From bd31a3e985587d868215cd870295c5243772c1f8 Mon Sep 17 00:00:00 2001
From: Daniel Vedder <daniel.vedder@idiv.de>
Date: Fri, 2 Aug 2024 23:33:54 +0200
Subject: [PATCH] Added skylark data output functions
---
src/analysis/makieplots.jl | 24 +++++++++
src/core/output.jl | 9 ++--
src/nature/ecologicaldata.jl | 94 +++++++++++++++++++++++++++++++++++
src/nature/species/skylark.jl | 8 ++-
4 files changed, 130 insertions(+), 5 deletions(-)
diff --git a/src/analysis/makieplots.jl b/src/analysis/makieplots.jl
index 7b1b901..1ec57dc 100644
--- a/src/analysis/makieplots.jl
+++ b/src/analysis/makieplots.jl
@@ -71,6 +71,30 @@ function populationtrends(model::SimulationModel)
f
end
+"""
+ skylarkpopulation(model)
+
+Plot a line graph of total population size and individual demographics of skylarks over time.
+Returns a Makie figure object.
+"""
+function skylarkpopulation(model::SimulationModel)
+ pops = model.datatables["skylark_abundance"]
+ update_theme!(palette=(color=cgrad(:seaborn_bright, 6),), cycle=[:color])
+ f = Figure()
+ dates = @param(core.startdate):@param(core.enddate)
+ axlimits = (1, length(dates), 0, maximum(pops[!,:TotalAbundance]))
+ ax = Axis(f[1,1], xlabel="Date", ylabel="Population size",
+ limits=axlimits, xticks=gettickmarks(dates))
+ lines!(f[1,1], Vector{Float32}(pops.TotalAbundance), linewidth=3, label="Total abundance")
+ lines!(f[1,1], Vector{Float32}(pops.Mating), linewidth=3, label="Mating")
+ lines!(f[1,1], Vector{Float32}(pops.Breeding), linewidth=3, label="Breeding")
+ lines!(f[1,1], Vector{Float32}(pops.Nonbreeding), linewidth=3, label="Non-breeding")
+ lines!(f[1,1], Vector{Float32}(pops.Juvenile), linewidth=3, label="Juvenile")
+ lines!(f[1,1], Vector{Float32}(pops.Migrants), linewidth=3, label="Migrants")
+ axislegend("Demographic"; position=:lt)
+ f
+end
+
"""
gettickmarks(dates)
diff --git a/src/core/output.jl b/src/core/output.jl
index a79a920..19a3743 100644
--- a/src/core/output.jl
+++ b/src/core/output.jl
@@ -158,9 +158,12 @@ struct DataOutput
header::Vector{String}
outputfunction::Function
frequency::String
- plotfunction::Union{Function,Nothing}
+ plotfunction::Union{Function,Nothing} #XXX remove this? (#81)
end
+##TODO what about output types that don't fit neatly into the standard CSV table format?
+## (e.g. end-of-run stats, map data)
+
"""
newdataoutput!(model, name, header, outputfunction, frequency)
@@ -169,7 +172,7 @@ that want to have their output functions called regularly.
"""
function newdataoutput!(model::SimulationModel, name::String, header::Vector{String},
outputfunction::Function, frequency::String,
- plotfunction::Union{Function,Nothing}=nothing)
+ plotfunction::Union{Function,Nothing}=nothing) #XXX remove this? (#81)
if !(frequency in ("daily", "monthly", "yearly", "end", "never"))
Base.error("Invalid frequency '$frequency' for $name.") #TODO replace with exception
end
@@ -235,7 +238,7 @@ end
Cycle through all data outputs and call their respective plot functions,
saving each figure to file.
"""
-function visualiseoutput(model::SimulationModel)
+function visualiseoutput(model::SimulationModel) #XXX remove this? (#81)
@debug "Visualising output."
CairoMakie.activate!() # make sure we're using Cairo
for output in model.dataoutputs
diff --git a/src/nature/ecologicaldata.jl b/src/nature/ecologicaldata.jl
index 06a2ad7..52c02e6 100644
--- a/src/nature/ecologicaldata.jl
+++ b/src/nature/ecologicaldata.jl
@@ -14,6 +14,7 @@ function initecologicaldata(model::SimulationModel)
savepopulationdata, @param(nature.popoutfreq), populationtrends)
newdataoutput!(model, "individuals", ["Date","ID","X","Y","Species","Sex","Age"],
saveindividualdata, @param(nature.indoutfreq), visualisemap)
+ initskylarkdata(model)
end
"""
@@ -58,3 +59,96 @@ function saveindividualdata(model::SimulationModel)
data
end
+
+## SKYLARK DATA OUTPUT
+
+function initskylarkdata(model::SimulationModel)
+ newdataoutput!(model, "skylark_abundance",
+ ["Date", "TotalAbundance", "Mating", "Breeding",
+ "Nonbreeding", "Juvenile", "Migrants"],
+ skylarkabundance, "daily", skylarkpopulation)
+ # newdataoutput!(model, "skylark_territories", ["Date", "ID", "X", "Y"],
+ # skylarkterritories, "monthly") #TODO add plotting function
+ newdataoutput!(model, "skylark_nests", ["Date", "ID", "X", "Y", "Landcover", "Crop"],
+ skylarknests, "monthly") #TODO add plotting function
+ # newdataoutput!(model, "skylark_mortality", ["Date", "N", "Cause"],
+ # skylarkmortality, "daily") #TODO add plotting function
+end
+
+"""
+ skylarkabundance(model)
+
+Save skylark abundance data, including total abundance and demographic data
+(abundances of breeding/non-breeding/juvenile/migrated individuals).
