From 4e876a092214445f09f32929705f5d745a7834d1 Mon Sep 17 00:00:00 2001
From: Daniel Vedder <daniel.vedder@idiv.de>
Date: Thu, 18 Jul 2024 16:03:44 +0200
Subject: [PATCH] Wrote skylark territory searching functions
---
CHANGELOG.md | 6 +-
src/crop/farmplot.jl | 4 +-
src/nature/individuals.jl | 13 +--
src/nature/macros.jl | 1 -
src/nature/nature.jl | 2 +-
src/nature/populations.jl | 4 +-
src/nature/species/skylark.jl | 149 +++++++++++++++++++++++++---------
7 files changed, 129 insertions(+), 50 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index aa0f220..2f9f15e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,10 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+## [1.0.0] - in planning
+
+*Aim: 3 species, 2 crop growth models, farm model, GAEC scenarios, experimental analysis*
+
## [0.6.0] - in planning
*Plan: integrate multiple crop growth models, set up first experiments*
@@ -33,7 +37,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- `EventType` renamed to `Management` for clarity
-- `insectbiomass()` uses units
### Deprecated
@@ -45,6 +48,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- all skylarks now migrate (#90)
+- `insectbiomass()` uses units
## [v0.5.1] - 13-06-2024
diff --git a/src/crop/farmplot.jl b/src/crop/farmplot.jl
index 13b7ad3..596da80 100644
--- a/src/crop/farmplot.jl
+++ b/src/crop/farmplot.jl
@@ -196,7 +196,7 @@ Return the height of the crop at this position, or nothing if there is no crop h
(utility wrapper).
"""
function cropheight(pos::Tuple{Int64,Int64}, model::SimulationModel)
- ismissing(model.landscape[pos...].fieldid) ? nothing :
+ ismissing(model.landscape[pos...].fieldid) ? 0cm : #FIXME should not return 0
model.farmplots[model.landscape[pos...].fieldid].height
end
@@ -208,7 +208,7 @@ here (utility wrapper).
"""
function cropcover(pos::Tuple{Int64,Int64}, model::SimulationModel)
#FIXME LAItotal != ground cover?
- ismissing(model.landscape[pos...].fieldid) ? nothing :
+ ismissing(model.landscape[pos...].fieldid) ? 0 : #FIXME should not return 0
model.farmplots[model.landscape[pos...].fieldid].LAItotal
end
diff --git a/src/nature/individuals.jl b/src/nature/individuals.jl
index f1f2488..5a056e7 100644
--- a/src/nature/individuals.jl
+++ b/src/nature/individuals.jl
@@ -81,10 +81,10 @@ Add the given location to the animal's territory.
"""
function occupy!(animal::Animal, model::SimulationModel, position::Tuple{Int64,Int64})
if isoccupied(model, speciesof(animal), position) #XXX should this be an error?
- @warn "Position $position is already occupied by a $(speciesof(animal))."
+ @warn "Position $position is already occupied by a $(speciesof(animal))." animal
end
- push!(animal.territories, position)
- push!(model.landscape[position...], animal.id)
+ push!(animal.territory, position)
+ push!(model.landscape[position...].territories, animal.id)
end
"""
@@ -144,7 +144,10 @@ Let the animal move a given number of steps in the given direction ("north", "no
"east", "southeast", "south", "southwest", "west", "northwest", "random").
"""
function walk!(animal::Animal, model::SimulationModel, direction::String, distance::Length=-1m)
- distance < 0m ? steps = 1 : steps = Int(floor(distance/@param(world.mapresolution)))
+ steps = 1
+ if distance > @param(world.mapresolution)
+ steps = Int(floor(distance/@param(world.mapresolution)))
+ end
if direction == "north"
shift = (0,-steps)
elseif direction == "northeast"
@@ -162,7 +165,7 @@ function walk!(animal::Animal, model::SimulationModel, direction::String, distan
elseif direction == "northwest"
shift = (-steps,-steps)
elseif direction == "random"
- shift = Tuple(@rand([-steps:steps], 2))
+ shift = Tuple(@rand(-steps:steps, 2))
else
@error "Invalid direction in @walk: "*direction
end
diff --git a/src/nature/macros.jl b/src/nature/macros.jl
index 1fa21f4..add747c 100644
--- a/src/nature/macros.jl
+++ b/src/nature/macros.jl
@@ -479,7 +479,6 @@ used nested within [`@phase`](@ref).
macro walk(args...)
#XXX add `ifempty` keyword?
:(walk!($(esc(:self)), $(esc(:model)), $(map(esc, args)...)))
- #FIXME MethodError: no method matching walk!(::Persefone.Skylark, ::AgricultureModel, ::Tuple{UnitRange{Int64}, UnitRange{Int64}}) -> due to map(esc())?
end
#TODO add own walking functions that respect habitat descriptors
diff --git a/src/nature/nature.jl b/src/nature/nature.jl
index d236343..317a19f 100644
--- a/src/nature/nature.jl
+++ b/src/nature/nature.jl
@@ -37,7 +37,7 @@ function speciesof(a::Union{Animal,Type})
# strip out the module name if necessary (`Persefone.<species>`)
(a isa Animal) && (a = typeof(a))
spstrings = split(string(a), ".")
