@species syntax now works as intended :-)

Translated the Wolpertinger to the new syntax, Wyvern to follow later.

src/Persephone.jl

@@ -46,7 +46,7 @@ include("nature/nature.jl")
 include("nature/lifehistory.jl")
 include("nature/ecologicaldata.jl")
 #include("nature/species/skylark.jl")
-#include("nature/species/wolpertinger.jl")
+include("nature/species/wolpertinger.jl")
 #include("nature/species/wyvern.jl")
 include("core/simulation.jl")
 

src/core/landscape.jl

+
 ### Persephone - a socio-economic-ecological model of European agricultural landscapes.
 ###
 ### This file manages the landscape maps that underlie the model.
@@ -40,7 +41,7 @@ function initlandscape()
             lc = landcover[x,y][1]
             (ismissing(lc)) && (lc = 0)
             lcv = LandCover(Int(lc/10))
-            landscape[x,y] = Pixel(lcv, farmfields[x,y][1])
+            landscape[x,y] = Pixel(lcv, farmfields[x,y][1], Vector{Symbol}())
         end
     end
     return landscape

src/nature/ecologicaldata.jl

@@ -14,7 +14,7 @@ Create output files for each data group collected by the nature model.
 function initecologicaldata()
     newdataoutput(POPFILE, "Date;Species;Abundance", savepopulationdata,
                   param("nature.popoutfreq"))
-    newdataoutput(INDFILE, "Date;ID;X;Y;Species;Sex;Age;Energy",
+    newdataoutput(INDFILE, "Date;ID;X;Y;Species;Sex;Age",
                   saveindividualdata, param("nature.indoutfreq"))
 end
 
@@ -29,7 +29,7 @@ function savepopulationdata(model::AgentBasedModel)
     pops = Dict{String,Int}(s=>0 for s = param("nature.targetspecies"))
     for a in allagents(model)
         (typeof(a) != Animal) && continue
-        pops[a.species.name] += 1
+        pops[a.traits["name"]] += 1
     end
     data = ""
     for p in keys(pops)
@@ -50,7 +50,7 @@ function saveindividualdata(model::AgentBasedModel)
     data = ""
     for a in allagents(model)
         (typeof(a) != Animal) && continue
-        entry = join([model.date,a.id,a.pos[1],a.pos[2],a.species.name,a.sex,a.age,a.energy], ";")
+        entry = join([model.date,a.id,a.pos[1],a.pos[2],a.traits["name"],a.sex,a.age], ";")
         data *= entry*"\n"
     end
     data

src/nature/species/wolpertinger.jl

@@ -5,49 +5,34 @@
 ### Although I dare say the Wolpertinger is probably rather endangered...
 ###
 
-##TODO convert to @species syntax
-
 """
-    initwolpertinger!(model)
-
-Initialise a population of Wolpertingers in random locations around the landscape.
+The wolpertinger is a mysterious beast, found in the hills and alps of Bavaria.
+It is purported to have the body of a hare, the wings of a bird, and the antlers
+of a deer.
 """
-function initwolpertinger!(model::AgentBasedModel)
-    species = getspecies("Wolpertinger")
-    x, y = size(model.landscape)
-    popsize = Int(round((x*y)*species.traits["popdensity"]))
-    for i in 1:popsize
-        add_agent!(Animal, model, species, hermaphrodite, 0, species.traits["birthenergy"])
-    end
-    @debug "Hid $(popsize) wolpertingers for gullible tourists to find."
-end
+@species Wolpertinger begin
+    popdensity = 1/100000
+    fecundity = 0.02
+    mortality = 0.01
+    maxspeed = 5
 
-"""
-    updatewolpertinger(animal, model)
+    initialise! = initrandompopulation(popdensity)
+    phase = "lifephase"
 
-Wolpertingers are rather stupid creatures, all they do is move around randomly
-and occasionally reproduce by spontaneous parthogenesis...
-"""
-function updatewolpertinger!(w::Animal, model::AgentBasedModel)
-    # walk in a random direction
-    direction = Tuple(rand([-1,1], 2))
-    speed = rand([1, trait(w, "maxspeed")])
-    for i in 1:speed
-        walk!(w, direction, model; ifempty=false)
-    end
-    w.energy -= speed
-    # reproduce every once in a blue moon
-    if rand() < trait(w, "fecundity")
-        @debug "Wolpertinger $(w.id) has reproduced."
-        add_agent!(w.pos, Animal, model, getspecies("Wolpertinger"),
-                   hermaphrodite, 0, trait(w, "birthenergy"))
+    """
+    Wolpertingers are rather stupid creatures, all they do is move around randomly
+    and occasionally reproduce by spontaneous parthogenesis...
+    """
+    @phase lifephase begin
+        direction = Tuple(rand([-1,1], 2))
+        for i in 1:rand(1:@trait(maxspeed))
+            walk!(animal, direction, model; ifempty=false)
+        end
+
+        if rand() < @trait(fecundity)
+            @reproduce
+        end
+
+        @kill @trait(mortality)
     end
 end
-
-newspecies("Wolpertinger",
-           initwolpertinger!,
-           updatewolpertinger!,
-           Dict("popdensity"=>1/10000,
-                "birthenergy"=>400,
-                "fecundity"=>0.01,
-                "maxspeed"=>5))

src/parameters.toml

@@ -18,10 +18,10 @@ startdate = 2020-01-01
 enddate = 2020-12-31
 
 [farm]
-
+farmmodel = "FieldManager" # which version of the farm model to use
 
 [nature]
-targetspecies = ["Wolpertinger", "Wyvern"] # list of target species to simulate
+targetspecies = ["Wolpertinger"] # list of target species to simulate
 popoutfreq = "daily" # output frequency population-level data, daily/monthly/yearly/end/never
 indoutfreq = "end" # output frequency individual-level data, daily/monthly/yearly/end/never