v0.4

Project.toml

@@ -4,36 +4,47 @@ authors = ["michael catchen <michael.catchen@colorado.edu>"]
 version = "0.2.1"
 
 [deps]
-CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
+Clustering = "aaaa29a8-35af-508c-8bc3-b662a17a0fe5"
+DelaunayTriangulation = "927a84f5-c5f4-47a5-9785-b46e178433df"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
+GeoInterface = "cf35fbd7-0cd7-5166-be24-54bfbe79505f"
+GeometryOps = "3251bfac-6a57-4b6d-aa61-ac1fef2975ab"
 HaltonSequences = "13907d55-377f-55d6-a9d6-25ac19e11b95"
 HiGHS = "87dc4568-4c63-4d18-b0c0-bb2238e4078b"
 JuMP = "4076af6c-e467-56ae-b986-b466b2749572"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+MultivariateStats = "6f286f6a-111f-5878-ab1e-185364afe411"
 ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
-Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 SimpleSDMLayers = "2c645270-77db-11e9-22c3-0f302a89c64c"
 SliceMap = "82cb661a-3f19-5665-9e27-df437c7e54c8"
 SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
+SpeciesDistributionToolkit = "72b53823-5c0b-4575-ad0e-8e97227ad13b"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 Term = "22787eb5-b846-44ae-b979-8e399b8463ab"
 TestItems = "1c621080-faea-4a02-84b6-bbd5e436b8fe"
 
 [weakdeps]
+Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
 NeutralLandscapes = "71847384-8354-4223-ac08-659a5128069f"
 
 [extensions]
+BONsMakieExt = "Makie"
 
 [compat]
+Clustering = "0.15.7"
+DelaunayTriangulation = "1.6.3"
 Distributions = "0.25"
+GeoInterface = "1.4.0"
+GeometryOps = "0.1.13"
 HaltonSequences = "0.2"
 HiGHS = "1.5"
 JuMP = "1.11"
+MultivariateStats = "0.10.3"
 ProgressMeter = "1.7.2"
-Requires = "1.3"
 SliceMap = "0.2.7"
 SpecialFunctions = "2.1"
+SpeciesDistributionToolkit = "1.2.0"
 StatsBase = "0.34"
 julia = "1.9"

_SCRATCH/Project.toml

@@ -0,0 +1,4 @@
+[deps]
+BiodiversityObservationNetworks = "a5b868d3-191d-4bba-a38a-ad28190da010"
+CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
+GeoMakie = "db073c08-6b98-4ee5-b6a4-5efafb3259c6"

_SCRATCH/scratchpad.jl

@@ -0,0 +1,39 @@
+using Pkg
+Pkg.activate(@__DIR__)
+
+using BiodiversityObservationNetworks
+using CairoMakie, GeoMakie
+
+
+import BiodiversityObservationNetworks as BONs
+import BiodiversityObservationNetworks.SpeciesDistributionToolkit as SDT
+import BiodiversityObservationNetworks.GeoInterface as GI
+import BiodiversityObservationNetworks.GeometryOps as GO
+
+
+col = SDT.gadm("COL")
+col_states = SDT.gadm("COL", 1)
+
+bioclim = RasterStack([SDT.mask!(SDT.SDMLayer(SDT.RasterData(SDT.WorldClim2, SDT.BioClim); layer=i, SDT.boundingbox(col)...), col) for i in 1:19])
+
+bon = sample(SimpleRandom(50), bioclim)
+bon = sample(SimpleRandom(10), col_states)
+bon = sample(SpatiallyStratified(100), col_states)
+bon = BONs.sample(Grid(), col)
+bon = BONs.sample(KMeans(75), bioclim)
+
+
+cornerplot(bioclim)
+
+
+
+begin 
+    f = Figure(size=(900,900))
+    ga = GeoAxis(f[1,1])
+    for (i,st) in enumerate(convert(Polygon, col_states))
+    poly!(ga, st.geometry, strokewidth=2, color=Symbol("grey", string(20+2*i)))
+    scatter!(ga, [node[1] for node in bon], [node[2] for node in bon], color=(:red))
+    end
+    f
+end 
+