+"""
+function skylarkabundance(model::SimulationModel)
+ pops = Dict{String,Int}("TotalAbundance" => 0, "Mating" => 0, "Breeding" => 0,
+ "Nonbreeding" => 0, "Juvenile" => 0, "Migrants" => 0)
+ for a in model.animals
+ (isnothing(a) || speciesof(a) != "Skylark") && continue
+ pops["TotalAbundance"] += 1
+ if a.phase == nonbreeding
+ pops["Nonbreeding"] += 1
+ elseif a.phase in (territorysearch, matesearch) || (a.phase == occupation && a.mate == -1)
+ pops["Mating"] += 1
+ else
+ pops["Breeding"] += 1
+ end
+ if a.sex == female && a.clutch > 0
+ pops["TotalAbundance"] += a.clutch
+ pops["Juvenile"] += a.clutch
+ end
+ end
+ for m in model.migrants
+ if speciesof(m.first) == "Skylark"
+ pops["TotalAbundance"] += 1
+ pops["Migrants"] += 1
+ end
+ end
+ return [[model.date, pops["TotalAbundance"], pops["Mating"], pops["Breeding"],
+ pops["Nonbreeding"], pops["Juvenile"], pops["Migrants"]]]
+end
+
+"""
+ skylarkterritories(model)
+
+Return a list of all coordinates occupied by a skylark territory, and the ID of the individual
+holding the territory. WARNING: produces very big files.
+"""
+function skylarkterritories(model::SimulationModel)
+ #TODO is there a way of outputting this that takes less space? For example as a landscape-size
+ # matrix where each position is the ID of the individual occupying this pixel?
+ data = []
+ for a in model.animals
+ (isnothing(a) || a.sex != male || speciesof(a) != "Skylark" || a.phase != occupation) && continue
+ for pos in a.territory
+ push!(data, [model.date, a.id, pos[1], pos[2]])
+ end
+ end
+ data
+end
+
+"""
+ skylarknests(model)
+
+Return a list of coordinates of active skylark nests, and the habitat type they occupy.
+"""
+function skylarknests(model::SimulationModel)
+ data = []
+ for a in model.animals
+ (isnothing(a) || a.sex != female || speciesof(a) != "Skylark" || isempty(a.nest)) && continue
+ push!(data, [model.date, a.id, a.nest[1], a.nest[2],
+ landcover(a.nest, model), cropname(a.nest, model)])
+ end
+ data
+end
+
+"""
+ skylarkmortality(model)
+
+
+"""
+function skylarkmortality(model::SimulationModel)
+ #TODO
+ #XXX may require an additional feature in output.jl to account for a different output type
+end
diff --git a/src/nature/species/skylark.jl b/src/nature/species/skylark.jl
index 8f511df..d45fc07 100644
--- a/src/nature/species/skylark.jl
+++ b/src/nature/species/skylark.jl
@@ -190,11 +190,13 @@ Females that have found a partner build a nest and lay eggs in a suitable locati
@setphase(nonbreeding) # stop trying to nest if it's too late (should be rare)
elseif isempty(self.nest)
# choose site, build nest & lay eggs
+ #XXX can I find a better solution that deepcopying & shuffling to randomise the location?
for pos in @shuffle!(deepcopy(@animal(self.mate).territory))
if allowsnesting(self, model, pos)
@move(pos)
self.nest = pos
self.clutch = @rand(self.eggsperclutch)
+ #XXX all skylarks laying on the same day lay the same number of eggs? RNG?!
# time to build + 1 day per egg laid
self.timer = @rand(self.nestbuildingtime) + self.clutch
if month(model.date) == month(self.nestingbegin)
@@ -207,9 +209,9 @@ Females that have found a partner build a nest and lay eggs in a suitable locati
end
#FIXME happens quite often (probably because the crop models don't work yet, so
# all agricultural areas have height == cover == 0)
- isempty(self.nest) && @warn("$(animalid(self)) didn't find a nesting location.")
+ #isempty(self.nest) && @warn("$(animalid(self)) didn't find a nesting location.")
elseif self.timer == 0
- @debug("$(animalid(self)) has laid $(self.clutch) eggs.") #FIXME 0 eggs laid?
+ @debug("$(animalid(self)) has laid $(self.clutch) eggs.")
@setphase(breeding)
else
self.timer -= 1
@@ -224,6 +226,7 @@ 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
+ #FIXME juveniles remain much too long
#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
@@ -246,6 +249,7 @@ chicks are independent or in case of brood loss.
@respond(harvesting, destroynest!(self, "harvesting"))
else # restart breeding cycle if there is time
self.timer = 0
+ self.nest = ()
if model.date <= self.nestingend - Month(1)
@setphase(nesting)
else
--
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