From b32fc6223e7b348e09d3b6f7559b9b6b2d739b80 Mon Sep 17 00:00:00 2001
From: Daniel Vedder <daniel.vedder@idiv.de>
Date: Wed, 7 Aug 2024 10:52:37 +0200
Subject: [PATCH] Added mortality data output
---
src/core/output.jl | 10 +++++-----
src/nature/ecologicaldata.jl | 1 +
src/nature/individuals.jl | 1 +
src/nature/macros.jl | 21 +++++++++++++++++++++
src/nature/species/skylark.jl | 29 ++++++++++++++++++-----------
5 files changed, 46 insertions(+), 16 deletions(-)
diff --git a/src/core/output.jl b/src/core/output.jl
index 555c4be..d59eb3d 100644
--- a/src/core/output.jl
+++ b/src/core/output.jl
@@ -194,7 +194,7 @@ function newdataoutput!(model::SimulationModel, name::String,
end
end
end
- ndo = DataOutput(frequency, [[]], df, outputfunction, plotfunction)
+ ndo = DataOutput(frequency, [], df, outputfunction, plotfunction)
model.dataoutputs[name] = ndo
end
@@ -221,7 +221,7 @@ function outputdata(model::SimulationModel, force=false)
(output.frequency == "yearly" && isnextyear(model.date)) ||
(output.frequency == "end" && model.date == @param(core.enddate))
!isnothing(output.outputfunction) && (output.databuffer = output.outputfunction(model))
- isempty(output.databuffer) && continue
+ (isempty(output.databuffer) || output.databuffer == [[]]) && continue
if @param(core.csvoutput)
open(joinpath(@param(core.outdir), o*".csv"), "a") do f
for row in output.databuffer
@@ -234,17 +234,17 @@ function outputdata(model::SimulationModel, force=false)
push!(output.datastore, row)
end
end
- output.databuffer = [[]]
+ output.databuffer = []
end
end
end
"""
- record(model, outputname, data)
+ record!(model, outputname, data)
Append an observation vector to the given output.
"""
-function record(model::SimulationModel, outputname::String, data::Vector)
+function record!(model::SimulationModel, outputname::String, data::Vector)
push!(model.dataoutputs[outputname].databuffer, data)
end
diff --git a/src/nature/ecologicaldata.jl b/src/nature/ecologicaldata.jl
index c350b99..8f0b7e8 100644
--- a/src/nature/ecologicaldata.jl
+++ b/src/nature/ecologicaldata.jl
@@ -14,6 +14,7 @@ function initecologicaldata(model::SimulationModel)
@param(nature.popoutfreq), savepopulationdata, populationtrends)
newdataoutput!(model, "individuals", ["Date","ID","X","Y","Species","Sex","Age"],
@param(nature.indoutfreq), saveindividualdata, visualisemap)
+ newdataoutput!(model, "mortality", ["Date", "Species", "Cause"], @param(nature.popoutfreq))
initskylarkdata(model)
end
diff --git a/src/nature/individuals.jl b/src/nature/individuals.jl
index 934d219..7cb9da5 100644
--- a/src/nature/individuals.jl
+++ b/src/nature/individuals.jl
@@ -47,6 +47,7 @@ function kill!(animal::Animal, model::SimulationModel,
# print the epitaph and remove the animal from the model
postfix = isempty(cause) ? "." : " from $cause."
@debug "$(animalid(animal)) has died$(postfix)"
+ @record("mortality", [model.date, speciesof(animal), cause])
model.animals[animal.id] = nothing
return true
end
diff --git a/src/nature/macros.jl b/src/nature/macros.jl
index 14a81d3..250d688 100644
--- a/src/nature/macros.jl
+++ b/src/nature/macros.jl
@@ -496,6 +496,7 @@ end
@thisyear(annualdate)
Construct a date object referring to the current model year from an AnnualDate.
+Only use in scopes where `model` is available.
