Added stats recording for the marbled white

src/nature/ecologicaldata.jl

@@ -137,11 +137,10 @@ function initmarbledwhitedata(model::SimulationModel)
     newdataoutput!(model, "marbledwhite_abundance",
                    ["Date", "TotalAbundance", "Eggs", "Larvae", "Pupae", "Adults"],
                    @param(nature.popoutfreq), marbledwhiteabundance, marbledwhitepopulation)
-    # newdataoutput!(model, "marbledwhite_territories", ["Date", "ID", "X", "Y"],
-    #                marbledwhiteterritories, "monthly") #TODO add plotting function
-    # newdataoutput!(model, "marbledwhite_breeding",
-    #                ["Date", "Female", "Male", "X", "Y", "Landcover", "Crop", "Territory"],
-    #                @param(nature.popoutfreq), nothing, marbledwhitestats) #TODO add
+    newdataoutput!(model, "marbledwhite_lifestats",
+                   ["ID", "Fecundity", "Daily movement", "Displacement", "Unmanaged grassland",
+                    "Extensive grassland", "Fallow", "Intensive grassland", "Arable", "Other"],
+                   @param(nature.popoutfreq), nothing, marbledwhitelifestats) #TODO add
 end
 
 """

src/nature/species/marbled_white.jl

@@ -3,10 +3,6 @@
 ### This file holds the code for the Marbled White (Melanargia galathea).
 ###
 
-##TODO
-## - population initialisation
-## - agglomeration?
-
 
 """
     Marbled White
@@ -41,6 +37,8 @@
     - Roy et al. (2001). Butterfly numbers and weather: Predicting historical
       trends in abundance and the future effects of climate change. Journal of
       Animal Ecology, 70(2), 201–217. https://doi.org/10.1111/j.1365-2656.2001.00480.x
+    - Schulte et al. (2007). Die Tagfalter der Pfalz—Band 2. Gesellschaft für
+      Naturschutz und Ornithologie Rheinland-Pfalz.
     - Vandewoestijne et al. (2004). Dispersal, landscape occupancy and population
       structure in the butterfly Melanargia galathea. Basic and Applied Ecology,
       5(6), 581–591. https://doi.org/10.1016/j.baae.2004.07.004
@@ -62,26 +60,32 @@
     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
 
     # lifecycle parameters
     # (eggsperday and time parameters from Reinhardt et al. 2007)
-    const maxeggsperday = 15 # number of eggs laid under optimal conditions
+    const maxeggsperday = 8 # 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 maturationtime = 5:8 # days from hatching to first oviposition
-    const juvenilesurvival = 0:25 # in percent (Wilson 1985, Dennis 1992)
+    const maturationtime = 5:8 # days from hatching to first oviposition #FIXME include
+    const juvenilesurvival = 0:5 #0:25 # in percent (Wilson 1985, Dennis 1992)
+    #TODO add mowing mortality
     const earliesteclosure::AnnualDate = (June, 15) # (Ebert & Rennwald 1991)
     const latesteclosure::AnnualDate = (August, 15) # (Ebert & Rennwald 1991)
     
     const enforceflyingperiod = true # make sure all pupa eclose in the flying period?
 
     ## INDIVIDUAL VARIABLES
+    # life-history related
     birthdate::Date = Date(2000, July, 1) # is redefined in @create
     # how many days this individual spends in each phase
     daysinphase::Vector{Int64} = [20, 300, 19, 25] # is redefined in @create
-    # following::Int64 = -1 # ID of the individual being followed #XXX include this?
+    # 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)
 end
 
 
@@ -124,7 +128,8 @@ Adults move a given number of steps each day, depending on the temperature (see
 Each step, an individual scans its surroundings in concentric circles, looking for
 the closest spot that offers suitable habitat which it hasn't visited today. (Depending
 on the `habitatpreference` and `selfavoidance` parameters, spots that are not suitable
-habitat or have been visited before may also be selected.) After each step, if it
+habitat or have been visited before may also be selected.) If `socialdistancing` is true,
+spots that are already occupied by a conspecific are avoided. After each step, if it
 is in a suitable habitat, the individual lays an egg, up to `maxeggsperday` (depending
 on temperature, see below).
 