- length(spstrings) == 1 ? spstrings[1] : spstrings[2]
+ length(spstrings) == 1 ? String(spstrings[1]) : String(spstrings[2])
end
"""
diff --git a/src/nature/populations.jl b/src/nature/populations.jl
index e47bcd2..d48d759 100644
--- a/src/nature/populations.jl
+++ b/src/nature/populations.jl
@@ -145,8 +145,8 @@ end
Test whether this location is part of the territory of an animal of the given species.
"""
function isoccupied(model::SimulationModel, species::String, position::Tuple{Int64,Int64})
- for terr in model.landscape[position...].territories
- (speciesof(model.animals[terr]) == species) && return true
+ for id in model.landscape[position...].territories
+ (speciesof(model.animals[id]) == species) && return true
end
return false
end
diff --git a/src/nature/species/skylark.jl b/src/nature/species/skylark.jl
index c564205..fd366ab 100644
--- a/src/nature/species/skylark.jl
+++ b/src/nature/species/skylark.jl
@@ -47,6 +47,7 @@ At the moment, this implementation is still in development.
const migrationmortality::Float64 = 0.33 # chance of dying during the winter
const minimumterritory = 5000m² # size of territory under ideal conditions
+ const mindistancetoedge = 60m # minimum distance of habitat to vertical structures
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
@@ -101,16 +102,20 @@ end
Males returning from migration move around to look for suitable habitats to establish a territory.
"""
@phase Skylark territorysearch begin
- #TODO
- #TODO Standorttreue
- # If we've found a territory, or the breeding season is over, move to the next phase
if !isempty(self.territory)
- @setphase(occupation)
+ @setphase(occupation) # If the male still has a territory, it is occupied again
elseif month(model.date) > self.nestingend
- @setphase(nonbreeding)
- else
- @walk("random", self.movementrange)
- #FIXME MethodError: no method matching walk!(::Persefone.Skylark, ::AgricultureModel, ::Tuple{UnitRange{Int64}, UnitRange{Int64}})
+ @setphase(nonbreeding) # If the breeding season is over, give up looking
+ else # otherwise check whether this is a suitable location
+ newterritory = findterritory(self, model)
+ if isempty(newterritory)
+ @walk("random", self.movementrange)
+ else
+ for p in newterritory
+ @occupy(p)
+ end
+ @debug("$(animalid(self)) has found a territory.")
+ end
end
end
@@ -121,7 +126,10 @@ adjusting it to new conditions when and as necessary.
@phase Skylark occupation begin
#move to a random location in the territory
@move(@rand(self.territory))
- #TODO adjust territory as needed
+ if month(model.date) > self.nestingend #XXX check that all the young have left the nest
+ @setphase(nonbreeding)
+ end
+ #TODO adjust territory as needed (e.g. once a week, or when a brood is done?)
end
"""
@@ -157,36 +165,35 @@ Females that have found a partner build a nest and lay eggs in a suitable locati
if model.date < Date(year(model.date), self.nestingbegin...)
# wait for nesting to begin, moving around in the territory
@move(@rand(@animal(self.mate).territory))
- elseif isempty(nest)
+ elseif month(model.date) > self.nestingend
+ @setphase(nonbreeding) # stop trying to nest if it's too late (should be rare)
+ elseif isempty(self.nest)
# choose site, build nest & lay eggs
for pos in @shuffle!(deepcopy(@animal(self.mate).territory))
- #TODO is this condition correct? -> needs validation!
- if (@landcover() == grass || @landcover() == soil ||
- (@landcover() == agriculture &&
- (self.nestingheight[1] <= @cropheight() <= self.nestingheight[2]) &&
- (self.nestingcover[1] <= @cropcover() <= self.nestingcover[2])))
+ if allowsnesting(self, model, pos)
@move(pos)
self.nest = pos
self.clutch = @rand(self.eggsperclutch)
- timer = self.nestbuildingtime + self.clutch # time to build + 1 day per egg laid
+ # time to build + 1 day per egg laid
+ self.timer = @rand(self.nestbuildingtime) + self.clutch
if month(model.date) == self.nestingbegin[1]
# the first nest takes twice as long to build
#XXX this may affect the first two nests
- timer += self.nestbuildingtime
+ self.timer += self.timer*2-self.clutch
end
break
end
end
- isempty(nest) && @warn("$(animalid(self)) didn't find a nesting location.")
- elseif timer == 0
+ isempty(self.nest) && @warn("$(animalid(self)) didn't find a nesting location.")
+ elseif self.timer == 0
@debug("$(animalid(self)) has laid $(self.clutch) eggs.")
