diff --git a/src/nature/individuals.jl b/src/nature/individuals.jl
index 863bb8f82ac0d9eaf0e39422b3eb9e60957f3a4e..f1f248890de3ad7f27e9bffafd0593b3c3cd08f4 100644
--- a/src/nature/individuals.jl
+++ b/src/nature/individuals.jl
@@ -162,7 +162,7 @@ function walk!(animal::Animal, model::SimulationModel, direction::String, distan
elseif direction == "northwest"
shift = (-steps,-steps)
elseif direction == "random"
- shift = Tuple(@rand([-steps,0,steps], 2))
+ shift = Tuple(@rand([-steps:steps], 2))
else
@error "Invalid direction in @walk: "*direction
end
diff --git a/src/nature/species/skylark.jl b/src/nature/species/skylark.jl
index 6400bbcd0c4b2a549eef4d11f8ddf491544759a3..dd959c3daae80733946d4651e52a308058bc949d 100644
--- a/src/nature/species/skylark.jl
+++ b/src/nature/species/skylark.jl
@@ -3,15 +3,6 @@
### This file holds the code for the Eurasian Skylark (Alauda arvensis).
###
-#XXX global variable/function
-skylarkhabitat = @habitat((@landcover() == grass ||
- (@landcover() == agriculture && @cropname() != "maize")) &&
- @distancetoedge() > 50m)
-#XXX this ought to check for distance to forest and builtup,
-# but that's very expensive (see below)
-# @distanceto(forest) > 5 && # at least 50m from forest edges
-# @distanceto(builtup) > 5) # and from anthropogenic structures
-
"""
Skylark
@@ -19,108 +10,78 @@ skylarkhabitat = @habitat((@landcover() == grass ||
At the moment, this implementation is still in development.
**Sources:**
- - Bauer, H.-G., Bezzel, E., & Fiedler, W. (Eds.). (2012).
- Das Kompendium der Vögel Mitteleuropas: Ein umfassendes
- Handbuch zu Biologie, Gefährdung und Schutz (Einbändige
- Sonderausg. der 2., vollständig überarb. und erw. Aufl. 2005).
- AULA-Verlag
- - Glutz von Blotzheim, Urs N. (Ed.). (1985). Handbuch der
- Vögel Mitteleuropas. Bd. 10. Passeriformes (Teil 1)
- 1. Alaudidae - Hirundidae. AULA-Verlag, Wiesbaden.
+ - Bauer, H.-G., Bezzel, E., & Fiedler, W. (Eds.). (2012). Das Kompendium
+ der Vögel Mitteleuropas: Ein umfassendes Handbuch zu Biologie, Gefährdung
+ und Schutz (Einbändige Sonderausg. der 2., vollständig überarb. und erw.
+ Aufl. 2005). AULA-Verlag
+ - Delius, J. D. (1965). A Population Study of Skylarks Alauda Arvensis.
+ Ibis, 107(4), 466–492. https://doi.org/10.1111/j.1474-919X.1965.tb07332.x
+ - Donald et al. (2002). Survival rates, causes of failure and productivity
+ of Skylark Alauda arvensis nests on lowland farmland. Ibis, 144(4), 652–664.
+ https://doi.org/10.1046/j.1474-919X.2002.00101.x
+ - Glutz von Blotzheim, Urs N. (Ed.). (1985). Handbuch der Vögel Mitteleuropas.
+ Bd. 10. Passeriformes (Teil 1) 1. Alaudidae - Hirundidae. AULA-Verlag, Wiesbaden.
ISBN 3-89104-019-9
+ - Jenny, M. (1990). Territorialität und Brutbiologie der Feldlerche Alauda
+ arvensis in einer intensiv genutzten Agrarlandschaft. Journal für Ornithologie,
+ 131(3), 241–265. https://doi.org/10.1007/BF01640998
+ - Püttmanns et al. (2022). Habitat use and foraging parameters of breeding Skylarks
+ indicate no seasonal decrease in food availability in heterogeneous farmland.
