Added parent field to animals

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"]`.

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

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)

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"

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)

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

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