Copernicus land cover data (#335)

* feat(data): copernicus layer * semver(data): v1.0.0 * doc(data): links to dataset * doc(data): use Copernicus example * doc(data): new layer * doc(data): typo * feat(data): copernicus lc forest type * doc: link Closes #327
PoisotLab · Dec 6, 2024 · aceb728 · aceb728 · tpoisot · Dec 6, 2024
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diff --git a/SimpleSDMDatasets/Project.toml b/SimpleSDMDatasets/Project.toml
@@ -1,7 +1,7 @@
 name = "SimpleSDMDatasets"
 uuid = "2c7d61d0-5c73-410d-85b2-d2e7fbbdcefa"
 authors = ["Timothée Poisot <[email protected]>"]
-version = "0.2.3"
+version = "1.0.0"
 
 [deps]
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"

diff --git a/SimpleSDMDatasets/src/SimpleSDMDatasets.jl b/SimpleSDMDatasets/src/SimpleSDMDatasets.jl
@@ -26,7 +26,7 @@ export MammalRichness, BirdRichness, AmphibianRichness
 
 include("types/providers.jl")
 export RasterProvider
-export WorldClim2, EarthEnv, CHELSA1, CHELSA2, BiodiversityMapping, PaleoClim
+export WorldClim2, EarthEnv, CHELSA1, CHELSA2, BiodiversityMapping, PaleoClim, Copernicus
 
 include("types/futures.jl")
 export FutureScenario, FutureModel
@@ -75,6 +75,9 @@ include("providers/BiodiversityMapping/biodiversitymapping.jl")
 
 include("providers/PaleoClim/bioclim.jl")
 
+include("providers/Copernicus/copernicus.jl")
+include("providers/Copernicus/landcover.jl")
+
 # Key checker
 include("keychecker.jl")
 

diff --git a/SimpleSDMDatasets/src/providers/Copernicus/copernicus.jl b/SimpleSDMDatasets/src/providers/Copernicus/copernicus.jl
@@ -0,0 +1,15 @@
+provides(::Type{Copernicus}, ::Type{LandCover}) = true
+
+url(::Type{Copernicus}) = "https://land.copernicus.eu/en/products/global-dynamic-land-cover"
+blurb(::Type{Copernicus}) = md"""
+The Global Dynamic Land Cover product offers annual global land cover maps and
+cover fraction layers, providing a detailed view of land cover at three
+classification levels. It uses modern data analysis techniques to ensure
+temporal consistency and accuracy, with the latest version achieving 80%
+accuracy at class level 1 on each continent. The product also includes
+continuous field layers, or "fraction maps", that provide proportional estimates
+for vegetation and ground cover for the land cover types. These features make it
+a versatile tool for a wide range of applications, including forest monitoring,
+rangeland management, crop monitoring, biodiversity conservation, climate
+modelling, and urban planning.
+"""
diff --git a/SimpleSDMDatasets/src/providers/Copernicus/landcover.jl b/SimpleSDMDatasets/src/providers/Copernicus/landcover.jl
@@ -0,0 +1,67 @@
+url(::RasterData{Copernicus, LandCover}) = "https://zenodo.org/records/3939050"
+
+blurb(::RasterData{Copernicus, LandCover}) = md"""
+Near real time epoch 2019 from the Collection 3 of annual, global 100m land
+cover maps.
+
+Produced by the global component of the Copernicus Land Service, derived from
+PROBA-V satellite observations and ancillary datasets.
+
+:::details Citation
+
+Marcel Buchhorn, Bruno Smets, Luc Bertels, Bert De Roo, Myroslava Lesiv,
+Nandin-Erdene Tsendbazar, Martin Herold, & Steffen Fritz. (2020). Copernicus
+Global Land Service: Land Cover 100m: collection 3: epoch 2019: Globe (V3.0.1)
+[Data set]. Zenodo. https://doi.org/10.5281/zenodo.3939050
+
+:::
+
+"""
+
+# Update the layers
+layers(::RasterData{Copernicus, LandCover}) = [
+    "Bare",
+    "Built-up",
+    "Crops",
+    "Grass",
+    "Moss and lichen",
+    "Permanent water",
+    "Seasonal water",
+    "Shrubs",
+    "Snow",
+    "Trees",
+    "Classification",
+    "Forest type"
+]
+
+function __copernify(str)
+    varnames = Dict(
+        "Bare" => "Bare-CoverFraction-layer",
+        "Built-up" => "BuiltUp-CoverFraction-layer",
+        "Crops" => "Crops-CoverFraction-layer",
+        "Grass" => "Grass-CoverFraction-layer",
+        "Moss and Lichen" => "MossLichen-CoverFraction-layer",
+        "Permanent water" => "PermanentWater-CoverFraction-layer",
+        "Seasonal water" => "SeasonalWater-CoverFraction-layer",
+        "Shrubs" => "Shrub-CoverFraction-layer",
+        "Snow" => "Snow-CoverFraction-layer",
+        "Trees" => "Tree-CoverFraction-layer",
+        "Classification" => "Discrete-Classification-map",
+        "Forest type" => "Forest-Type-layer",
+    )
+
+    return varnames[str]
+end
+
+function source(
+    data::RasterData{Copernicus, LandCover};
+    layer = "Classification",
+)
+    var_code = __copernify(layer)
+    dlurl = "https://zenodo.org/records/3939050/files/PROBAV_LC100_global_v3.0.1_2019-nrt_$(var_code)_EPSG-4326.tif?download=1"
+    return (
+        url = dlurl,
+        filename = lowercase("PROBAV_LC100_global_v3.0.1_2019-nrt_$(var_code)_EPSG-4326.tif"),
+        outdir = destination(data),
+    )
+end
diff --git a/SimpleSDMDatasets/src/types/providers.jl b/SimpleSDMDatasets/src/types/providers.jl
@@ -40,4 +40,11 @@ struct BiodiversityMapping <: RasterProvider end
 
