Merge pull request #107 from EcoJulia/claireh93/landcover

ClimatePref updates

.github/workflows/testing.yaml

@@ -16,7 +16,7 @@ jobs:
     strategy:
       matrix:
         julia-version:
-          - '1.6'
+          - '1.8'
         os:
           - ubuntu-latest
           - macOS-10.15

Project.toml

@@ -34,9 +34,9 @@ Pluto = "c3e4b0f8-55cb-11ea-2926-15256bba5781"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 REPL = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+RasterDataSources = "3cb90ccd-e1b6-4867-9617-4276c8b2ca36"
 Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 SHA = "ea8e919c-243c-51af-8825-aaa63cd721ce"
-SimpleSDMLayers = "2c645270-77db-11e9-22c3-0f302a89c64c"
 SpatialEcology = "348f2d5d-71a3-5ad4-b565-8af070f99681"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
@@ -59,17 +59,16 @@ JLD2 = "0.4.3"
 MPI = "0.17.2, 0.18, 0.19, 0.20"
 Measures = "0.3.1"
 Missings = "0.4.5, 1.0"
-NetCDF = "0.11.3"
+NetCDF = "0.11"
 OnlineStats = "1.5.8"
 Optim = "0.18, 0.19, 0.20, 0.21, 0.22, 1"
 Phylo = "0.4.18"
 Plots = "0.28.4, 0.29, 1"
 Requires = "1"
-SimpleSDMLayers = "0.7, 0.8"
 SpatialEcology = "0.9"
 StatsBase = "0.32.2, 0.33"
 Unitful = "1.7"
-julia = "1.6"
+julia = "1.6, 1.8"
 
 [extras]
 MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195"

examples/LandCover_africa.jl

@@ -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")