Adaptations to marbled white model

In the process of validation here...

Project.toml

 name = "Persefone"
 uuid = "039acd1d-2a07-4b33-b082-83a1ff0fd136"
 authors = ["Daniel Vedder <daniel.vedder@idiv.de>"]
-version = "0.7.0"
+version = "0.8.0beta"
 
 [deps]
 AquaCrop = "8f16cebd-c0b4-44a3-857f-c101f083256c"

src/analysis/makieplots.jl

@@ -59,7 +59,7 @@ function populationtrends(model::SimulationModel)
     pops = @data("populations")
     ncolors = max(2, length(@param(nature.targetspecies)))
     update_theme!(palette=(color=cgrad(:seaborn_bright, ncolors),), cycle=[:color])
-    f = Figure()
+    f = Figure(size=(1600,800))
     dates = @param(core.startdate):@param(core.enddate)
     axlimits = (1, length(dates), 0, max(MIN_AXISLIMIT, maximum(pops[!,:Abundance]; init=0)*1.1))
     ax = Axis(f[1,1], xlabel="Date", ylabel="Population size",
@@ -144,7 +144,7 @@ Returns a Makie figure object.
 function marbledwhitepopulation(model::SimulationModel)
     !("MarbledWhite" in @param(nature.targetspecies)) && return nothing
     pops = @data("marbledwhite_abundance")
-    f = Figure()
+    f = Figure(size=(1600,800))
     dates = @param(core.startdate):@param(core.enddate)
     axlimits = (1, length(dates), 0, max(MIN_AXISLIMIT, maximum(pops[!,:TotalAbundance]; init=0)))
     ax = Axis(f[1,1], xlabel="Date", ylabel="Population size",
@@ -165,13 +165,12 @@ Plot various statistics from the marbled white model: fecundity, movement, habit
 """
 function marbledwhitelifestats(model::SimulationModel)
     !("MarbledWhite" in @param(nature.targetspecies)) && return nothing
-    f = Figure(size=(1500,800))
+    f = Figure(size=(1600,800))
     data = @data("marbledwhite_lifestats")
     n = length(data[!, "ID"])
-    # fecundity
+    # fecundity / population density / displacement
     violin(f[1,1], repeat([1], n), data[!, "Fecundity"], axis=(ylabel="Eggs/Female", xticks=([1], [""]), title="Fecundity"))
-    # movement / displacement
-    violin(f[1,2], repeat([1], n), data[!, "Daily movement"], axis=(ylabel="Meters", xticks=([1], [""]), title="Mean daily movement"))
+    violin(f[1,2], repeat([1], n), data[!, "Population density"], axis=(ylabel="Individuals/Hectare", xticks=([1], [""]), title="Population density"))
     violin(f[1,3], repeat([1], n), data[!, "Displacement"]./1000, axis=(ylabel="Kilometers", xticks=([1], [""]), title="Lifetime displacement"))
     # habitat use
     boxplot(f[2,1:3], repeat(1:6, n), collect(Iterators.flatten(zip(data[!, "Unmanaged grassland"],

src/nature/ecologicaldata.jl

@@ -138,9 +138,10 @@ function initmarbledwhitedata(model::SimulationModel)
                    ["Date", "TotalAbundance", "Eggs", "Larvae", "Pupae", "Adults"],
                    @param(nature.popoutfreq), marbledwhiteabundance, marbledwhitepopulation)
     newdataoutput!(model, "marbledwhite_lifestats",
-                   ["ID", "Year", "Fecundity", "Daily movement", "Displacement", "Unmanaged grassland",
-                    "Extensive grassland", "Fallow", "Intensive grassland", "Arable", "Other"],
-                   @param(nature.popoutfreq), nothing, marbledwhitelifestats) #TODO add
+                   ["ID", "Year", "Fecundity", "Population density",
+                    "Displacement", "Unmanaged grassland", "Extensive grassland",
+                    "Fallow", "Intensive grassland", "Arable", "Other"],
+                   @param(nature.popoutfreq), nothing, marbledwhitelifestats)
 end
 
 """

src/nature/species/marbled_white.jl

@@ -51,26 +51,26 @@
     #  see Ebert & Rennwald 1991, Gotthard et al., 2007, and Evans et al. 2019)
     const minheight = 30cm # minimum height of vegetation for egg-laying
     const maxheight = 60cm # maximum height of vegetation for egg-laying
-    const mintemp = 18 # minimum temperature for activity (°C)
-    const maxtemp = 30 # maximum temperature for activity (°C)
+    const mintemp = 17 # minimum temperature for activity (°C)
+    const maxtemp = 31 # maximum temperature for activity (°C)
 
     # movement parameters
     #FIXME these are arbitrary guesses!
-    const maxstepsperday = 80 # daily movement steps under optimal temperatures
+    const maxstepsperday = 100 # daily movement steps under optimal temperatures
     const selfavoidance = 0.9
     const habitatpreference = 0.9
     const perception = 100m # perceptual range (cf. Cant et al. 2005)
-    const socialdistancing = true # avoid pixels already occupied by conspecifics
+    const socialdistancing = false #true # avoid pixels already occupied by conspecifics
 
