Merge pull request #72 from PoisotLab/feature/human-names

Add additional metadata to the providers

SimpleSDMDatasets/src/SimpleSDMDatasets.jl

@@ -51,6 +51,7 @@ export RasterData, Projection
 
 # Common interface
 include("interface.jl")
+export layers, layerdescriptions
 
 # Providers
 include("providers/CHELSA/chelsa_v1.jl")

SimpleSDMDatasets/src/interface.jl

@@ -151,10 +151,9 @@ layers(data::R, ::F) where {R <: RasterData, F <: Projection} = layers(data)
 """
     layerdescriptions(data::R) where {R <: RasterData}
 
-Human-readable names the layers. This will by default print the value of
-`layers`, but can be overloaded if these names are not informative.
+Human-readable names the layers. This *must* be a dictionary mapping the layer names (as returned by `layers`) to a string explaining the contents of the layers.
 """
-layerdescriptions(data::R) where {R <: RasterData} = layers(data)
+layerdescriptions(data::R) where {R <: RasterData} = Dict(zip(layers(data), layers(data)))
 layerdescriptions(data::R, ::F) where {R <: RasterData, F <: Projection} =
     layerdescriptions(data)
 
@@ -223,4 +222,7 @@ bandnumber(::R; kwargs...) where {R <: RasterData} = 1
 bandnumber(::R, ::F; kwargs...) where {R <: RasterData, F <: Projection} = 1
 
 crs(::R) where {R <: RasterData} = _wgs84
-crs(data::R, future::F) where {R <: RasterData, F <: Projection} = crs(data)
+crs(data::R, ::F) where {R <: RasterData, F <: Projection} = crs(data)
+
+url(::R) where {R <: RasterData} = ""
+url(data::R, ::F) where {R <: RasterData, F <: Projection} = url(data)

SimpleSDMDatasets/src/providers/CHELSA/chelsa_v1.jl

@@ -9,8 +9,31 @@ CHELSA1Dataset = Union{
 # Update provisioning
 provides(::Type{CHELSA1}, ::Type{T}) where {T <: CHELSA1Dataset} = true
 
+url(::RasterData{CHELSA1, D}) where {D <: CHELSA1Dataset} = "https://chelsa-climate.org/"
+
 # Update the layers
 layers(::RasterData{CHELSA1, BioClim}) = "BIO" .* string.(1:19)
+layerdescriptions(::RasterData{CHELSA1, BioClim}) = Dict([
+    "BIO1" => "Annual Mean Temperature",
+    "BIO2" => "Mean Diurnal Range (Mean of monthly (max temp - min temp))",
+    "BIO3" => "Isothermality (BIO2/BIO7) (×100)",
+    "BIO4" => "Temperature Seasonality (standard deviation ×100)",
+    "BIO5" => "Max Temperature of Warmest Month",
+    "BIO6" => "Min Temperature of Coldest Month",
+    "BIO7" => "Temperature Annual Range (BIO5-BIO6)",
+    "BIO8" => "Mean Temperature of Wettest Quarter",
+    "BIO9" => "Mean Temperature of Driest Quarter",
+    "BIO10" => "Mean Temperature of Warmest Quarter",
+    "BIO11" => "Mean Temperature of Coldest Quarter",
+    "BIO12" => "Annual Precipitation",
+    "BIO13" => "Precipitation of Wettest Month",
+    "BIO14" => "Precipitation of Driest Month",
+    "BIO15" => "Precipitation Seasonality (Coefficient of Variation)",
+    "BIO16" => "Precipitation of Wettest Quarter",
+    "BIO17" => "Precipitation of Driest Quarter",
+    "BIO18" => "Precipitation of Warmest Quarter",
+    "BIO19" => "Precipitation of Coldest Quarter",
+])
 
 # Months for climate variables
 months(::RasterData{CHELSA1, T}) where {T <: CHELSA1Dataset} = Month.(1:12)
@@ -56,4 +79,4 @@ function source(data::RasterData{CHELSA1, BioClim}; layer = "BIO1")
         filename = lowercase(stem),
         outdir = destination(data),
     )
-end
+end

