From 7aa6d64a72e2d5ebb9c51727609890f8e97f5512 Mon Sep 17 00:00:00 2001
From: Daniel Vedder <daniel.vedder@idiv.de>
Date: Wed, 12 Jun 2024 11:52:44 +0200
Subject: [PATCH] Reorganised skylark species parameters
---
src/nature/species/skylark.jl | 68 ++++++++++++++++++++++-------------
src/parameters.toml | 2 +-
2 files changed, 44 insertions(+), 26 deletions(-)
diff --git a/src/nature/species/skylark.jl b/src/nature/species/skylark.jl
index c9ecca8..72e4102 100644
--- a/src/nature/species/skylark.jl
+++ b/src/nature/species/skylark.jl
@@ -3,10 +3,11 @@
### This file holds the code for the Eurasian Skylark (Alauda arvensis).
###
+#XXX global variable
skylarkhabitat = @habitat((@landcover() == grass ||
# settle on grass or arable land (but not maize)
(@landcover() == agriculture && @cropname() != "maize")) &&
- @distancetoedge() >= 5) # at least 50m from other habitats
+ @distancetoedge() > 5) # at least 50m from other habitats
#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
@@ -31,32 +32,36 @@ At the moment, this implementation is still in development.
"""
@species Skylark begin
#XXX use Unitful.jl
- eggtime::Int64 = 11 # 11 days from laying to hatching
- eggpredationmortality::Float64 = 0.03 # per-day egg mortality from predation
- nestharvestmortality::Float64 = 0.9 # egg/nestling mortality after a harvest event (XXX guess)
- nestlingtime::Union{Int64,UnitRange{Int64}} = 7:11 # 7-11 days from hatching to leaving nest
- nestlingpredationmortality::Float64 = 0.03 # per-day nestling mortality from predation
+ # species parameters
+ const eggtime::Int64 = 11 # 11 days from laying to hatching
+ const nestlingtime::UnitRange{Int64} = 7:11 # 7-11 days from hatching to leaving nest
+ const fledglingtime::UnitRange{Int64} = 25:30 # 25-30 days from hatching to independence
- fledglingtime::Union{Int64,UnitRange{Int64}} = 25:30 # 25-30 days from hatching to independence
- fledglingharvestmortality::Float64 = 0.5 # fledgling mortality after harvest
- fledglingpredationmortality::Float64 = 0.01 # per-day fledgling mortality from predation
- firstyearmortality::Float64 = 0.38 # total mortality in the first year after 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 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 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 # 2-5 eggs laid per clutch
+ const breedingdelay::Int64 = 18 # wait 18 days after hatching to start a new brood
+ const nestingend::Int64 = July # last month of nesting
- migrationdates::Tuple = () # is defined by each individual in @create(Skylark)
- migrationmortality::Float64 = 0.33 # chance of dying during the winter
+ const habitats::Function = skylarkhabitat
+ # individual variables
+ daystonextphase::Int64 = 0 # days remaining until fledging or maturity
+ 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
- nestingbegin::Tuple{Int64,Int64} = (April, 10) # begin nesting in the middle of April
- nestbuildingtime::Union{Int64,UnitRange{Int64}} = 4:5 # 4-5 days needed to build a nest (doubled for first nest)
nestcompletion::Int64 = 0 # days left until the nest is built
- eggsperclutch::Union{Int64,UnitRange{Int64}} = 2:5 # 2-5 eggs laid per clutch
clutch::Vector{Int64} = Vector{Int64}() # IDs of offspring in current clutch
- breedingdelay::Int64 = 18 # wait 18 days after hatching to start a new brood
- nestingend::Int64 = July # last month of nesting
-
- habitats::Function = skylarkhabitat
+
end
"""
@@ -66,6 +71,7 @@ As an egg, simply check for mortality and hatching.
@kill(self.eggpredationmortality, "predation")
@respond(harvesting, @kill(self.nestharvestmortality, "harvest"))
if self.age == self.eggtime
+ self.daystonextphase = @rand(self.nestlingtime)
@setphase(nestling)
end
end
@@ -77,8 +83,14 @@ As a nestling, simply check for mortality and fledging.
#TODO add feeding & growth
@kill(self.nestlingpredationmortality, "predation")
@respond(harvesting, @kill(self.nestharvestmortality, "harvest"))
- if self.age == self.nestlingtime+self.eggtime
+ # 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
@@ -90,9 +102,15 @@ check mortality.
#TODO add feeding & growth
@kill(self.fledglingpredationmortality, "predation")
@walk("random") #TODO add movement following the parents
- if self.age == self.fledglingtime+self.eggtime
+ # 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
@@ -123,6 +141,8 @@ 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)
@@ -152,6 +172,7 @@ 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)
@@ -193,7 +214,7 @@ end
Do lots of foraging (not yet implemented).
"""
@phase Skylark breeding begin
- #TODO forage (move random)
+ #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
@@ -243,9 +264,6 @@ should currently be on migration. Also sets other individual-specific variables.
model.date != @param(core.startdate) && (returndate += Year(1))
@migrate(returndate)
end
- # set individual life-history parameters that are defined as ranges for the species
- self.nestlingtime = @rand(self.nestlingtime)
- self.fledglingtime = @rand(self.fledglingtime)
#TODO other stuff?
end
diff --git a/src/parameters.toml b/src/parameters.toml
index d956e37..f9da32f 100644
--- a/src/parameters.toml
+++ b/src/parameters.toml
@@ -10,7 +10,7 @@
configfile = "src/parameters.toml" # location of the configuration file
outdir = "results" # location and name of the output folder
overwrite = "ask" # overwrite the output directory? (true/false/"ask")
-logoutput = "both" # log output to screen/file/none/both
+logoutput = "both" # log output to screen/file/none/both #XXX default "both"
csvoutput = true # save collected data in CSV files
visualise = true # generate result graphs
storedata = true # keep collected data in memory
--
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