Wrote test.sh for development purposes

run.jl

@@ -7,4 +7,4 @@ using Pkg
 Pkg.activate(".")
 using Persephone
 
-simulate()
+@time simulate()

src/analysis/analyse_nature.R

@@ -12,7 +12,7 @@ library(terra)
 
 autorun = TRUE ## automatically run all analyses?
 
-datadir = "results" ## "results" by default
+datadir = "test_results" ## "results" by default
 popfile = "populations.csv"
 indfile = "individuals.csv"
 mapfile = "landcover_jena.tif"
@@ -26,7 +26,7 @@ populationTrends = function() {
         mutate(Date = as.POSIXct(strptime(Date,format="%Y-%m-%d")))
     ggplot(data=popdata, aes(x=Date, y=Abundance, color=Species)) +
         geom_point() +
-        geom_smooth() +
+        ##geom_smooth() +
         scale_color_viridis_d() +
         theme_bw()
     ggsave(paste0(datadir, "/", population_output_file, ".pdf"), width=8, height=4)

src/nature/wolpertinger.jl

@@ -47,5 +47,5 @@ newspecies("Wolpertinger",
            updatewolpertinger!,
            Dict("popdensity"=>1/10000,
                 "birthenergy"=>400,
-                "fecundity"=>0.02,
+                "fecundity"=>0.01,
                 "maxspeed"=>5))

src/parameters.toml

@@ -15,7 +15,7 @@ loglevel = "debug" # verbosity level: "debug", "info", "quiet"
 seed = 0 # seed value for the RNG (0 -> random value)
 # dates to start and end the simulation
 startdate = 2020-01-01
-enddate = 2020-01-31
+enddate = 2020-12-31
 
 [farm]
 

test.sh

+#!/bin/bash
+## A short shell script to test the current development version of Persephone.
+
+if [[ -d "test_results" ]]
+then
+    rm -r test_results
+fi
+
+./run.jl -o test_results -s 1
+
+src/analysis/analyse_nature.R