Jaccard similarity here

EcoJulia · Nov 10, 2023 · 3801b38 · 3801b38
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commit 3801b38
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Showing 4 changed files with 14 additions and 13 deletions.
diff --git a/NEWS.md b/NEWS.md
@@ -3,7 +3,7 @@
 - v0.5.8
   - Add in Pielou diversity measures
   - Add docs for PRs
-  - Fix Jaccard to be differentiation measure
+  - Generalise Jaccard with similarity
 - v0.5.7
   - Update compat and some doc fixes
 - v0.5.6

diff --git a/src/Ecology.jl b/src/Ecology.jl
@@ -213,7 +213,7 @@ end
     generalisedjaccard(proportions::AbstractArray, qs, sim::AbstractTypes)
     generalisedjaccard(meta::AbstractAssemblage, qs)
 
-Calculates a generalisation of the Jaccard index of two columns
+Calculates a generalisation of the Jaccard similarity of two columns
 representing the counts of two subcommunities. This evaluates to raw
 alpha / gamma - 1 for a series of orders, repesented as a vector of qs
 (or a single number). It also includes an optional similarity matrix
@@ -244,7 +244,7 @@ generalisedjaccard(proportions::AbstractMatrix, sim::AbstractTypes) =
 function generalisedjaccard(meta::AbstractAssemblage)
     countsubcommunities(meta) == 2 ||
     error("Can only calculate Jaccard index for 2 subcommunities")
-    num = sum(abs.(diff(getordinariness!(meta), dims = 2)))
+    num = sum(minimum(getordinariness!(meta), dims = 2))
     denom = sum(maximum(getordinariness!(meta), dims = 2))
     jac = metadiv(Gamma(meta), 0)
     jac[!,:diversity] .= num / denom
@@ -257,12 +257,13 @@ end
     jaccard(proportions::AbstractMatrix)
     jaccard(asm::AbstractAssemblage)
 
-Calculates Jaccard index (Jaccard similarity coefficient) of two
+Calculates Jaccard similarity coefficient of two
 columns representing independent subcommunity counts
 
 #### Arguments:
 
 - `proportions`: population proportions
+- `asm`: assemblage / metacommunity
 
 #### Returns:
 

diff --git a/test/run_rcall.jl b/test/run_rcall.jl
@@ -82,8 +82,8 @@ if !skipR
             jag = gower(pops, countzeros = false).diversity[1]
             jag1 = gower([x > 0 ? 1 : 0 for x in pops], countzeros = false).diversity[1]
 
-            @test jj ≈ rj
-            @test jj1 ≈ rj1
+            @test jj ≈ 1.0 - rj
+            @test jj1 ≈ 1.0 - rj1
             @test jg ≈ rg
             @test jg1 ≈ rg1
             @test jag ≈ rag
@@ -123,8 +123,8 @@ if !skipR
             jag = gower(pops, countzeros = false).diversity[1]
             jag1 = gower([x > 0 ? 1 : 0 for x in pops], countzeros = false).diversity[1]
 
-            @test jj ≈ rj
-            @test jj1 ≈ rj1
+            @test jj ≈ 1.0 - rj
+            @test jj1 ≈ 1.0 - rj1
             @test jg ≈ rg
             @test jg1 ≈ rg1
             @test jag ≈ rag

diff --git a/test/test_Ecology.jl b/test/test_Ecology.jl
@@ -36,12 +36,12 @@ Z1 = ones(typeof(weights[1]), (length(weights), length(weights)));
     @test_throws ErrorException simpson(Metacommunity(communities,
         GeneralTypes(rand(numspecies,numspecies))))
 
-    @test jaccard([1 0 0; 0 1 1]'/3)[!,:diversity][1] ≈ 1.0
+    @test jaccard([1 0 0; 0 1 1]'/3)[!,:diversity][1] + 1.0 ≈ 1.0
     @test jaccard(Metacommunity([1 0 1; 0 1 1]'/4))[!,:diversity] ==
         jaccard([1 0 1; 0 1 1]'/4)[!,:diversity]
     @test_throws ErrorException jaccard(Metacommunity([1 0 1; 0 1 1]'/4,
                                                       GeneralTypes(rand(3, 3))))
-    @test jaccard([1 0 1; 0 1 1]'/4)[!,:diversity][1] ≈ 2.0 / 3.0
+    @test jaccard([1 0 1; 0 1 1]'/4)[!,:diversity][1] ≈ 1.0 / 3.0
     @test_throws ErrorException jaccard([1 1 0; 0 1 1; 1 1 1]/7)
     @test_throws ErrorException jaccard(Metacommunity([1 1 0; 0 1 1; 1 1 1]/7))
 
@@ -82,9 +82,9 @@ end
     @test_throws ErrorException generalisedsimpson(individualDiversity,
                                                    communities, Z1)
 
-    @test generalisedjaccard([1 0 1; 0 1 1]'/4, UniqueTypes(3))[!,:diversity][1] ≈ 2.0/3.0
-    @test generalisedjaccard([1 0 1; 0 1 1]'/4, ones(Float64, 3, 3))[!,:diversity][1] ≈ 0.0
-    @test generalisedjaccard([1 1 1; 1 1 1]'/6, Matrix(1.0I, 3, 3))[!,:diversity][1] ≈ 0.0
+    @test generalisedjaccard([1 0 1; 0 1 1]'/4, UniqueTypes(3))[!,:diversity][1] ≈ 1.0/3.0
+    @test generalisedjaccard([1 0 1; 0 1 1]'/4, ones(Float64, 3, 3))[!,:diversity][1] ≈ 1.0
+    @test generalisedjaccard([1 1 1; 1 1 1]'/6, Matrix(1.0I, 3, 3))[!,:diversity][1] ≈ 1.0
 
     @test all(Diversity.Ecology.generalisedpielou(subcommunityDiversity, [1/6 2/6; 1/6 2/6]).diversity .≈ 1.0)