@@ -146,6 +151,7 @@ weather data.
     opttemp = (self.mintemp + self.maxtemp)/2
     optimality = bounds(1 - (abs(opttemp-@maxtemp()) / (opttemp-self.mintemp)))
     stepsremaining::Int64 = Int(round(self.maxstepsperday*optimality))
+    #FIXME consider maturationtime
     eggsremaining::Int64 = self.maxeggsperday
     if @maxtemp() < opttemp || @maxtemp() > self.maxtemp
         eggsremaining = Int(round(self.maxeggsperday*optimality))
@@ -168,11 +174,15 @@ weather data.
                 push!(coords, (y, xrange[2]))
             end
             for c in @shuffle!(coords)
+                # ignore undesirable habitats
                 (c[1] <= 0 || c[2] <= 0 || c[1] > width || c[2] > height) && continue
+                (self.socialdistancing && countanimals(c, model, species="MarbledWhite") > 0) && continue
                 (c in path && @chance(self.selfavoidance)) && continue
                 (!suitablehabitat(self, model, c) && @chance(self.habitatpreference)) && continue
-                radius = self.perception / @param(world.mapresolution)
+                # move to the new location and record habitat stats
+                radius = self.perception / @param(world.mapresolution) # end the outer loop
                 @move(c)
+                recordmovementstats(self, model)
                 break
             end
             radius += 1
@@ -182,13 +192,16 @@ weather data.
             if @chance(@randn(self.juvenilesurvival)/100)
                 @reproduce() # only create an individual that will survive to adulthood
             end
+            self.lifestats["Fecundity"] += 1
             eggsremaining -= 1
         end
         push!(path, self.pos)
         stepsremaining -= 1
     end
+    #XXX record daily displacement?
     # die once the lifespan has been reached
     if self.age >= sum(self.daysinphase)
+        recordlifestats(self, model)
         @kill()
     end
 end
@@ -210,6 +223,56 @@ function suitablehabitat(butterfly::MarbledWhite, model::SimulationModel, pos::T
         @cropheight() <= butterfly.maxheight)))
 end
 
+"""
+    recordmovementstats(butterfly, model)
+
+Record the habitat category of the butterfly's current location in its life stats.
+"""
+function recordmovementstats(butterfly::MarbledWhite, model::SimulationModel)
+    pos = butterfly.pos
+    if @cropname() == "permanent grassland (low yield)"
+        butterfly.lifestats["Extensive grassland"] +=1
+    elseif @cropname() == "permanent grassland (grazed)"
+        butterfly.lifestats["Intensive grassland"] +=1
+    elseif @cropname() == "set-aside"
+        butterfly.lifestats["Fallow"] +=1
+    elseif @cropname() == ""
+        if @landcover() == "grass"
+            butterfly.lifestats["Unmanaged grassland"] +=1
+        else
+            butterfly.lifestats["Other"] +=1
+        end
+    else
+        butterfly.lifestats["Arable"] += 1
+    end
+end
+
+"""
+    recordlifestats(butterfly, model)
+
+Save this butterfly's life stats to file.
+"""
+function recordlifestats(butterfly::MarbledWhite, model::SimulationModel)
+    stats = butterfly.lifestats
+    totalmovement = stats["Unmanaged grassland"] + stats["Extensive grassland"] +
+        stats["Fallow"] + stats["Intensive grassland"] +
+        stats["Arable"] + stats["Other"]
+    # use Pythagoras to calculate the lifetime displacement
+    displacement = round(sqrt(sum(abs.(butterfly.birthplace .- butterfly.pos).^2)))
+    record!(model, "marbledwhite_lifestats",
+            [butterfly.id,
+             stats["Fecundity"],
+             # save average daily movement and lifetime displacement distances (but strip out units)
+             Int(round((totalmovement/butterfly.daysinphase[4]))*@param(world.mapresolution)/1m),
+             Int(displacement*@param(world.mapresolution)/1m),
+             # save percentage time spent in different habitats
+             Int(round(stats["Unmanaged grassland"]/totalmovement*100)),
+             Int(round(stats["Extensive grassland"]/totalmovement*100)),
+             Int(round(stats["Fallow"]/totalmovement*100)),
+             Int(round(stats["Intensive grassland"]/totalmovement*100)),
+             Int(round(stats["Arable"]/totalmovement*100)),
+             Int(round(stats["Other"]/totalmovement*100))])
+end
 
 ## INITIALISATION
 
@@ -238,15 +301,16 @@ random, but I don't have data for that.)
     if self.enforceflyingperiod
         eclose = self.birthdate+Day(self.daysinphase[1]+self.daysinphase[2]+self.daysinphase[3])
         if eclose < self.earliesteclosure
-            diff = @thisyear(self.earliesteclosure) - eclose
+            diff = @nextyear(self.earliesteclosure) - eclose
             self.daysinphase[2] += diff.value
             @debug("Increased larval time by $(diff) to stay in flying period.")
         elseif eclose > self.latesteclosure
-            diff = eclose - @thisyear(self.latesteclosure)
+            diff = eclose - @nextyear(self.latesteclosure)
             self.daysinphase[2] -= diff.value
             @debug("Reduced larval time by $(diff) to stay in flying period.")
         end
     end
+    self.birthplace = self.pos
 end
 
 """