From be69f7fedfb9cf4dd6402ec8dba3da0ab0195c00 Mon Sep 17 00:00:00 2001
From: Daniel Vedder <daniel.vedder@idiv.de>
Date: Thu, 20 Jun 2024 12:12:48 +0200
Subject: [PATCH] Addressed the remaining comments from the first code review
closes #40
---
README.md | 16 +++++++-----
src/Persefone.jl | 1 -
src/core/input.jl | 7 ++---
src/core/output.jl | 22 +++++++++++-----
src/nature/ecologicaldata.jl | 13 +++++-----
src/nature/energy.jl | 3 ++-
src/nature/populations.jl | 50 ++++++++++++++++++++++--------------
test/io_tests.jl | 13 +++++-----
8 files changed, 77 insertions(+), 48 deletions(-)
diff --git a/README.md b/README.md
index 935fcfc..0f785a0 100644
--- a/README.md
+++ b/README.md
@@ -9,8 +9,8 @@
[Persefone.jl](https://persefone-model.eu/) models agricultural practice and
how it impacts animal species at a landscape scale. It includes a farm submodel, a crop
growth submodel, and individual-based models of multiple indicator species. Its aim is to
-investigate how changes in farm operations (e.g. through policy changes in the CAP)
-influence biodiversity.
+investigate how changes in farm operations (e.g. through changes in the European Common
+Agricultural Policy) influence biodiversity.
**The model is still in development. A first version will be available in summer 2024.**
@@ -22,9 +22,9 @@ To use Persefone.jl with a graphical user interface, see [here](https://git.idiv
### Installation
Install the latest version of the [Julia](https://julialang.org/downloads/) programming
-language (1.9+). The recommended editors are [VSCode](https://www.julia-vscode.org/) or
+language (1.10+). The recommended editors are [VSCode](https://www.julia-vscode.org/) or
[Emacs](https://www.emacswiki.org/emacs/JuliaProgrammingLanguage).
-To install package dependencies, open a Julia REPL in this folder and run
+To install package dependencies, open a Julia REPL in the Persefone root folder and run
`using Pkg; Pkg.activate("."); Pkg.instantiate()`.
### Running from the command line
@@ -81,8 +81,12 @@ Pkg.activate(".") # assuming you're in the Persefone root folder
using Persefone
```
-You can then access all Persefone functions, such as `simulate()`. (See
-`src/Persefone.jl` for a list of exported functions.)
+You can then access all Persefone functions, such as
+[`simulate()`](https://persefone-model.eu/documentation/simulation.html#Persefone.simulate)
+(which runs a complete simulation, as when calling `julia run.jl` from the commandline).
+See [`src/Persefone.jl`](https://git.idiv.de/persefone/persefone-model/-/blob/master/src/Persefone.jl?ref_type=heads)
+or the [documentation](https://persefone-model.eu/documentation/simulation.html) for a
+list of exported functions.
---
diff --git a/src/Persefone.jl b/src/Persefone.jl
index 12e1faf..6c4df60 100644
--- a/src/Persefone.jl
+++ b/src/Persefone.jl
@@ -22,7 +22,6 @@ using
DataFramesMeta,
Distributed,
FileIO,
- #FIXME an upstream update broke GeoArrays for TableTransforms > 1.15.0
GeoArrays, #XXX this is another big dependency
Logging,
LoggingExtras,
diff --git a/src/core/input.jl b/src/core/input.jl
index 5c22b60..a8bc2a4 100644
--- a/src/core/input.jl
+++ b/src/core/input.jl
@@ -4,7 +4,8 @@
###
## Note: much of this code was adapted from the GeMM model by Leidinger et al.
-## (https://github.com/CCTB-Ecomods/gemm/blob/master/src/input.jl)
+## (https://github.com/CCTB-Ecomods/gemm/blob/master/src/input.jl, archived at
+## https://doi.org/10.5281/zenodo.5602906)
"""
The file that stores all default parameters: `src/parameters.toml`
@@ -75,8 +76,8 @@ end
"""
preprocessparameters(settings)
-Take the raw input parameters and process them (convert types, perform checks, etc.).
-This is a helper function for [`getsettings`](@ref).
