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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,111 @@ | ||
| #### SINGLE SPECIES #### | ||
| # Code to run single species across Africa with WorldClim data. | ||
| using EcoSISTEM | ||
| using EcoSISTEM.ClimatePref | ||
| using EcoSISTEM.Units | ||
| using RasterDataSources | ||
| using AxisArrays | ||
| using Unitful | ||
| using Unitful.DefaultSymbols | ||
| using StatsBase | ||
| using Plots | ||
|
|
||
| # Download landcover data | ||
| if !isdir("assets") | ||
| mkdir("assets") | ||
| end | ||
| ENV["RASTERDATASOURCES_PATH"] = "assets" | ||
| getraster(EarthEnv{LandCover}) | ||
| world = readlc("assets/EarthEnv/LandCover/without_DISCover/", -180.0°, 180.0°, -56.0°, 90.0°) | ||
| world = compressLC(world) | ||
| africa_lc = world[-25°.. 50°, -35° .. 40°] | ||
| bio_africa_lc = Landcover(africa_lc) | ||
| heatmap(africa_lc') | ||
|
|
||
| getraster(WorldClim{BioClim}) | ||
| world = readbioclim("assets/WorldClim/BioClim/") | ||
| africa_water = world.array[-25°.. 50°, -35° .. 40°, 12] | ||
| africa_water = upresolution(africa_water, 2) | ||
| africa_water = Worldclim_bioclim(AxisArray(africa_water .* mm, AxisArrays.axes(africa_water))) | ||
| bio_africa_water = WaterBudget(africa_water) | ||
|
|
||
| # Find which grid cells are land | ||
| active = Array{Bool, 2}(africa_lc .!= 4) | ||
|
|
||
| # Set up initial parameters for ecosystem | ||
| numSpecies = 1; grid = size(active); req= 10.0mm; individuals=0; area = 64e6km^2; totalK = 1000.0kJ/km^2 | ||
|
|
||
| # Set up how much water each species consumes | ||
| energy_vec = WaterRequirement(fill(req, numSpecies)) | ||
|
|
||
| # Set rates for birth and death | ||
| birth = 0.6/year | ||
| death = 0.6/year | ||
| longevity = 1.0 | ||
| survival = 0.2 | ||
| boost = 1.0 | ||
| # Collect model parameters together | ||
| param = EqualPop(birth, death, longevity, survival, boost) | ||
|
|
||
| # Create kernel for movement | ||
| kernel = fill(GaussianKernel(15.0km, 10e-10), numSpecies) | ||
| movement = AlwaysMovement(kernel, Torus()) | ||
|
|
||
| # Create species list, including their temperature preferences, seed abundance and native status | ||
| opts = fill(collect(1:8), numSpecies) | ||
| traits = LCtrait(opts) | ||
| native = fill(true, numSpecies) | ||
| abun = fill(div(individuals, numSpecies), numSpecies) | ||
| sppl = SpeciesList(numSpecies, traits, abun, energy_vec, | ||
| movement, param, native) | ||
|
|
||
| # Create abiotic environment - with temperature and water resource | ||
| abenv = lcAE(bio_africa_lc, bio_africa_water, active) | ||
|
|
||
| # Set relationship between species and environment (gaussian) | ||
| rel = LCmatch{Int64}() | ||
|
|
||
| # Create ecosystem and fill every active grid square with an individual | ||
| eco = Ecosystem(sppl, abenv, rel) | ||
| rand_start = findall(active) | ||
| for i in rand_start | ||
| eco.abundances.grid[1, i[1], i[2]] += 1 | ||
| end | ||
|
|
||
| # Run simulation | ||
| times = 10years; timestep = 1month; record_interval = 1month; repeats = 1 | ||
| lensim = length(0years:record_interval:times) | ||
| abuns = zeros(Int64, numSpecies, prod(grid), lensim) | ||
| @time simulate_record!(abuns, eco, times, record_interval, timestep); | ||
|
|
||
| # Reshape abundances for plotting | ||
| abuns = reshape(abuns[1, :, :, 1], grid[1], grid[2], lensim) | ||
|
|
||
| # Create a gif (warning, slow!) | ||
| anim = @animate for i in 1:lensim | ||
| africa_abun = Float64.(abuns[:, :, i]) | ||
| africa_abun[.!(active)] .= NaN | ||
| heatmap(africa_abun, clim = (0, maximum(abuns)), | ||
| background_color = :lightblue, background_color_outside=:white, | ||
| grid = false, color = cgrad(:algae, scale = :exp)) | ||
| end | ||
| gif(anim, "examples/Africa.gif", fps = 15) | ||
|
|
||
| # Plot start and end abundances, next to temperature and rainfall | ||
| africa_startabun = Float64.(abuns[:, :, 1]) | ||
| africa_startabun[.!(active)] .= NaN | ||
| africa_endabun = Float64.(abuns[:, :, end]) | ||
| africa_endabun[.!(active)] .= NaN | ||
| heatmap(africa_startabun', clim = (0, maximum(abuns)), | ||
| background_color = :lightblue, background_color_outside=:white, | ||
| grid = false, color = cgrad(:algae, scale = :exp), | ||
| layout = (@layout [a b; c d]), title = "Start abundance") | ||
| heatmap!(africa_endabun', clim = (0, maximum(abuns)), | ||
| background_color = :lightblue, background_color_outside=:white, | ||
| grid = false, color = cgrad(:algae, scale = :exp), | ||
| subplot = 2, title = "End Abundance") | ||
| africa_lc = Float64.(africa_lc.data) | ||
| africa_lc[.!active] .= NaN | ||
| heatmap!(africa_lc', grid = false, subplot = 3, title = "Land Cover") | ||
| africa_water = world.array[-25°.. 50°, -35° .. 40°, 12] | ||
| heatmap!(africa_water', grid = false, subplot = 4, title = "Precipitation") |
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