Model now saves per-species abundances each time step

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

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
 
 """