From 11803d92b52a0f869ac1d2e6cde2164bc405f506 Mon Sep 17 00:00:00 2001
From: Daniel Vedder <daniel.vedder@idiv.de>
Date: Fri, 6 Jan 2023 11:58:38 +0100
Subject: [PATCH] Wrote the `initpopulation()` function
Still needs to be tested.
---
src/core/output.jl | 2 +-
src/core/simulation.jl | 10 +++---
src/crop/crops.jl | 2 +-
src/nature/nature.jl | 7 ++--
src/nature/populations.jl | 63 ++++++++++++++++++++++++++++++++---
src/nature/species/skylark.jl | 2 +-
6 files changed, 70 insertions(+), 16 deletions(-)
diff --git a/src/core/output.jl b/src/core/output.jl
index 830303f..db3ce30 100644
--- a/src/core/output.jl
+++ b/src/core/output.jl
@@ -42,7 +42,7 @@ function setupdatadir()
simulationlogger = TeeLogger(ConsoleLogger(logfile, loglevel),
ConsoleLogger(stdout, loglevel))
global_logger(simulationlogger)
- @info "Setting up output directory $(param("core.outdir"))"
+ @debug "Setting up output directory $(param("core.outdir"))"
# Export a copy of the current parameter settings to the output folder.
# This can be used to replicate this exact run in future, and also
# records the current time and git commit.
diff --git a/src/core/simulation.jl b/src/core/simulation.jl
index b94b8d6..f8c94f9 100644
--- a/src/core/simulation.jl
+++ b/src/core/simulation.jl
@@ -10,7 +10,8 @@ Initialise the model: read in parameters, create the output data directory,
and instantiate the AgentBasedModel object.
"""
function initialise(config::String=PARAMFILE)
- #XXX add a seed parameter?
+ @info "Simulation run started at $(Dates.now())."
+ #TODO add a seed parameter - requires mutable parameters
# do some housekeeping
initsettings(config)
Random.seed!(param("core.seed"))
@@ -29,7 +30,6 @@ function initialise(config::String=PARAMFILE)
initfarms!(model)
initfields!(model)
initnature!(model)
- @info "Simulation initialised at $(Dates.now())."
model
end
@@ -52,11 +52,11 @@ end
"""
finalise(model)
-Wrap up the simulation. Output all remaining data and exit.
+Wrap up the simulation. Currently doesn't do anything except print some information.
"""
function finalise(model::AgentBasedModel)
- @info "Simulated $(model.date-param("core.startdate"))."
- @info "Simulation completed at $(Dates.now()),\nwrote output to $(param("core.outdir"))."
+ @info "Simulated $(model.date-param("core.startdate")) days."
+ @info "Simulation run completed at $(Dates.now()),\nwrote output to $(param("core.outdir"))."
#XXX is there anything to do here?
#genocide!(model)
end
diff --git a/src/crop/crops.jl b/src/crop/crops.jl
index c96c7c0..c84c75d 100644
--- a/src/crop/crops.jl
+++ b/src/crop/crops.jl
@@ -59,7 +59,7 @@ function initfields!(model::AgentBasedModel)
end
end
end
- @debug "Initialised $n farm plots."
+ @info "Initialised $n farm plots."
end
#XXX only needed during development, can be deleted again?
diff --git a/src/nature/nature.jl b/src/nature/nature.jl
index bae1428..186c476 100644
--- a/src/nature/nature.jl
+++ b/src/nature/nature.jl
@@ -304,12 +304,11 @@ macro distancetoedge()
end
"""
- @countanimals(speciesname)
+ @countanimals(speciesname, radius=0)
Count the number of animals of the given species in this location.
This is a utility wrapper that can only be used nested within `@phase` or `@habitat`.