+Take the raw input parameters and process them where necessary (e.g. convert types or
+perform checks). This is a helper function for [`getsettings`](@ref).
"""
function preprocessparameters(settings::Dict{String,Any}, defaultoutdir::String)
(settings["core.seed"] == 0) && (settings["core.seed"] = abs(rand(RandomDevice(), Int32)))
diff --git a/src/core/output.jl b/src/core/output.jl
index 5028dde..a79a920 100644
--- a/src/core/output.jl
+++ b/src/core/output.jl
@@ -1,10 +1,16 @@
### Persefone.jl - a model of agricultural landscapes and ecosystems in Europe.
###
-### This file includes functions for saving the model output.
+### This file contains functions for saving the model output. This includes logging
+### facilities, but also functions for collecting and outputting data from the
+### different submodels.
###
+"Log output is saved to `simulation.log` in the output directory"
const LOGFILE = "simulation.log"
+"All input data are copied to the `inputs` folder within the output directory"
+const RECORDDIR = "inputs"
+
## Much of this code was adapted from the GeMM model by Leidinger et al.
## (https://github.com/CCTB-Ecomods/gemm/blob/master/src/output.jl)
@@ -26,6 +32,7 @@ function createdatadir(outdir::String, overwrite::Union{Bool,String})
@warn "Overwriting existing output directory $(outdir)."
#TODO replace with exception
end
+ @debug "Setting up output directory $outdir."
mkpath(outdir)
end
@@ -81,9 +88,9 @@ settings used. This allows replicating a run in future.
function saveinputfiles(model::SimulationModel)
#XXX If this is a parallel run, we should save the global config to the top-level
# output directory
- @debug "Setting up output directory $(@param(core.outdir))."
currentcommit = read(`git rev-parse HEAD`, String)[1:8]
- open(joinpath(@param(core.outdir), basename(@param(core.configfile))), "w") do f
+ mkpath(joinpath(@param(core.outdir), RECORDDIR))
+ open(joinpath(@param(core.outdir), RECORDDIR, basename(@param(core.configfile))), "w") do f
println(f, "#\n# --- Persefone configuration parameters ---")
println(f, "# This file was generated automatically.")
println(f, "# Simulation run on $(string(Dates.format(Dates.now(), "d u Y HH:MM:SS"))),")
@@ -96,14 +103,17 @@ function saveinputfiles(model::SimulationModel)
end
TOML.print(f, prepareTOML(deepcopy(model.settings)))
end
- # Copy the map files to the output folder
+ # Copy the map and weather files to the output folder
lcmap = joinpath(@param(world.mapdirectory), @param(world.landcovermap))
ffmap = joinpath(@param(world.mapdirectory), @param(world.farmfieldsmap))
+ wfile = joinpath(@param(world.mapdirectory), @param(world.weatherfile))
#TODO replace errors with exceptions
!(isfile(lcmap)) && Base.error("The map file $(lcmap) doesn't exist.")
!(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)
+ !(isfile(wfile)) && Base.error("The map file $(wfile) doesn't exist.")
+ cp(lcmap, joinpath(@param(core.outdir), RECORDDIR, basename(lcmap)), force = true)
+ cp(ffmap, joinpath(@param(core.outdir), RECORDDIR, basename(ffmap)), force = true)
+ cp(wfile, joinpath(@param(core.outdir), RECORDDIR, basename(wfile)), force = true)
end
"""
diff --git a/src/nature/ecologicaldata.jl b/src/nature/ecologicaldata.jl
index 78e85b7..06a2ad7 100644
--- a/src/nature/ecologicaldata.jl
+++ b/src/nature/ecologicaldata.jl
@@ -1,6 +1,7 @@
### Persefone.jl - a model of agricultural landscapes and ecosystems in Europe.
###
-### This file includes the functions for collecting and saving ecological output data.
+### This file includes the functions for collecting ecological output data, which
+### are then passed on to the `core/output.jl`.