     # lifecycle parameters
     # (eggsperday and time parameters from Reinhardt et al. 2007)
-    const maxeggsperday = 7 # number of eggs laid under optimal conditions #TODO recalculate
+    const maxeggsperday = 6 # number of eggs laid under optimal conditions #TODO recalculate
     const eggtime = 18:22 # days as egg
     const larvatime = 290:320 # days as larva
     const pupatime = 16:29 # days as pupa
-    const adulttime = 17:34 # days as adult
+    const maxadulttime = 34 # maximum lifespan in days as adult #XXX Reinhardt et al. say 17-34
     const maturationtime = 5:8 # days from hatching to first oviposition
-    const juvenilemortality = 0.9 #0:25 # in percent (Wilson 1985, Dennis 1992) #TODO check up
+    const juvenilemortality = 0.98 #0:25 # in percent (Wilson 1985, Dennis 1992) #TODO check up
     const mowingmortality = 0.3 # juvenile mortality from mowing events
     const earliesteclosure::AnnualDate = (June, 15) # (Ebert & Rennwald 1991)
     const latesteclosure::AnnualDate = (August, 15) # (Ebert & Rennwald 1991)
@@ -85,8 +85,10 @@
     timetomaturity::Int64 = 0 # is redefined in @create
     # needed for statistics
     birthplace::Tuple{Int64,Int64} = (0,0) # is redefined in @create
-    lifestats::Dict{String,Int64} = Dict("Fecundity"=>0, "Unmanaged grassland"=>0, "Extensive grassland"=>0,
-                                         "Fallow"=>0, "Intensive grassland"=>0, "Arable"=>0, "Other"=>0)
+    lifestats::Dict{String,Int64} = Dict("Fecundity"=>0, "Neighbours"=>0,
+                                         "Unmanaged grassland"=>0, "Fallow"=>0,
+                                         "Extensive grassland"=>0, "Arable"=>0,
+                                         "Intensive grassland"=>0, "Other"=>0)
 end
 
 
@@ -166,6 +168,7 @@ weather data.
         end
     end
     # movement
+    #FIXME butterflies drift west, ending up on a lot of arable land
     path::Vector{Tuple{Int64,Int64}} = [pos]
     width, height = size(model.landscape)
     while stepsremaining > 0
@@ -189,14 +192,15 @@ weather data.
                 (c in path && @chance(self.selfavoidance)) && continue
                 (!suitablehabitat(self, model, c) && @chance(self.habitatpreference)) && continue
                 # move to the new location and record habitat stats
-                radius = self.perception / @param(world.mapresolution) # end the outer loop
                 @move(c)
                 recordmovementstats(self, model)
+                radius = Inf # end the outer loop
                 break
             end
             radius += 1
         end
         # lay an egg if possible
+        #XXX butterflies lay fewer eggs when they get older, see Gotthard et al. 2007
         if eggsremaining > 0 && suitablehabitat(self, model, pos)
             if @chance(1-self.juvenilemortality)
                 @reproduce() # only create an individual that will survive to adulthood
@@ -266,13 +270,14 @@ function recordlifestats(butterfly::MarbledWhite, model::SimulationModel)
     totalmovement = stats["Unmanaged grassland"] + stats["Extensive grassland"] +
         stats["Fallow"] + stats["Intensive grassland"] +
         stats["Arable"] + stats["Other"]
+    iszero(totalmovement) && (totalmovement = 1) # avoid division-by-zero below
     # use Pythagoras to calculate the lifetime displacement
     displacement = round(sqrt(sum(abs.(butterfly.birthplace .- butterfly.pos).^2)))
     record!(model, "marbledwhite_lifestats",
             [butterfly.id, Year(model.date),
              stats["Fecundity"],
-             # save average daily movement and lifetime displacement distances (but strip out units)
-             Int(round((totalmovement/butterfly.daysinphase[4]))*@param(world.mapresolution)/1m),
+             # save current population density and lifetime displacement distances (but strip out units)
+             countanimals(butterfly.pos, model, radius=500m, species="MarbledWhite"),
              Int(displacement*@param(world.mapresolution)/1m),
              # save percentage time spent in different habitats
              Int(round(stats["Unmanaged grassland"]/totalmovement*100)),
@@ -299,13 +304,13 @@ random, but I don't have data for that.)
     else
         self.birthdate = model.date
         if model.date <= self.earliesteclosure &&
-            model.date >= (self.latesteclosure + Day(maximum(self.adulttime)))
+            model.date >= (self.latesteclosure + Day(self.maxadulttime))
             @warn("$(animalid(self)) born outside of flying period.")
         end
     end
     # choose a normally-distributed random number of days to spend in each phase
     self.daysinphase = [@randn(self.eggtime), @randn(self.larvatime),
-                        @randn(self.pupatime), @randn(self.adulttime)]
+                        @randn(self.pupatime), @rand(1:self.maxadulttime)]
     # check whether eclosure is during the flight period, change the larval time if not
     if self.enforceflyingperiod
         eclose = self.birthdate+Day(self.daysinphase[1]+self.daysinphase[2]+self.daysinphase[3])
@@ -334,7 +339,6 @@ Initialise the marbled white population with one individual on every grassland p
     birthphase = egg
     #popsize = 200 #FIXME use something else
     indarea = 1ha # initialise 1 individual per 100 suitable pixels #XXX
-    #popsize = -1 # one individual per suitable location
     sex = female #TODO change to hermaphrodite to force all individuals to have the same sex
 end