"""
macro thisyear(annualdate)
:(thisyear($(esc(annualdate)), $(esc(:model))))
@@ -505,6 +506,7 @@ end
@nextyear(annualdate)
Construct a date object referring to the next year in the model from an AnnualDate.
+Only use in scopes where `model` is available.
"""
macro nextyear(annualdate)
:(nextyear($(esc(annualdate)), $(esc(:model))))
@@ -514,7 +516,26 @@ end
@lastyear(annualdate)
Construct a date object referring to the last year in the model from an AnnualDate.
+Only use in scopes where `model` is available.
"""
macro lastyear(annualdate)
:(lastyear($(esc(annualdate)), $(esc(:model))))
end
+
+"""
+ @record(outputname, data)
+
+Record an observation / data point. Only use in scopes where `model` is available.
+"""
+macro record(args...)
+ :(record!($(esc(:model)), $(map(esc, args)...)))
+end
+
+"""
+ @destroynest(reason)
+
+Utility wrapper for `destroynest!()` in the Skylark model.
+"""
+macro destroynest(reason)
+ :(destroynest!($(esc(:self)), $(esc(:model)), $(esc(reason))))
+end
diff --git a/src/nature/species/skylark.jl b/src/nature/species/skylark.jl
index cced022..547f1cd 100644
--- a/src/nature/species/skylark.jl
+++ b/src/nature/species/skylark.jl
@@ -229,8 +229,8 @@ 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, destroynest!(self, "tillage"))
- @respond(harvesting, destroynest!(self, "harvesting"))
+ @respond(tillage, @destroynest("tillage"))
+ @respond(harvesting, @destroynest("harvesting"))
end
"""
@@ -243,24 +243,27 @@ chicks are independent or in case of brood loss.
self.timer += 1
#TODO this should be habitat-dependent!
if self.timer <= self.eggtime
- @chance(self.eggpredationmortality) && destroynest!(self, "predation")
+ @chance(self.eggpredationmortality) && @destroynest("predation")
elseif self.timer <= self.eggtime + self.nestlingtime
- @chance(self.nestlingpredationmortality) && destroynest!(self, "predation")
+ @chance(self.nestlingpredationmortality) && @destroynest("predation")
elseif self.timer <= self.eggtime + self.nestlingtime + self.fledglingtime
- @chance(self.fledglingpredationmortality) && destroynest!(self, "predation")
+ @chance(self.fledglingpredationmortality) && @destroynest("predation")
else
# create new young, reset timer and clutch counter
for o in 1:self.clutch #XXX is this the best way of doing first-year mortality?
- @chance(self.firstyearmortality) ?
- @debug("A skylark has died from first year mortality") :
+ if @chance(self.firstyearmortality)
+ @debug("A skylark has died from first year mortality")
+ @record("mortality", [model.date, "Skylark", "firstyearmortality"])
+ else
@reproduce(1, self.mate)
+ end
end
self.clutch = 0
end
if self.clutch > 0
# tillage and harvest destroys the nest
- @respond(tillage, destroynest!(self, "tillage"))
- @respond(harvesting, destroynest!(self, "harvesting"))
+ @respond(tillage, @destroynest("tillage"))
+ @respond(harvesting, @destroynest("harvesting"))
else # restart breeding cycle if there is time
self.timer = 0
self.nest = ()
@@ -358,16 +361,20 @@ function allowsnesting(skylark::Skylark, model::SimulationModel, pos::Tuple{Int6
end
"""
- destroynest!(skylark, reason)
+ destroynest!(skylark, model, reason)
Remove the skylark's nest and offspring due to disturbance or predation.
"""
-function destroynest!(self::Skylark, reason::String)
+function destroynest!(self::Skylark, model::SimulationModel, reason::String)
+ for c in self.clutch
+ @record("mortality", [model.date, "Skylark", reason])
+ end
self.nest = ()
self.clutch = 0
@debug("$(animalid(self)) had her nest destroyed by $reason.")
end
+
## INITIALISATION
"""
--
GitLab