From 1c0f44e3c262b9ce571a092050a532dea0be083a Mon Sep 17 00:00:00 2001
From: Daniel Vedder <daniel.vedder@idiv.de>
Date: Sat, 26 Nov 2022 18:12:13 +0100
Subject: [PATCH] Model now saves per-species abundances each time step
---
src/core/output.jl | 27 ++++++++++++++++++++++++++-
src/core/simulation.jl | 1 +
2 files changed, 27 insertions(+), 1 deletion(-)
diff --git a/src/core/output.jl b/src/core/output.jl
index 75a37a3..de9047a 100644
--- a/src/core/output.jl
+++ b/src/core/output.jl
@@ -3,6 +3,9 @@
### This file includes functions for saving the model output.
###
+const LOGFILE = "simulation.log"
+const POPFILE = "populations.csv"
+
## Note: `setupdatadir()` was adapted from the GeMM model by Leidinger et al.
## (https://github.com/CCTB-Ecomods/gemm/blob/master/src/output.jl)
@@ -29,7 +32,7 @@ function setupdatadir()
elseif param("core.loglevel") == "quiet"
loglevel = Logging.Warn
end
- logfile = open(joinpath(param("core.outdir"), "simulation.log"), "w+")
+ logfile = open(joinpath(param("core.outdir"), LOGFILE), "w+")
simulationlogger = TeeLogger(ConsoleLogger(logfile, loglevel),
ConsoleLogger(stdout, loglevel))
global_logger(simulationlogger)
@@ -51,5 +54,27 @@ function setupdatadir()
!(isfile(ffmap)) && Base.error("The map file $(ffmap) doesn't exist.")
cp(lcmap, joinpath(param("core.outdir"), basename(lcmap)), force = true)
cp(ffmap, joinpath(param("core.outdir"), basename(ffmap)), force = true)
+ # Create the data output file(s)
+ open(joinpath(param("core.outdir"), POPFILE), "w") do f
+ println(f, "Date;Species;Abundance")
+ end
end
+"""
+ savepopulationdata(model)
+
+Print a comma-separated set of lines to `populations.csv`, giving the
+current date and population size for each animal species.
+"""
+function savepopulationdata(model::AgentBasedModel)
+ pops = Dict{String,Int}(s=>0 for s = param("nature.targetspecies"))
+ for a in allagents(model)
+ (typeof(a) != Animal) && continue
+ pops[a.species.name] += 1
+ end
+ open(joinpath(param("core.outdir"), POPFILE), "a") do f
+ for p in keys(pops)
+ println(f, "$(model.date);$(p);$(pops[p])")
+ end
+ end
+end
diff --git a/src/core/simulation.jl b/src/core/simulation.jl
index 48744d9..8e6f61a 100644
--- a/src/core/simulation.jl
+++ b/src/core/simulation.jl
@@ -44,6 +44,7 @@ function stepsimulation!(model::AgentBasedModel)
for a in Schedulers.ByType((Farmer,Animal,CropPlot), true)(model)
stepagent!(getindex(model, a), model)
end
+ savepopulationdata(model)
end
"""
--
GitLab