SimpleSDMDatasets/src/providers/CHELSA/chelsa_v2.jl

@@ -9,8 +9,31 @@ CHELSA2Dataset = Union{
 # Update provisioning
 provides(::Type{CHELSA2}, ::Type{T}) where {T <: CHELSA2Dataset} = true
 
+url(::RasterData{CHELSA2, D}) where {D <: CHELSA2Dataset} = "https://chelsa-climate.org/"
+
 # Update the layers
 layers(::RasterData{CHELSA2, BioClim}) = "BIO" .* string.(1:19)
+layerdescriptions(::RasterData{CHELSA2, BioClim}) = Dict([
+    "BIO1" => "Annual Mean Temperature",
+    "BIO2" => "Mean Diurnal Range (Mean of monthly (max temp - min temp))",
+    "BIO3" => "Isothermality (BIO2/BIO7) (×100)",
+    "BIO4" => "Temperature Seasonality (standard deviation ×100)",
+    "BIO5" => "Max Temperature of Warmest Month",
+    "BIO6" => "Min Temperature of Coldest Month",
+    "BIO7" => "Temperature Annual Range (BIO5-BIO6)",
+    "BIO8" => "Mean Temperature of Wettest Quarter",
+    "BIO9" => "Mean Temperature of Driest Quarter",
+    "BIO10" => "Mean Temperature of Warmest Quarter",
+    "BIO11" => "Mean Temperature of Coldest Quarter",
+    "BIO12" => "Annual Precipitation",
+    "BIO13" => "Precipitation of Wettest Month",
+    "BIO14" => "Precipitation of Driest Month",
+    "BIO15" => "Precipitation Seasonality (Coefficient of Variation)",
+    "BIO16" => "Precipitation of Wettest Quarter",
+    "BIO17" => "Precipitation of Driest Quarter",
+    "BIO18" => "Precipitation of Warmest Quarter",
+    "BIO19" => "Precipitation of Coldest Quarter",
+])
 
 # Months
 months(::RasterData{CHELSA2, T}) where {T <: CHELSA2Dataset} = Month.(1:12)
@@ -45,4 +68,4 @@ function source(data::RasterData{CHELSA2, T}; month = Month(1)) where {T <: CHEL
         filename = lowercase(stem),
         outdir = destination(data),
     )
-end
+end

SimpleSDMDatasets/src/providers/EarthEnv/earthenv.jl

@@ -4,7 +4,10 @@ EarthEnvDataset = Union{LandCover, HabitatHeterogeneity}
 provides(::Type{EarthEnv}, ::Type{T}) where {T <: EarthEnvDataset} = true
 
 # Additional keys for search
-extrakeys(::RasterData{EarthEnv, LandCover}) = Dict([:full=>(true,false)])
+extrakeys(::RasterData{EarthEnv, LandCover}) = Dict([:full => (true, false)])
+
+url(::RasterData{EarthEnv, LandCover}) = "https://www.earthenv.org/landcover"
+url(::RasterData{EarthEnv, HabitatHeterogeneity}) = "https://www.earthenv.org/texture"
 
 # Update the layers
 layers(::RasterData{EarthEnv, LandCover}) = [
@@ -110,4 +113,4 @@ function source(
         filename = lowercase(stem),
         outdir = destination(data),
     )
-end
+end

SimpleSDMDatasets/src/providers/WorldClim/worldclim_v2.jl

@@ -12,6 +12,9 @@ wcdat = [
 ]
 WorldClim2Dataset = Union{wcdat...}
 
+url(::RasterData{WorldClim2, D}) where {D <: WorldClim2Dataset} =
+    "https://www.worldclim.org/data/index.html"
+
 # Update provisioning
 provides(::Type{WorldClim2}, ::Type{T}) where {T <: WorldClim2Dataset} = true
 