+ Ecology and Evolution, 12(1), e8461. https://doi.org/10.1002/ece3.8461
"""
@species Skylark begin
# species parameters
+ const movementrange = 500m #XXX arbitrary
+ const visionrange = 200m #XXX arbitrary
+
const eggtime::Int64 = 11 # days from laying to hatching
const nestlingtime::UnitRange{Int64} = 7:11 # days from hatching to leaving nest
const fledglingtime::UnitRange{Int64} = 25:30 # days from hatching to independence
const eggpredationmortality::Float64 = 0.03 # per-day egg mortality from predation
- const nestharvestmortality::Float64 = 0.9 # egg/nestling mortality after a harvest event (XXX guess)
+ const nestharvestmortality::Float64 = 1.0 # egg/nestling mortality after a harvest event
const nestlingpredationmortality::Float64 = 0.03 # per-day nestling mortality from predation
const fledglingharvestmortality::Float64 = 0.5 # fledgling mortality after harvest
const fledglingpredationmortality::Float64 = 0.01 # per-day fledgling mortality from predation
const firstyearmortality::Float64 = 0.38 # total mortality in the first year after independence
const migrationmortality::Float64 = 0.33 # chance of dying during the winter
+ const minimumterritory = 5000m² # size of territory under ideal conditions
+ const maxforageheight = 50cm # maximum preferred vegetation height for foraging
+ const maxforagecover = 0.7 # maximum preferred vegetation cover for foraging
+ const nestingheight = (15cm, 25cm) # min and max preferred vegetation height for nesting
+ const nestingcover = (0.2, 0.5) # min and max preferred vegetation cover for nesting
+
const nestingbegin::Tuple{Int64,Int64} = (April, 10) # begin nesting in the middle of April
const nestbuildingtime::UnitRange{Int64} = 4:5 # 4-5 days needed to build a nest (doubled for first nest)
const eggsperclutch::UnitRange{Int64} = 2:5 # eggs laid per clutch
const breedingdelay::Int64 = 18 # days after hatching before starting a new brood
const nestingend::Int64 = July # last month of nesting
-
- const habitats::Function = skylarkhabitat
# individual variables
- daystonextphase::Int64 = 0 # days remaining until fledging or maturity
+ #FIXME check what needs to be rewritten
+ timer::Int64 = 0 # a count-down timer that can be used for different purposes
migrationdates::Tuple = () # is defined by each individual in @create(Skylark)
- territory::Vector = [] # pixels that this skylark claims as its territory
mate::Int64 = -1 # the agent ID of the mate (-1 if none)
nest::Tuple = () # coordinates of current nest
nestcompletion::Int64 = 0 # days left until the nest is built
- clutch::Vector{Int64} = Vector{Int64}() # IDs of offspring in current clutch
+ clutch::Int64 = 0 # number of offspring in current clutch
end
-"""
-As an egg, simply check for mortality and hatching.
-"""
-@phase Skylark egg begin
- @kill(self.eggpredationmortality, "predation")
- @respond(harvesting, @kill(self.nestharvestmortality, "harvest"))
- if self.age == self.eggtime
- self.daystonextphase = @rand(self.nestlingtime)
- @setphase(nestling)
- end
-end
-"""
-As a nestling, simply check for mortality and fledging.
-"""
-@phase Skylark nestling begin
- #TODO add feeding & growth
- @kill(self.nestlingpredationmortality, "predation")
- @respond(harvesting, @kill(self.nestharvestmortality, "harvest"))
- # if self.age == self.nestlingtime+self.eggtime
- # @setphase(fledgling)
- # end
- if self.daystonextphase == 0
- self.daystonextphase = @rand(self.fledglingtime)
- @setphase(fledgling)
- else
- self.daystonextphase -= 1
- end
-end
+## LIFE PHASES
-"""
-As a fledgling, move around a little, but mainly wait for maturity and
-check mortality.
-"""
-@phase Skylark fledgling begin
- #TODO add feeding & growth
- @kill(self.fledglingpredationmortality, "predation")
- @walk("random", 10m) #TODO add movement following the parents
- # if self.age == self.fledglingtime+self.eggtime
- # @kill(self.firstyearmortality, "first year mortality") #XXX mechanistic?
- # @setphase(nonbreeding)
- # end
- if self.daystonextphase == 0
- @kill(self.firstyearmortality, "first year mortality") #XXX mechanistic?
- @setphase(nonbreeding)
- else
- self.daystonextphase -= 1
- end
-end
+#TODO respect habitat when moving
"""
As a non-breeding adult, move around with other individuals and check for migration.
