diff --git a/src/crop/farmplot.jl b/src/crop/farmplot.jl
index 596da80ea50f0db4bba5bdbe50da85270f99b236..359c0c00d53ac50f5614f8cd71f8f3a7faf5ffad 100644
--- a/src/crop/farmplot.jl
+++ b/src/crop/farmplot.jl
@@ -192,23 +192,23 @@ end
"""
cropheight(model, position)
-Return the height of the crop at this position, or nothing if there is no crop here
+Return the height of the crop at this position, or 0 if there is no crop here
(utility wrapper).
"""
function cropheight(pos::Tuple{Int64,Int64}, model::SimulationModel)
- ismissing(model.landscape[pos...].fieldid) ? 0cm : #FIXME should not return 0
- model.farmplots[model.landscape[pos...].fieldid].height
+ ismissing(model.landscape[pos...].fieldid) ? 0cm : #FIXME can I return something better than 0?
+ model.farmplots[model.landscape[pos...].fieldid].height*1cm #FIXME units
end
"""
cropcover(model, position)
-Return the percentage ground cover of the crop at this position, or nothing if there is no crop
+Return the percentage ground cover of the crop at this position, or 0 if there is no crop
here (utility wrapper).
"""
function cropcover(pos::Tuple{Int64,Int64}, model::SimulationModel)
#FIXME LAItotal != ground cover?
- ismissing(model.landscape[pos...].fieldid) ? 0 : #FIXME should not return 0
+ ismissing(model.landscape[pos...].fieldid) ? 0 : #FIXME can I return something better than 0?
model.farmplots[model.landscape[pos...].fieldid].LAItotal
end
diff --git a/src/nature/species/skylark.jl b/src/nature/species/skylark.jl
index 606ebc478ecad982421ba6d38cdbbd0218251cb0..6da29352cc3eed3f90ee3e2d67396db9bff86542 100644
--- a/src/nature/species/skylark.jl
+++ b/src/nature/species/skylark.jl
@@ -35,13 +35,12 @@ At the moment, this implementation is still in development.
const visionrange::Length = 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 nestlingtime::Int64 = 9 # days from hatching to leaving nest
+ const fledglingtime::Int64 = 21 # days from leaving the nest to independence
+ #XXX predation mortality should be habitat-dependent
const eggpredationmortality::Float64 = 0.03 # per-day egg mortality from predation
- 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
@@ -57,17 +56,14 @@ At the moment, this implementation is still in development.
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 #XXX ??
const nestingend::Int64 = July # last month of nesting
# individual variables
- #FIXME check what needs to be rewritten
- timer::Int64 = 0 # a count-down timer that can be used for different purposes
+ timer::Int64 = 0 # a counter that can be used for different purposes
migrationdates::Tuple = () # is defined by each individual in @create(Skylark)
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::Int64 = 0 # number of offspring in current clutch
+ clutch::Int64 = 0 # number and life stage of offspring in current clutch
end
@@ -203,8 +199,8 @@ Females that have found a partner build a nest and lay eggs in a suitable locati
self.timer -= 1
end
# tillage and harvest destroys the nest
- @respond(tillage, self.nest = ())
- @respond(harvesting, self.nest = ())
+ @respond(tillage, destroynest!(self, "tillage"))
+ @respond(harvesting, destroynest!(self, "harvesting"))
end
"""
@@ -212,12 +208,32 @@ Females that have laid eggs take care of their chicks, restarting the nesting pr
chicks are independent or in case of brood loss.
"""
@phase Skylark breeding begin
- #TODO wait for eggs to hatch & chicks to mature, checking for mortality
- # restart breeding cycle if there is time
- if self.clutch == 0 && month(model.date) <= self.nestingend
- @setphase(nesting) #TODO breeding delay?
- elseif month(model.date) > self.nestingend
- @setphase(nonbreeding)
+ #XXX Schachtelbruten - sometimes skylarks start a new nest before the previous young are gone
+ # wait for eggs to hatch & chicks to mature, checking for predation and disturbance mortality
+ self.timer += 1
+ #XXX this should be habitat-dependent!