###
"""
@@ -18,9 +19,9 @@ end
"""
savepopulationdata(model)
-Return a comma-separated set of lines (to be printed to `populations.csv`), giving
-the current date and population size for each animal species. May be called never,
-daily, monthly, yearly, or at the end of a simulation, depending on the parameter
+Return a data table (to be printed to `populations.csv`), giving the current
+date and population size for each animal species. May be called never, daily,
+monthly, yearly, or at the end of a simulation, depending on the parameter
`nature.popoutfreq`.
"""
function savepopulationdata(model::SimulationModel)
@@ -42,8 +43,8 @@ end
"""
saveindividualdata(model)
-Return a comma-separated set of lines (to be printed to `individuals.csv`), listing
-all properties of all animal individuals in the model. May be called never, daily,
+Return a data table (to be printed to `individuals.csv`), listing all
+properties of all animal individuals in the model. May be called never, daily,
monthly, yearly, or at the end of a simulation, depending on the parameter
`nature.indoutfreq`. WARNING: Produces very big files!
"""
diff --git a/src/nature/energy.jl b/src/nature/energy.jl
index feb3a94..1d2c46a 100644
--- a/src/nature/energy.jl
+++ b/src/nature/energy.jl
@@ -3,6 +3,7 @@
### This file contains structs and functions for implementing Dynamic Energy Budgets.
###
+#TODO add units
## STRUCTS
@@ -42,7 +43,7 @@ in a reserve buffer, before being used for maintenance, growth, and reproduction
- Sibly et al. (2013). Representing the acquisition and use of energy by individuals in agent-based models of animal populations. Methods in Ecology and Evolution, 4(2), 151–161. https://doi.org/10.1111/2041-210x.12002
- Sousa et al. (2010). Dynamic energy budget theory restores coherence in biology. Philosophical Transactions of the Royal Society B: Biological Sciences, 365(1557), 3413–3428. https://doi.org/10.1098/rstb.2010.0166
- Kooijman, S. A. L. M. (2009). Dynamic energy and mass budgets in biological systems (3rd ed). Cambridge University Press. https://www.researchgate.net/profile/Edgar-Meza-3/post/Is_there_a_toxicokinetic_model_for_daphnia_magna_or_other_zooplankton/attachment/59d62cf579197b807798b396/AS%3A348547653357569%401460111644286/download/Dynamic+Energy+Budget+theory+-+Kooijman.pdf
-- *see also:* Brown et al. (2004). Toward a metabolic theory of ecology. Ecology, 85(7), 1771–1789. https://doi.org/10.1890/03-9000
+- *compare with:* Brown et al. (2004). Toward a metabolic theory of ecology. Ecology, 85(7), 1771–1789. https://doi.org/10.1890/03-9000
"""
mutable struct EnergyBudget
params::DEBparameters
diff --git a/src/nature/populations.jl b/src/nature/populations.jl
index 4292ba1..187157e 100644
--- a/src/nature/populations.jl
+++ b/src/nature/populations.jl
@@ -70,10 +70,11 @@ end
initpopulation!(speciestype, popinitparams, model)
Initialise the population of the given species, based on the given initialisation parameters.
-This is an internal function called by initpopulation!(), and was split off from it to allow
+This is an internal function called by `initpopulation!()`, and was split off from it to allow
better testing.
"""
-function initpopulation!(species::Type, p::PopInitParams, model::SimulationModel)
+function initpopulation!(species::Type, p::PopInitParams, model::SimulationModel)
+ #XXX this is a pretty complicated function - can we make it simpler?
(p.popsize <= 0 && p.indarea <= 0m²) && # can be legit if a habitat descriptor is provided
@warn("initpopulation!() called with popsize and indarea both <= 0")
(p.popsize > 0 && p.indarea > 0m²) && #XXX not sure what this would do
@@ -93,22 +94,7 @@ function initpopulation!(species::Type, p::PopInitParams, model::SimulationModel
#XXX `n==0` above guarantees that at least one individual is created, even
# in a landscape that is otherwise too small for the specified indarea -
# do we want this?
- if p.pairs
- a1 = species(length(model.animals)+1, male, (-1, -1), (x,y), p.initphase)
- a2 = species(length(model.animals)+2, female, (-1, -1), (x,y), p.initphase)
- push!(model.animals, a1, a2)
- push!(model.landscape[x,y].animals, a1.id, a2.id)
- create!(a1, model)
- create!(a2, model)
- n += 2
- else
- sex = p.asexual ? hermaphrodite : @rand([male, female])
- a = species(length(model.animals)+1, sex, (-1, -1), (x,y), p.initphase)
- push!(model.animals, a)
- push!(model.landscape[x,y].animals, a.id)
- create!(a, model)
- n += 1
- end
+ n += initindividuals!(species, (x,y), p, model)
end
#XXX break randomly to avoid initialising all individuals in a single column?
