Fix the sample function

src/SpeciesDistributionToolkit.jl

@@ -42,5 +42,6 @@ include("io/read_write.jl")
 include("pseudoabsences.jl")
 export WithinRadius, SurfaceRangeEnvelope, RandomSelection
 export pseudoabsencemask
+export rarefy
 
 end # module SpeciesDistributionToolkit

src/pseudoabsences.jl

@@ -36,7 +36,10 @@ end
 """
     _random_point(ref, d; R = 6371.0)
 
-This function is used _internally_ to create a random point located within a distance `d` of point `ref`, assuming that the radius of the Earth is `R`. All it does is to generate a random angle in degrees, and the using the `_known_point` method to generate the new point.
+This function is used _internally_ to create a random point located within a
+distance `d` of point `ref`, assuming that the radius of the Earth is `R`. All
+it does is to generate a random angle in degrees, and the using the
+`_known_point` method to generate the new point.
 """
 function _random_point(ref, d; R = 6371.0)
     α = deg2rad(rand() * 360.0)
@@ -46,7 +49,8 @@ end
 """
     _known_point(ref, d, α; R = 6371.0)
 
-This function will generate a new point set at a distance `d` and angle `α` from the `ref` point, assuming the radius of the Earth is `R`.
+This function will generate a new point set at a distance `d` and angle `α` from
+the `ref` point, assuming the radius of the Earth is `R`.
 """
 function _known_point(ref, d, α; R = 6371.0)
     # Convert the coordinates from degrees to radians
@@ -106,10 +110,10 @@ end
 """
     pseudoabsencemask(::Type{RandomSelection}, presence::T) where {T <: SimpleSDMLayer}
 
-Generates a mask for pseudo-absences using the random selection method. Candidate
-cells for the pseudo-absence mask are (i) within the bounding box of the _layer_
-(use `SurfaceRangeEnvelope` to use the presences bounding box), and (ii) valued in the
-layer.
+Generates a mask for pseudo-absences using the random selection method.
+Candidate cells for the pseudo-absence mask are (i) within the bounding box of
+the _layer_ (use `SurfaceRangeEnvelope` to use the presences bounding box), and
+(ii) valued in the layer.
 """
 function pseudoabsencemask(
     ::Type{RandomSelection},
@@ -151,13 +155,13 @@ function pseudoabsencemask(
 end
 
 """
-    sample(layer::T, n::Integer = 1; kwargs...) where {T <: SimpleSDMLayer}
+    rarefy(layer::T, n::Integer = 1; kwargs...) where {T <: SimpleSDMLayer}
 
 Sample a series of background points from a Boolean layer. The `kwargs`
 arguments are passed to `StatsBase.sample`. This method returns a Boolean layer
 where the values of `true` correspond to a background point.
 """
-function sample(layer::T, n::Integer = 1; kwargs...) where {T <: SimpleSDMLayer}
+function rarefy(layer::T, n::Integer = 1; kwargs...) where {T <: SimpleSDMLayer}
     @assert SimpleSDMLayers._inner_type(layer) <: Bool
     pseudoabs = similar(layer, Bool)
     for k in StatsBase.sample(keys(replace(layer, false => nothing)), n; kwargs...)
@@ -167,14 +171,14 @@ function sample(layer::T, n::Integer = 1; kwargs...) where {T <: SimpleSDMLayer}
 end
 
 """
-    sample( layer::T, weights::T2, n::Integer = 1; kwargs..., ) where {T <: SimpleSDMLayer, T2 <: SimpleSDMLayer}
+    rarefy(layer::T, weights::T2, n::Integer = 1; kwargs..., ) where {T <: SimpleSDMLayer, T2 <: SimpleSDMLayer}
 
 Sample a series of background points from a Boolean layer, where each point has
 a probability of being included in the background given by the second layer.
 This methods works like (and is, in fact, a wrapper around) `StatsBase.sample`,
 where the cell values in the weight layers are transformed into weights.
 """
-function sample(
+function rarefy(
     layer::T,
     weights::T2,
     n::Integer = 1;

test/02_rarefy.jl

@@ -0,0 +1,8 @@
+module TestThatRarefyWorks
+
+using Test
+using SpeciesDistributionToolkit
+
+@test error("Rarefy tests are not implemented yet")
+
+end

test/Project.toml

@@ -1,3 +1,4 @@
 [deps]
 GDAL = "add2ef01-049f-52c4-9ee2-e494f65e021a"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+TestItems = "1c621080-faea-4a02-84b6-bbd5e436b8fe"

test/edgecases/03_layers_keycheck.jl

@@ -1,7 +1,4 @@
-module TestThatWrongKeywordsAreCaught
-
-using SpeciesDistributionToolkit
-using Test
+@testitem "Layers are correctly keychecked" begin
 
 provider = RasterData(WorldClim2, BioClim)
 @test_throws "The keyword argument layers is not" SimpleSDMPredictor(provider; layers=3)

test/rarefy.jl

@@ -0,0 +1,9 @@
+@testitem "Rarefy returns the correct number of points" begin
+
+    random_layer = SimpleSDMResponse(rand(Bool, (20, 30)))
+
+    rarefied_layer = rarefy(random_layer, 100)
+    replace!(rarefied_layer, false => nothing)
+    @info rarefied_layer
+
+end

test/runtests.jl

@@ -5,6 +5,7 @@ global anyerrors = false
 
 tests = [
     "read/write layers" => "01_integration_read.jl",
+    "rarefy pseudo-absences" => "02_rarefy.jl",
     "EDGE: stitch bounding box" => "edgecases/01_stitch_wrong_bb.jl",
     "EDGE: clip & GDAL" => "edgecases/02_clip_gdalwarp.jl",
     "EDGE: keychecker" => "edgecases/03_layers_keycheck.jl",