"""
@phase Skylark nonbreeding begin
# flocking behaviour - follow a random neighbour or move randomly
- #TODO add feeding and mortality, respect habitat when moving
- neighbours = @neighbours(100m) #XXX magic number
+ neighbours = @neighbours(self.visionrange) #XXX check for the closest neighbour(s)?
isempty(neighbours) ?
- @walk("random", 50m) :
- @follow(@rand(neighbours), 20m)
+ @walk("random", self.movementrange) :
+ @follow(@rand(neighbours), 30m) #XXX magic number
# check if the bird migrates
leave, arrive = self.migrationdates
month, day = monthday(model.date)
@@ -129,111 +90,72 @@ As a non-breeding adult, move around with other individuals and check for migrat
if migrate
@kill(self.migrationmortality, "migration")
returndate = Date(year(model.date)+1, arrive[1], arrive[2])
- @setphase(mating)
+ self.sex == male ?
+ @setphase(territory-search) :
+ @setphase(mate-search)
@migrate(returndate)
end
end
-"""
-Move around until a mate is found.
-"""
-@phase Skylark mating begin
- #TODO mortality and feeding
- #TODO territoriality
- # if we've found a mate, wait for nesting begin and then go to the next phase
- if self.mate != -1
- if !@isalive(self.mate)
- self.mate = -1
- return
- end
- mon, day = monthday(model.date)
- nest = ((mon == self.nestingbegin[1] && day >= self.nestingbegin[2]
- && @chance(0.05)) || (mon > self.nestingbegin[1])) #XXX why the chance?
- nest && @setphase(nestbuilding)
- return
+@phase Skylark territory-search begin
+ #TODO move around, searching for a suitable area to establish a territory
+
+ # If we've found a territory, or the breeding season is over, move to the next phase
+ if !isempty(self.territory)
+ @setphase(occupation)
+ elseif month(model.date) > nestingend
+ @setphase(nonbreeding)
+ else
+ @walk("random", self.movementrange)
end
+end
+
+@phase Skylark mate-search begin
+ #TODO move around, looking for a male with an established territory
+
# look for a mate among the neighbouring birds, or move randomly
- for n in @neighbours(500m) #XXX magic number
- if n.sex != self.sex && n.phase == mating && n.mate == -1
+ for n in @neighbours(self.visionrange)
+ if n.sex == male && n.mate == -1 && n.phase == occupation
self.mate = n.id
n.mate = self.id
@debug "$(animalid(self)) and $(animalid(n)) have mated."
- return
+ break
end
end
#@debug("$(animalid(self)) didn't find a mate.")
- if month(model.date) > self.nestingend # stop trying to find a mate if it's too late
+ if self.mate != -1
+ mon, day = monthday(model.date)
+ nest = ((mon == self.nestingbegin[1] && day >= self.nestingbegin[2]
+ && @chance(0.1)) || (mon > self.nestingbegin[1])) #XXX magic number
+ nest && @setphase(breeding)
+ elseif month(model.date) > self.nestingend # stop trying to find a mate if it's too late
@setphase(nonbreeding)
else
- @walk("random", 100m) #XXX magic number
+ @walk("random", self.movementrange)
end
end
-"""
-Females select a location and build a nest. Males do nothing. (Sound familiar?)
-"""
-@phase Skylark nestbuilding begin
- #TODO mortality and feeding
- if !@isalive(self.mate)
- self.mate = -1
- @setphase(nonbreeding)
- return
- end
- if self.sex == female
- if isempty(self.nest)
- # try to find a nest in the neighbourhood, or move on
- nestlocation = @randompixel(100m, self.habitats) #XXX magic number
- if isnothing(nestlocation)
- @walk("random", 200m) #XXX magic number
- else
- # if we've found a location, start the clock on the building time
- # (building time doubles for the first nest of the year)
- self.nest = nestlocation
- self.nestcompletion = @rand(self.nestbuildingtime)
- month(model.date) == self.nestingbegin[1] && (self.nestcompletion *= 2)
- @debug "$(animalid(self)) is building a nest."