@@ -29,6 +32,27 @@ months(::RasterData{WorldClim2, Elevation}) = nothing
 
 # Update the layers
 layers(::RasterData{WorldClim2, BioClim}) = "BIO" .* string.(1:19)
+layerdescriptions(::RasterData{WorldClim2, BioClim}) = Dict([
+    "BIO1" => "Annual Mean Temperature",
+    "BIO2" => "Mean Diurnal Range (Mean of monthly (max temp - min temp))",
+    "BIO3" => "Isothermality (BIO2/BIO7) (×100)",
+    "BIO4" => "Temperature Seasonality (standard deviation ×100)",
+    "BIO5" => "Max Temperature of Warmest Month",
+    "BIO6" => "Min Temperature of Coldest Month",
+    "BIO7" => "Temperature Annual Range (BIO5-BIO6)",
+    "BIO8" => "Mean Temperature of Wettest Quarter",
+    "BIO9" => "Mean Temperature of Driest Quarter",
+    "BIO10" => "Mean Temperature of Warmest Quarter",
+    "BIO11" => "Mean Temperature of Coldest Quarter",
+    "BIO12" => "Annual Precipitation",
+    "BIO13" => "Precipitation of Wettest Month",
+    "BIO14" => "Precipitation of Driest Month",
+    "BIO15" => "Precipitation Seasonality (Coefficient of Variation)",
+    "BIO16" => "Precipitation of Wettest Quarter",
+    "BIO17" => "Precipitation of Driest Quarter",
+    "BIO18" => "Precipitation of Warmest Quarter",
+    "BIO19" => "Precipitation of Coldest Quarter",
+])
 
 # The following functions are the list of URL codes for the datasets. Note that
 # they dispatch on the dataset within the context of WorldClim2
@@ -88,4 +112,4 @@ function layername(
     res_code = get(resolutions(data), resolution, "10m")
     var_code = _var_slug(data)
     return "wc2.1_$(res_code)_$(var_code).tif"
-end
+end

SimpleSDMDatasets/test/chelsa_v1.jl

@@ -13,38 +13,40 @@ for T in Base.uniontypes(SimpleSDMDatasets.CHELSA1Dataset)
     @test SimpleSDMDatasets.resolutions(data) |> isnothing
 end
 
+@test layerdescriptions(RasterData(CHELSA1, BioClim))["BIO1"] == "Annual Mean Temperature"
+
 @test SimpleSDMDatasets.months(RasterData(CHELSA1, BioClim)) |> isnothing
 @test SimpleSDMDatasets.extrakeys(RasterData(CHELSA1, BioClim)) |> isnothing
 @test SimpleSDMDatasets.layers(RasterData(CHELSA1, BioClim)) |> !isnothing
 
 begin
-    out = downloader(RasterData(CHELSA1, BioClim); layer = "BIO12")
+    out = downloader(RasterData(CHELSA1, BioClim); layer="BIO12")
     @test isfile(first(out))
     @test out[2] == SimpleSDMDatasets.filetype(RasterData(CHELSA1, BioClim))
 end
 
 begin
-    out = downloader(RasterData(CHELSA1, AverageTemperature); month = Month(6))
+    out = downloader(RasterData(CHELSA1, AverageTemperature); month=Month(6))
     @test isfile(first(out))
     @test out[2] == SimpleSDMDatasets.filetype(RasterData(CHELSA1, AverageTemperature))
 end
 
 begin
-    out = downloader(RasterData(CHELSA1, MinimumTemperature); month = Month(12))
+    out = downloader(RasterData(CHELSA1, MinimumTemperature); month=Month(12))
     @test isfile(first(out))
     @test out[2] == SimpleSDMDatasets.filetype(RasterData(CHELSA1, MinimumTemperature))
 end
 
 begin
-    out = downloader(RasterData(CHELSA1, MaximumTemperature); month = Month(1))
+    out = downloader(RasterData(CHELSA1, MaximumTemperature); month=Month(1))
     @test isfile(first(out))
     @test out[2] == SimpleSDMDatasets.filetype(RasterData(CHELSA1, MaximumTemperature))
 end
 
 begin
-    out = downloader(RasterData(CHELSA1, Precipitation); month = Month(10))
+    out = downloader(RasterData(CHELSA1, Precipitation); month=Month(10))
     @test isfile(first(out))
     @test out[2] == SimpleSDMDatasets.filetype(RasterData(CHELSA1, Precipitation))
 end
 