docs/make.jl

@@ -8,7 +8,7 @@ using BiodiversityObservationNetworks
 bib = CitationBibliography(joinpath(@__DIR__, "BONs.bib"))
 
 makedocs(
-    sitename = "BiodiversityObservationNetwork.jl",
+    sitename = "BiodiversityObservationNetworks.jl",
     authors = "Michael D. Catchen, Timothée Poisot, Kari Norman, Hana Mayall, Tom Malpas",
     modules = [BiodiversityObservationNetworks],
     format = DocumenterVitepress.MarkdownVitepress(

docs/src/index.md

@@ -4,49 +4,12 @@ The purpose of this package is to provide a high-level, extensible, modular
 interface to the selection of sampling point for biodiversity processes in
 space. It is based around a collection of types representing point selection
 algorithms, used to select the most informative sampling points based on raster
-data. Specifically, many algorithms work from a layer indicating *entropy* of a
-model based prediction at each location.
+data. 
 
 !!! warning "This package is in development"
     The `BiodiversityObservationNetworks.jl` package is currently under development. The API is not expected to change a lot, but it may change in order to facilitate the integration of new features.
 
-## High-level types
-
-```@docs
-BONSampler
-BONSeeder
-BONRefiner
-```
-
-## Seeder and refiner functions
-
-```@docs
-seed
-seed!
-```
-
-```@docs
-refine
-refine!
-```
-
-## Seeder algorithms
-
-```@docs
-BalancedAcceptance
-```
-
-## Refiner algorithms
-
-```@docs
-AdaptiveSpatial
-Uniqueness
-```
-
-## Helper functions
-
-```@docs
-squish
-entropize!
-entropize
+```@autodocs
+Modules = [BiodiversityObservationNetworks]
+Order   = [:type, :function]
 ```

ext/BONsMakieExt/BONsMakieExt.jl

@@ -0,0 +1,13 @@
+module BONsMakieExt
+
+@info "Loading Makie Extension for BiodiversityObservationNetworks.jl..."
+
+@static if isdefined(Base, :get_extension)
+    using Makie, BiodiversityObservationNetworks
+else    
+    using ..Makie, ..BiodiversityObservationNetworks
+end
+
+include(joinpath(@__DIR__, "recipes.jl"))
+
+end

ext/BONsMakieExt/recipes.jl

@@ -0,0 +1,33 @@
+const MAX_CORNERPLOT_DIMS_BEFORE_PCA = 20
+
+function BiodiversityObservationNetworks.cornerplot(
+    layers::RasterStack;
+    pca_layers = false
+)
+
+    _, mat = BiodiversityObservationNetworks.features(layers)
+    num_layers = length(layers)
+    if num_layers > MAX_CORNERPLOT_DIMS_BEFORE_PCA || pca_layers
+        pca = BiodiversityObservationNetworks.MultivariateStats.fit(BiodiversityObservationNetworks.MultivariateStats.PCA, mat)
+        @info length(pca.prinvars)
+        num_layers = length(pca.prinvars)
+        mat = BiodiversityObservationNetworks.MultivariateStats.transform(pca, mat)    
+    end 
+
+    f = Figure(size=(900,900))
+    for i in 1:num_layers-1, j in 1:num_layers
+        if j > i
+            ax = Axis(
+                f[j-1,i],
+                xlabel = j == num_layers ? "$i" : "",
+                ylabel = i == 1 ? "$j" : "",
+                xticksvisible=false,
+                yticksvisible=false,
+                xticklabelsvisible=false,
+                yticklabelsvisible=false,
+            )
+            hexbin!(ax, mat[i,:], mat[j,:], bins=40)
+        end
+    end 
+    f
+end