(p.popsize > 0 && n >= p.popsize) && break
@@ -124,6 +110,32 @@ function initpopulation!(species::Type, p::PopInitParams, model::SimulationModel
@info "Initialised $(n) $(speciesof(species))s."
end
+"""
+ initindividuals!(species, pos, popinitparams, model)
+
+Initialise one or two individuals (depending on the `pairs` parameter) in the
+given location. Returns the number of created individuals. (Internal helper
+function for `initpopulation!()`.)
+"""
+function initindividuals!(species::Type, pos::Tuple{Int64,Int64}, p::PopInitParams, model::SimulationModel)
+ if p.pairs
+ a1 = species(length(model.animals)+1, male, (-1, -1), pos, p.initphase)
+ a2 = species(length(model.animals)+2, female, (-1, -1), pos, p.initphase)
+ push!(model.animals, a1, a2)
+ push!(model.landscape[pos...].animals, a1.id, a2.id)
+ create!(a1, model)
+ create!(a2, model)
+ return 2
+ else
+ sex = p.asexual ? hermaphrodite : @rand([male, female])
+ a = species(length(model.animals)+1, sex, (-1, -1), pos, p.initphase)
+ push!(model.animals, a)
+ push!(model.landscape[pos...].animals, a.id)
+ create!(a, model)
+ return 1
+ end
+end
+
#XXX initpopulation with dispersal from an original source?
#XXX initpopulation based on known occurences in real-life?
@@ -143,6 +155,7 @@ function reproduce!(animal::Animal, model::SimulationModel,
sex = @rand([male, female])
end
bphase = populationparameters(typeof(animal)).birthphase
+ #TODO add DEB?
child = typeof(animal)(length(model.animals)+1, sex, (animal.id, mate), animal.pos, bphase)
push!(model.animals, child)
push!(animal.offspring, child.id)
@@ -219,7 +232,6 @@ function nearby_ids(pos::Tuple{Int64,Int64}, model::SimulationModel, radius::Len
ids
end
-
"""
nearby_animals(pos, model; radius= 0, species="")
diff --git a/test/io_tests.jl b/test/io_tests.jl
index 71c8f0c..2275990 100644
--- a/test/io_tests.jl
+++ b/test/io_tests.jl
@@ -17,14 +17,15 @@ end
model = inittestmodel()
# test that the output directory is created with all files
outdir = @param(core.outdir)
- Ps.createdatadir(outdir, @param(core.overwrite))
- @test isdir(outdir)
@test_logs((:debug, "Setting up output directory results_testsuite."),
min_level=Logging.Debug, match_mode=:any,
- Ps.saveinputfiles(model))
- @test isfile(joinpath(outdir, @param(world.landcovermap)))
- @test isfile(joinpath(outdir, @param(world.farmfieldsmap)))
- @test isfile(joinpath(outdir, @param(core.configfile)))
+ Ps.createdatadir(outdir, @param(core.overwrite)))
+ @test isdir(outdir)
+ Ps.saveinputfiles(model)
+ @test isfile(joinpath(outdir, Ps.RECORDDIR, @param(world.landcovermap)))
+ @test isfile(joinpath(outdir, Ps.RECORDDIR, @param(world.farmfieldsmap)))
+ @test isfile(joinpath(outdir, Ps.RECORDDIR, @param(world.weatherfile)))
+ @test isfile(joinpath(outdir, Ps.RECORDDIR, @param(core.configfile)))
# test log output to screen/file/both
#XXX cannot test logger output due to https://github.com/JuliaLang/julia/issues/48456
logger1 = Ps.modellogger(@param(core.loglevel), outdir, "screen")
--
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