- end
- else
- # wait while nest is being built, then lay eggs and go to next phase
- if self.nestcompletion > 0
- self.nestcompletion -= 1
- else
- #XXX more accurately, a female lays one egg per day, not all at once
- @reproduce(@rand(self.eggsperclutch),self.mate)
- @setphase(breeding)
- end
- end
- else
- # males stay near the female
- mate = @animal(self.mate)
- @follow(mate, 50m)
- mate.phase == breeding && @setphase(breeding)
- end
+@phase Skylark occupation begin
+ #move to a random location in the territory
+ @move(@rand(self.territory))
+ #TODO adjust territory as needed
end
-"""
-Do lots of foraging (not yet implemented).
-"""
@phase Skylark breeding begin
- #TODO forage (move inside the territory)
- for offspring in self.clutch
- # check if offspring are still alive and juvenile, else remove from clutch
- if !@isalive(offspring) || @animal(offspring).phase == nonbreeding
- filter!(x -> x != offspring, self.clutch)
- end
- end
- # if all young have fledged, move to nonbreeding (if it's July) or breed again
- if isempty(self.clutch)
- self.nest = ()
- if month(model.date) >= self.nestingend
- self.territory = []
- @setphase(nonbreeding)
- else
- @setphase(nestbuilding)
- end
+ if isempty(nest)
+ #TODO choose site, build nest & lay eggs
+ elseif clutch > 0
+ #TODO wait for eggs to hatch & chicks to mature, checking for mortality
+ elseif month(model.date) > self.nestingend
+ #TODO restart cycle, if time
+ @setphase(nonbreeding)
end
end
+
+
+## SUPPORTING FUNCTIONS
+
"""
migrationdates(skylark, model)
@@ -251,14 +173,40 @@ function migrationdates(skylark::Animal, model::SimulationModel)
(leave, arrive)
end
+"""
+ foragequality(maxcover, maxheight, position, model)
+
+Calculate the relative quality of the habitat at this position for foraging.
+(Approximated from Püttmanns et al., 2021; Jeromin, 2002; Jenny, 1990b.)
+"""
+function foragequality(maxcover::Float64, maxheight::Float64, position::Tuple{Int64,Int64},
+ model::SimulationModel)
+ #TODO this is a key function that needs to be validated thoroughly
+ px = model.landscape[position...]
+ !(px.landcover in (grass, soil, agriculture)) && return 0.0
+ quality = 1.0
+ if !is.missing(px.fieldid)
+ f = model.farmplots[px.fieldid]
+ groundcoverfactor = x -> bounds(-1/maxcover + 1.0, max=1.0)
+ plantheightfactor = x -> bounds(-1/maxheight + 1.0, max=1.0)
+ #FIXME need percentage cover, not LAI
+ quality = bounds(groundcoverfactor(f.LAItotal) + plantheightfactor(f.height), max=1.0)
+ else
+ @warn "No field assigned to location $position" px
+ end
+ return quality
+end
+
+
+## INITIALISATION
+
"""
Initialise a skylark individual. Selects migration dates and checks if the bird
should currently be on migration. Also sets other individual-specific variables.
"""
@create Skylark begin
@debug "Added $(animalid(self)) at $(self.pos)"
- # calculate migration dates for this individual
- self.migrationdates = migrationdates(self, model)
+ self.migrationdates = migrationdates(self, model) #XXX should be dynamic
leave, arrive = self.migrationdates
mon, day = monthday(model.date)
migrate = (((mon < arrive[1]) || (mon == arrive[1] && day < arrive[2])) ||
@@ -266,15 +214,19 @@ should currently be on migration. Also sets other individual-specific variables.
if migrate
returndate = Date(year(model.date), arrive[1], arrive[2])
model.date != @param(core.startdate) && (returndate += Year(1))
+ self.sex == male ?
+ @setphase(territory-search) :
+ @setphase(mate-search)
@migrate(returndate)
end
- #TODO other stuff?
end
@populate Skylark begin
- habitat = skylarkhabitat
- initphase = mating
- birthphase = egg
+ # initialise on open land, at least 60m from vertical structures
+ habitat = @habitat((@landcover() == grass || @landcover() == agriculture) &&
+ @distanceto(forest) >= 60m && @distanceto(builtup) >=60m)
+ initphase = nonbreeding
+ birthphase = nonbreeding
indarea = 3ha
pairs = true
end