From ada453071d3706d835f367fd96acff916b239084 Mon Sep 17 00:00:00 2001
From: Denis Barucic <barucic.d@gmail.com>
Date: Fri, 19 Aug 2022 16:27:38 +0200
Subject: [PATCH] Improve speed of `shannon` and `ginisimpson` (#135)

This commit improves the speed of `shannon` and `ginisimpsons` by
avoiding creation of temporary arrays. The `shannon` function is also
simplified a little.
---
 src/diversity.jl | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/diversity.jl b/src/diversity.jl
index ce033bf..768a242 100644
--- a/src/diversity.jl
+++ b/src/diversity.jl
@@ -11,8 +11,9 @@ See also [`shannon!`](@ref).
 """
 function shannon(v::Union{AbstractVector{T}, AbstractSparseMatrix{T}}) where T<:Real
     total = sum(v)
-    relab = map(x-> x/total, v)
-    return -sum([log(x^x) for x in relab])
+    logtotal = log(total)
+    # The iszero condition is necessary to prevent log(0)
+    return logtotal - sum(x -> iszero(x) ? x : x * log(x), v) / total
 end
 
 function shannon(abt::AbstractAbundanceTable)
@@ -49,8 +50,7 @@ See also [`ginisimpson!`](@ref).
 """
 function ginisimpson(v::Union{AbstractVector{T}, AbstractSparseMatrix{T}}) where T<:Real
     total = sum(v)
-    relab = map(x-> x/total, v)
-    return 1 - sum([x^2 for x in relab])
+    return 1 - sum(x -> x^2, v) / (total^2)
 end
 
 function ginisimpson(abt::AbstractAbundanceTable)