-end
+end

SimpleSDMDatasets/test/chelsa_v2.jl

@@ -13,6 +13,8 @@ for T in Base.uniontypes(SimpleSDMDatasets.CHELSA2Dataset)
     @test SimpleSDMDatasets.resolutions(data) |> isnothing
 end
 
+@test layerdescriptions(RasterData(CHELSA2, BioClim))["BIO1"] == "Annual Mean Temperature"
+
 @test SimpleSDMDatasets.months(RasterData(CHELSA2, BioClim)) |> isnothing
 @test SimpleSDMDatasets.extrakeys(RasterData(CHELSA2, BioClim)) |> isnothing
 @test SimpleSDMDatasets.layers(RasterData(CHELSA2, BioClim)) |> !isnothing
@@ -22,33 +24,33 @@ end
 @test SimpleSDMDatasets.layers(RasterData(CHELSA2, MinimumTemperature)) |> isnothing
 
 begin
-    out = downloader(RasterData(CHELSA2, BioClim); layer = "BIO12")
+    out = downloader(RasterData(CHELSA2, BioClim); layer="BIO12")
     @test isfile(first(out))
     @test out[2] == SimpleSDMDatasets.filetype(RasterData(CHELSA2, BioClim))
 end
 
 begin
-    out = downloader(RasterData(CHELSA2, AverageTemperature); month = Month(6))
+    out = downloader(RasterData(CHELSA2, AverageTemperature); month=Month(6))
     @test isfile(first(out))
     @test out[2] == SimpleSDMDatasets.filetype(RasterData(CHELSA2, AverageTemperature))
 end
 
 begin
-    out = downloader(RasterData(CHELSA2, MinimumTemperature); month = Month(12))
+    out = downloader(RasterData(CHELSA2, MinimumTemperature); month=Month(12))
     @test isfile(first(out))
     @test out[2] == SimpleSDMDatasets.filetype(RasterData(CHELSA2, MinimumTemperature))
 end
 
 begin
-    out = downloader(RasterData(CHELSA2, MaximumTemperature); month = Month(1))
+    out = downloader(RasterData(CHELSA2, MaximumTemperature); month=Month(1))
     @test isfile(first(out))
     @test out[2] == SimpleSDMDatasets.filetype(RasterData(CHELSA2, MaximumTemperature))
 end
 
 begin
-    out = downloader(RasterData(CHELSA2, Precipitation); month = Month(10))
+    out = downloader(RasterData(CHELSA2, Precipitation); month=Month(10))
     @test isfile(first(out))
     @test out[2] == SimpleSDMDatasets.filetype(RasterData(CHELSA2, Precipitation))
 end
 
-end
+end

SimpleSDMDatasets/test/worldclim_v2.jl

@@ -10,7 +10,7 @@ using Dates
 for T in Base.uniontypes(SimpleSDMDatasets.WorldClim2Dataset)
     @test SimpleSDMDatasets.provides(WorldClim2, T)
     data = RasterData(WorldClim2, T)
-    @test typeof(data) == RasterData{WorldClim2, T}
+    @test typeof(data) == RasterData{WorldClim2,T}
     @test SimpleSDMDatasets.resolutions(data) |> !isnothing
 end
 
@@ -20,29 +20,31 @@ end
 @test SimpleSDMDatasets.layers(RasterData(WorldClim2, AverageTemperature)) |> isnothing
 @test SimpleSDMDatasets.layers(RasterData(WorldClim2, BioClim)) |> !isnothing
 