"""
-macro countanimals(speciesname)
- #XXX this also counts the enquiring agent
- :(countanimals($(esc(:pos)), $(esc(:model)), $speciesname))
+macro countanimals(speciesname, radius=0)
+ :(countanimals($(esc(:pos)), $(esc(:model)), $speciesname, $radius))
end
diff --git a/src/nature/populations.jl b/src/nature/populations.jl
index 28b9528..bd6577f 100644
--- a/src/nature/populations.jl
+++ b/src/nature/populations.jl
@@ -4,6 +4,63 @@
### reproduction, and mortality.
###
+"""
+ initpopulation(habitatdescriptor; popsize=-1, pairs=false, asexual=false)
+
+Creates a function that initialises individuals at random locations across the landscape.
+This can be used to create the `initialise!` variable in a species definition block.
+
+- `habitatdescriptor` is a function that determines whether a given location is suitable
+ or not (create this using `@habitat`).
+
+- `popsize` determines the number of individuals that will be created. If this is zero or
+ negative, one individual will be created in every suitable location in the landscape.
+ If `popsize` is greater than the number of suitable locations, multiple individuals
+ will be created in one place. (Maximum population density can be set in the habitat
+ descriptor using the `@countanimals` macro.)
+
+- If `pairs` is true, a male and a female individual will be created in each selected
+ location, otherwise, only one individual will be created at a time.
+
+- If `asexual` is true, all created individuals are assigned the sex `hermaphrodite`,
+ otherwise, they are randomly assigned male of female. (If `pairs` is true, `asexual`
+ is ignored.)
+"""
+function initpopulation(habitatdescriptor::Function;
+ popsize::Int64=-1, pairs::Bool=false, asexual=false)
+ function(species::Dict{String,Any}, model::AgentBasedModel)
+ n = 0
+ lastn = 0
+ specname = species["name"]
+ width, height = size(model.landscape)
+ while n == 0 || n < popsize
+ for x in shuffle!(Vector(1:width))
+ for y in shuffle!(Vector(1:height))
+ if habitatdescriptor((x,y), model)
+ if pairs
+ add_agent!(Animal, (x,y), model, species, female, 0)
+ add_agent!(Animal, (x,y), model, species, male, 0)
+ n += 2
+ else
+ sex = asexual ? hermaphrodite : rand([male, female])
+ add_agent!(Animal, (x,y), model, species, sex, 0)
+ n += 1
+ end
+ end
+ (n >= popsize) && break
+ end
+ (n >= popsize) && break
+ end
+ if lastn == n # prevent an infinite loop - we don't have a Cray...
+ @warn "There are not enough suitable locations for $(specname) in the landscape."
+ break
+ end
+ lastn = n
+ end
+ @info "Initialised $(n) $(specname)s."
+ end
+end
+
"""
initrandompopulation(popsize, asexual=true)
@@ -12,7 +69,7 @@ A simplified version of `initpopulation()`. Creates a function that initialises
than 1, it is interpreted as a population density (i.e. 1 animal per `popsize` pixels).
"""
function initrandompopulation(popsize::Union{Int64,Float64}, asexual::Bool=true)
- initfunc = function(species::Dict{String,Any}, model::AgentBasedModel)
+ function(species::Dict{String,Any}, model::AgentBasedModel)
if popsize < 1.0
x, y = size(model.landscape)
popsize = Int(round(x*y*popsize))
@@ -21,12 +78,10 @@ function initrandompopulation(popsize::Union{Int64,Float64}, asexual::Bool=true)
sex = asexual ? hermaphrodite : rand([male, female])
add_agent!(Animal, model, species, sex, 0)
end
- @debug "Initialised $(popsize) $(species["name"])s."
+ @info "Initialised $(popsize) $(species["name"])s."
end
- return initfunc
end
-#TODO initpopulation with habitat descriptor
#XXX initpopulation with dispersal from an original source?
#XXX initpopulation based on known occurences in real-life?
diff --git a/src/nature/species/skylark.jl b/src/nature/species/skylark.jl
index d29ab65..0f877bd 100644
--- a/src/nature/species/skylark.jl
+++ b/src/nature/species/skylark.jl
@@ -35,7 +35,7 @@ At the moment, this implementation is still in development.
@respond harvest @kill(@trait(eggharvestmortality), "harvest")
- if animal.age == 14
+ if @trait(age) == 14
@trait(phase) = "nestling"
end
end
--
GitLab