+ if self.timer <= self.eggtime
+ @chance(self.eggpredationmortality) && destroynest!(self, "predation")
+ elseif self.timer <= self.eggtime + self.nestlingtime
+ @chance(self.nestlingpredationmortality) && destroynest!(self, "predation")
+ elseif self.timer <= self.eggtime + self.nestlingtime + self.fledglingtime
+ @chance(self.fledglingpredationmortality) && destroynest!(self, "predation")
+ else
+ # create new young, reset timer and clutch counter
+ @reproduce(self.clutch, self.mate)
+ self.clutch = 0
+ end
+ if self.clutch > 0
+ # tillage and harvest destroys the nest
+ @respond(tillage, destroynest!(self, "tillage"))
+ @respond(harvesting, destroynest!(self, "harvesting"))
+ else # restart breeding cycle if there is time
+ self.timer = 0
+ if month(model.date) <= self.nestingend
+ @setphase(nesting)
+ elseif month(model.date) > self.nestingend
+ @setphase(nonbreeding)
+ end
end
end
@@ -236,8 +252,8 @@ function migrationdates(skylark::Skylark, model::SimulationModel)
minarrive = skylark.sex == male ? (February, 15) : (March, 1)
deltaleave = @rand(0:45) #XXX ought to be normally distributed
deltaarrive = @rand(0:15) #XXX ought to be normally distributed
- leave = Date(year(model.date), minleave[1], minleave[2]) + Day(deltaleave))
- arrive = Date(year(model.date)+1, minarrive[1], minarrive[2]) + Day(deltaarrive))
+ leave = Date(year(model.date), minleave[1], minleave[2]) + Day(deltaleave)
+ arrive = Date(year(model.date)+1, minarrive[1], minarrive[2]) + Day(deltaarrive)
(leave, arrive)
end
@@ -292,7 +308,9 @@ end
foragequality(skylark, model, pos)
Calculate the relative quality of the habitat at this position for foraging.
-(Approximated from Püttmanns et al., 2021; Jeromin, 2002; Jenny, 1990b.)
+This assumes that open habitat is best (quality = 1.0), and steadily decreases as vegetation
+height and/or cover increase. (Linear regressions based on Püttmanns et al., 2021; Jeromin, 2002;
+Jenny, 1990b.)
"""
function foragequality(skylark::Skylark, model::SimulationModel, pos::Tuple{Int64,Int64})
#TODO this is a key function that needs to be validated thoroughly
@@ -301,18 +319,9 @@ function foragequality(skylark::Skylark, model::SimulationModel, pos::Tuple{Int6
(@distanceto(builtup) < skylark.mindistancetoedge)
return 0.0
end
- quality = 1.0
- f = farmplot(pos, model)
- # Assume that grass and soil have a habitat quality of 1.0. For fields, calculate quality
- # as the sum of cover quality and height quality (each modelled using a linear regression).
- if !isnothing(f)
- groundcoverfactor = x -> bounds((-1/skylark.maxforagecover)*x + 1.0, max=1.0)
- plantheightfactor = x -> bounds((-1/skylark.maxforageheight)*(x |> cm) + 1.0, max=1.0)
- #FIXME need percentage cover in FarmPlot, not LAI
- #FIXME height is currently dimensionless in FarmPlot, hence the conversion to cm
- quality = bounds(groundcoverfactor(f.LAItotal) + plantheightfactor(f.height*1cm), max=1.0)
- end
- return quality
+ groundcoverfactor = x -> bounds((-1/skylark.maxforagecover)*x + 1.0, max=1.0)
+ plantheightfactor = x -> bounds((-1/skylark.maxforageheight)*(x |> cm) + 1.0, max=1.0)
+ return bounds(groundcoverfactor(@cropcover()) + plantheightfactor(@cropheight()), max=1.0)
end
"""
@@ -324,12 +333,24 @@ function allowsnesting(skylark::Skylark, model::SimulationModel, pos::Tuple{Int6
#TODO is this condition correct? -> needs validation!
(@landcover() == grass ||
(@landcover() == agriculture &&
- (skylark.nestingheight[1] <= @cropheight() <= skylark.nestingheight[2]) &&
+ (skylark.nestingheight[1] <= (@cropheight()) <= skylark.nestingheight[2]) &&
(skylark.nestingcover[1] <= @cropcover() <= skylark.nestingcover[2]))) #&&
+ #FIXME if we add the distance requirement, females don't find a nesting spot?
#(@distanceto(forest) < skylark.mindistancetoedge) &&
#(@distanceto(builtup) < skylark.mindistancetoedge)
end
+"""
+ destroynest!(skylark, reason)
+
+Remove the skylark's nest and offspring due to disturbance or predation.
+"""
+function destroynest!(self::Skylark, reason::String)
+ self.nest = ()
+ self.clutch = 0
+ @debug("$(animalid(self)) had her nest destroyed by $reason.")
+end
+
## INITIALISATION
"""
@@ -345,7 +366,7 @@ should currently be on migration. Also sets other individual-specific variables.
@setphase(territorysearch) :
@setphase(matesearch)
@migrate(arrive)
- self.migrationdates = self.migrationdates .+ Year(1))
+ self.migrationdates = self.migrationdates .+ Year(1)
end
end