+@test layerdescriptions(RasterData(WorldClim2, BioClim))["BIO1"] == "Annual Mean Temperature"
+
 begin
-    out = downloader(RasterData(WorldClim2, BioClim); resolution = 10.0, layer = "BIO8")
+    out = downloader(RasterData(WorldClim2, BioClim); resolution=10.0, layer="BIO8")
     @test isfile(first(out))
     @test out[2] == SimpleSDMDatasets.filetype(RasterData(WorldClim2, BioClim))
 end
 
 begin
-    out = downloader(RasterData(WorldClim2, BioClim); resolution = 5.0, layer = "BIO4")
+    out = downloader(RasterData(WorldClim2, BioClim); resolution=5.0, layer="BIO4")
     @test isfile(first(out))
     @test out[2] == SimpleSDMDatasets.filetype(RasterData(WorldClim2, BioClim))
 end
 
 begin
-    out = downloader(RasterData(WorldClim2, Elevation); resolution = 5.0)
+    out = downloader(RasterData(WorldClim2, Elevation); resolution=5.0)
     @test isfile(first(out))
     @test out[2] == SimpleSDMDatasets.filetype(RasterData(WorldClim2, Elevation))
 end
 
 begin
     out = downloader(
         RasterData(WorldClim2, MaximumTemperature);
-        resolution = 10.0,
-        month = Month(4),
+        resolution=10.0,
+        month=Month(4)
     )
     @test isfile(first(out))
     @test out[2] == SimpleSDMDatasets.filetype(RasterData(WorldClim2, MaximumTemperature))
@@ -51,8 +53,8 @@ end
 begin
     out = downloader(
         RasterData(WorldClim2, MinimumTemperature);
-        resolution = 2.5,
-        month = Month(12),
+        resolution=2.5,
+        month=Month(12)
     )
     @test isfile(first(out))
     @test out[2] == SimpleSDMDatasets.filetype(RasterData(WorldClim2, MinimumTemperature))
@@ -61,8 +63,8 @@ end
 begin
     out = downloader(
         RasterData(WorldClim2, AverageTemperature);
-        resolution = 10.0,
-        month = Month(4),
+        resolution=10.0,
+        month=Month(4)
     )
     @test isfile(first(out))
     @test out[2] == SimpleSDMDatasets.filetype(RasterData(WorldClim2, AverageTemperature))
@@ -71,8 +73,8 @@ end
 begin
     out = downloader(
         RasterData(WorldClim2, SolarRadiation);
-        resolution = 10.0,
-        month = Month(4),
+        resolution=10.0,
+        month=Month(4)
     )
     @test isfile(first(out))
     @test out[2] == SimpleSDMDatasets.filetype(RasterData(WorldClim2, SolarRadiation))
@@ -81,8 +83,8 @@ end
 begin
     out = downloader(
         RasterData(WorldClim2, WindSpeed);
-        resolution = 10.0,
-        month = Month(4),
+        resolution=10.0,
+        month=Month(4)
     )
     @test isfile(first(out))
     @test out[2] == SimpleSDMDatasets.filetype(RasterData(WorldClim2, WindSpeed))
@@ -91,11 +93,11 @@ end
 begin
     out = downloader(
         RasterData(WorldClim2, WaterVaporPressure);
-        resolution = 10.0,
-        month = Month(4),
+        resolution=10.0,
+        month=Month(4)
     )
     @test isfile(first(out))
     @test out[2] == SimpleSDMDatasets.filetype(RasterData(WorldClim2, WaterVaporPressure))
 end
 
-end
+end

docs/src/SimpleSDMDatasets/dev/interface.md

@@ -83,8 +83,8 @@ SimpleSDMDatasets.resolutions
 ## Available layers
 
 ```@docs
-SimpleSDMDatasets.layers
-SimpleSDMDatasets.layerdescriptions
+layers
+layerdescriptions
 ```
 
 ## Available months
@@ -115,4 +115,4 @@ SimpleSDMDatasets.source
 
 ```@docs
 SimpleSDMDatasets.destination
-```
+```