@setphase(breeding)
else
self.timer -= 1
end
# tillage and harvest destroys the nest
- @respond(tillage, nest = ())
- @respond(harvesting, nest = ())
+ @respond(tillage, self.nest = ())
+ @respond(harvesting, self.nest = ())
end
"""
@@ -196,7 +203,7 @@ 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 clutch == 0 && month(model.date) <= self.nestingend
+ if self.clutch == 0 && month(model.date) <= self.nestingend
@setphase(nesting) #TODO breeding delay?
elseif month(model.date) > self.nestingend
@setphase(nonbreeding)
@@ -212,7 +219,7 @@ end
Select the dates on which this skylark will leave for / return from its migration,
based on observed migration patterns.
"""
-function migrationdates(skylark::Animal, model::SimulationModel)
+function migrationdates(skylark::Skylark, model::SimulationModel)
#TODO this ought to be temperature-dependent and dynamic
minleave = skylark.sex == female ? (September, 15) : (October, 1)
minarrive = skylark.sex == male ? (February, 15) : (March, 1)
@@ -224,29 +231,95 @@ function migrationdates(skylark::Animal, model::SimulationModel)
end
"""
- foragequality(maxcover, maxheight, position, model)
+ findterritory(skylark, model)
+
+Check whether the habitat surrounding the skylark is suitable for establishing a territory.
+If it is, return the list of coordinates that make up the new territory, else return an empty list.
+"""
+function findterritory(skylark::Skylark, model::SimulationModel)
+ effectivesize::Area = 0m² # the usable size of the territory, weighted by habitat quality
+ territory::Vector{Tuple{Int64,Int64}} = []
+ msize = size(model.landscape)
+ radius = 0
+ constrained = false
+ # Inspect the landscape in concentric circles around the individual until enough pixels have
+ # been found to provide a territory of sufficient size and quality. If there are no suitable
+ # pixels in one circle, break off the search (territories must be contiguous).
+ while !constrained && effectivesize < skylark.minimumterritory
+ constrained = true
+ if radius == 0
+ coords = [skylark.pos]
+ else # list all coordinates in the next circle...
+ coords = []
+ xrange = (skylark.pos[1]-radius, skylark.pos[1]+radius)
+ yrange = (skylark.pos[2]-radius, skylark.pos[2]+radius)
+ for x in xrange[1]:xrange[2]
+ push!(coords, (x, yrange[1]))
+ push!(coords, (x, yrange[2]))
+ end
+ for y in (yrange[1]+1):(yrange[2]-1) #avoid duplicating the corners
+ push!(coords, (y, xrange[1]))
+ push!(coords, (y, xrange[2]))
+ end
+ end
+ #FIXME some duplicates remain?
+ for c in coords # ...then inspect them
+ (c[1] <= 0 || c[2] <= 0 || c[1] > msize[1] || c[2] > msize[2]) && continue
+ (isoccupied(model, "Skylark", c)) && continue
+ quality = foragequality(skylark, model, c)
+ #XXX check for nesting habitats?
+ if quality > 0
+ constrained = false
+ push!(territory, c)
+ effectivesize += @param(world.mapresolution)^2*quality
+ end
+ end
+ radius +=1
+ end
+ constrained ? [] : territory
+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.)
"""
-function foragequality(maxcover::Float64, maxheight::Float64, position::Tuple{Int64,Int64},
- model::SimulationModel)
+function foragequality(skylark::Skylark, model::SimulationModel, pos::Tuple{Int64,Int64})
#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
+ if !(@landcover() in (grass, soil, agriculture)) ||
+ (@distanceto(forest) < skylark.mindistancetoedge) ||
+ (@distanceto(builtup) < skylark.mindistancetoedge)
+ return 0.0
+ end
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
+ 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
end
+"""
+ allowsnesting(skylark, model, pos)
+
+Check whether the given position is suitable for nesting.
+"""
+function allowsnesting(skylark::Skylark, model::SimulationModel, pos::Tuple{Int64,Int64})
+ #TODO is this condition correct? -> needs validation!
+ (@landcover() == grass ||
+ (@landcover() == agriculture &&
+ (skylark.nestingheight[1] <= @cropheight() <= skylark.nestingheight[2]) &&
+ (skylark.nestingcover[1] <= @cropcover() <= skylark.nestingcover[2]))) #&&
+ #(@distanceto(forest) < skylark.mindistancetoedge) &&
+ #(@distanceto(builtup) < skylark.mindistancetoedge)
+end
## INITIALISATION
@@ -274,9 +347,9 @@ end
@populate Skylark begin
# initialise on open land, at least 60m from vertical structures
habitat = @habitat((@landcover() == grass || @landcover() == agriculture) &&
- @distanceto(forest) >= 60m && @distanceto(builtup) >=60m)
+ @distanceto(forest) >= 60m && @distanceto(builtup) >=60m) #XXX magic numbers
initphase = nonbreeding
birthphase = nonbreeding
- indarea = 3ha
+ indarea = 3ha #XXX magic number
pairs = true
end
--
GitLab