Merge pull request #27 from kescobo/kevdev

Some beta diversity functions

src/Microbiome.jl

@@ -33,7 +33,10 @@ export
     optimalorder,
     optimalorder!,
     ginisimpson,
-    shannon
+    shannon,
+    present,
+    prevalence
+
 
 using Reexport
 @reexport using SpatialEcology

src/abundances.jl

@@ -84,3 +84,14 @@ function relativeabundance(a::AbstractComMatrix; kind::Symbol=:fraction)
     relativeabundance!(relab, kind=kind)
     return relab
 end
+
+"""
+Check if a given (non-zero) value is greater than a minimum value.
+If the minimum abundance is 0, just checks if value is non-zero
+"""
+present(t::Float64, minabundance::Float64=0.0001) = t == 0 ? false : t >= minabundance
+
+"""
+Return the fraction of values that are greater than a minimum
+"""
+prevalence(a::AbstractArray{<:Real}, minabundance::Float64=0.0001) = mean(x-> present(x, minabundance), a)

test/runtests.jl

@@ -62,6 +62,15 @@ using Test
     end
 
     @test featurenames(filt)[end] == "other"
+
+    @test present(0.1, 0.001)
+    @test !present(0.001, 0.1)
+    @test present(rand(), 0.)
+
+    a = zeros(100)
+    a[randperm(100)[1:10]] .= rand(10)
+
+    @test prevalence(a, 0.) == 0.1
 end
 
 @testset "Distances" begin