event that can be simulated"
@enum EventType tillage sowing fertiliser pesticide harvesting
@@ -160,6 +160,7 @@ Calculate the distance from the given location to the closest habitat of the spe
Caution: can be computationally expensive!
"""
function distanceto(pos::Tuple{Int64,Int64}, model::AgentBasedModel, habitattype::LandCover)
+ #XXX allow testing for multiple habitat types?
# can't use @habitat here because nature.jl is loaded later than this file
distanceto(pos, model, function(p,m) landcover(p,m) == habitattype end)
end
diff --git a/test/nature_tests.jl b/test/nature_tests.jl
index dddbb64ada3a88773f37efcdafbfab46e518a577..ef945ffdb6e455da0f25c5943af5279b129b57ea 100644
--- a/test/nature_tests.jl
+++ b/test/nature_tests.jl
@@ -83,7 +83,7 @@ end
@debug "Animal: $animal"
if @trait(sex) == Persefone.female && @countanimals() < 3 &&
@trait(age) >= @trait(ageofmaturity) && @landcover() == Persefone.water
- @reproduce()
+ @reproduce(-1)
end
end
@phase drought begin