 Paleoclimate data from http://www.paleoclim.org/ - see this website for citation information
 """
-struct PaleoClim <: RasterProvider end
+struct PaleoClim <: RasterProvider end
+
+"""
+    Copernicus
+
+Produced by the global component of the Copernicus Land Service, derived from PROBA-V satellite observations and ancillary datasets -- see https://land.copernicus.eu/en/products/global-dynamic-land-cover
+"""
+struct Copernicus <: RasterProvider end
diff --git a/docs/src/.vitepress/config.mts b/docs/src/.vitepress/config.mts
@@ -51,12 +51,13 @@ export default defineConfig({
             {
                 text: 'Datasets',
                 items: [
+                    { text: "BiodiversityMapping", link: "/datasets/BiodiversityMapping" },
                     { text: "CHELSA 1", link: "/datasets/CHELSA1" },
                     { text: "CHELSA 2", link: "/datasets/CHELSA2" },
-                    { text: "WorldClim 2", link: "/datasets/WorldClim2" },
-                    { text: "PaleoClim", link: "/datasets/PaleoClim" },
+                    { text: "Copernicus", link: "/datasets/Copernicus" },
                     { text: "EarthEnv", link: "/datasets/EarthEnv" },
-                    { text: "BiodiversityMapping", link: "/datasets/BiodiversityMapping" },
+                    { text: "PaleoClim", link: "/datasets/PaleoClim" },
+                    { text: "WorldClim 2", link: "/datasets/WorldClim2" },
                 ]
             },
             {
@@ -96,7 +97,7 @@ export default defineConfig({
                         {text: "... list provided layers?", link: "/howto/list-provided-layers/"},
                         {text: "... do arithmetic on layers?", link: "/howto/layer-arithmetic/"},
                         {text: "... mask a layer?", link: "/howto/mask-layer/"},
-                        {text: "... mask with polygons", link: "/howto/mask-polygons/"},
+                        {text: "... mask with polygons?", link: "/howto/mask-polygons/"},
                         {text: "... read part of a layer?", link: "/howto/read-part-layer/"},
                         {text: "... get the bounding box for an object?", link: "/howto/get-boundingbox/"},
                         {text: "... calculate statistics on layers?", link: "/howto/layer-statistics/"},

diff --git a/docs/src/howto/get-boundingbox.jl b/docs/src/howto/get-boundingbox.jl
@@ -7,7 +7,7 @@ CairoMakie.activate!(; type = "png", px_per_unit = 2) #hide
 # The `boundingbox` method accepts most types that `SpeciesDistributionToolkit`
 # knows about, and returns a tuple:
 
-occ = occurrences("hasCoordinate" => true, "country" => "BR", "limit" => 300)
+occ = occurrences("hasCoordinate" => true, "country" => "CH", "limit" => 300)
 SpeciesDistributionToolkit.boundingbox(occ)
 
 # We can also specify a padding (in degrees) that is added to the bounding box:
@@ -24,11 +24,12 @@ SpeciesDistributionToolkit.boundingbox(occ; padding = 1.0)
 # 
 # :::
 
-# This is useful to restrict the part of a layer that is loaded:
+# This is useful to restrict the part of a layer that is loaded, here one of the
+# fractional layers from the copernicus landcover dataset:
 
 L = SDMLayer(
-    RasterData(CHELSA1, BioClim);
-    layer = 1,
+    RasterData(Copernicus, LandCover);
+    layer = "Crops",
     SpeciesDistributionToolkit.boundingbox(occ; padding = 0.5)...,
 )
 

diff --git a/docs/src/manual.md b/docs/src/manual.md
@@ -9,7 +9,7 @@ distribution modeling and biodiversity research, for the
 This package is now used in pipelines in [BON in a
 Box](https://boninabox.geobon.org/index), [GEOBON](https://geobon.org/)'s
 project to automate the calculation and representation of the post-2020 [GBF
-indicators](https://www.cbd.int/gbf).
+indicators](https://www.cbd.int/gbf). See the [BON in a Box tool page](https://boninabox.geobon.org/tool-detail?id=236).
 
 :::
 

diff --git a/docs/src/reference/datasets/CHANGELOG.md b/docs/src/reference/datasets/CHANGELOG.md
@@ -5,7 +5,7 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-<!-- Added, Changed, Deprecated, Removed, Fixed -->
+## `v1.0.0`
 
-## [Unreleased]
+- **added** support for the [Copernicus Global Land Service](https://zenodo.org/records/3939050) landcover data