From 0cc0b18fca95afa7df954783170c6a23bf63c4a4 Mon Sep 17 00:00:00 2001
From: Philip Swannell <philip.swannell@gmail.com>
Date: Sat, 23 Jan 2021 14:54:11 +0000
Subject: [PATCH] fix type instabilities, more use of @inbounds

---
 src/rankcorr.jl | 33 +++++++++++++++++----------------
 1 file changed, 17 insertions(+), 16 deletions(-)

diff --git a/src/rankcorr.jl b/src/rankcorr.jl
index e87d701..ea094c1 100644
--- a/src/rankcorr.jl
+++ b/src/rankcorr.jl
@@ -22,7 +22,7 @@ function corkendall!(x::RealVector, y::RealVector, permx=sortperm(x))
     npairs = div(n * (n - 1), 2)
     ntiesx, ntiesy, ndoubleties, k, nswaps = 0, 0, 0, 0, 0
 
-    for i ∈ 2:n
+    @inbounds for i ∈ 2:n
         if x[i - 1] == x[i]
             k += 1
         elseif k > 0
@@ -30,14 +30,14 @@ function corkendall!(x::RealVector, y::RealVector, permx=sortperm(x))
             # sorted first on x, then (where x values are tied) on y. Hence 
             # double ties can be counted by calling countties.
             mergesort!(y,  i - k - 1, i - 1)
-            ntiesx += k * (k + 1) / 2
+            ntiesx += div(k * (k + 1) , 2)
             ndoubleties += countties(y,  i - k - 1, i - 1)
             k = 0
         end
     end
     if k > 0
         mergesort!(y,  n - k, n)
-        ntiesx += k * (k + 1) / 2
+        ntiesx += div(k * (k + 1) , 2)
         ndoubleties += countties(y,  n - k, n)
     end
 
@@ -55,17 +55,18 @@ Assumes `x` is sorted. Returns the number of ties within `x[lo:hi]`.
 """
 function countties(x::AbstractVector, lo::Integer, hi::Integer)
     thistiecount, result = 0, 0
-    for i ∈ (lo + 1):hi
+    (lo < 1 || hi > length(x)) && error("Bounds error")
+    @inbounds for i ∈ (lo + 1):hi
         if x[i] == x[i - 1]
             thistiecount += 1
         elseif thistiecount > 0
-            result += (thistiecount * (thistiecount + 1)) / 2
+            result += div(thistiecount * (thistiecount + 1) , 2)
             thistiecount = 0
         end
     end
 
     if thistiecount > 0
-        result += (thistiecount * (thistiecount + 1)) / 2
+        result += div(thistiecount * (thistiecount + 1), 2)
     end
     result
 end
@@ -85,7 +86,7 @@ corkendall(x::RealVector, Y::RealMatrix) = (n = size(Y, 2); permx = sortperm(x);
 function corkendall(X::RealMatrix)
     n = size(X, 2)
     C = ones(float(eltype(X)), n, n)# avoids dependency on LinearAlgebra
-    for j ∈ 2:n
+    @inbounds for j ∈ 2:n
         permx = sortperm(X[:,j])
         for i ∈ 1:j - 1
             C[j,i] = corkendall!(X[:,j], X[:,i], permx)
@@ -99,7 +100,7 @@ function corkendall(X::RealMatrix, Y::RealMatrix)
     nr = size(X, 2)
     nc = size(Y, 2)
     C = zeros(float(eltype(X)), nr, nc)
-    for j ∈ 1:nr
+    @inbounds for j ∈ 1:nr
         permx = sortperm(X[:,j])
         for i ∈ 1:nc
             C[j,i] = corkendall!(X[:,j], Y[:,i], permx)
@@ -110,10 +111,11 @@ end
 
 # Auxilliary functions for Kendall's rank correlation
 
-# Same value for this constant as in base/sort.jl. Method speedtestmergesort seems
-# to show that a value of 64 is fractionaly (2% ?) faster but safer to follow base/sort.jl, which has it at 20.
+# Method speedtest_mergesort appears to to show that a value of 64 is optimal,
+# but note that the equivalent constant in base/sort.jl is 20.
 const SMALL_THRESHOLD  = 64
 
+#Copy was from https://github.com/JuliaLang/julia/commit/28330a2fef4d9d149ba0fd3ffa06347b50067647 dated 20 Sep 2020
 """
     mergesort!(v::AbstractVector, lo::Integer, hi::Integer, t=similar(v, 0))    
 
@@ -160,19 +162,18 @@ function mergesort!(v::AbstractVector, lo::Integer, hi::Integer, t=similar(v, 0)
     return nswaps
 end
 
-# This implementation of `midpoint` is performance-optimized but safe
-# only if `lo <= hi`.
-# This function is copied from base/sort.jl
+# This implementation of `midpoint` is performance-optimized but safe only if `lo <= hi`.
+# This function is also copied from base/sort.jl
 midpoint(lo::T, hi::T) where T <: Integer = lo + ((hi - lo) >>> 0x01)
 midpoint(lo::Integer, hi::Integer) = midpoint(promote(lo, hi)...)
 
-
+#Copy was from https://github.com/JuliaLang/julia/commit/28330a2fef4d9d149ba0fd3ffa06347b50067647 dated 20 Sep 2020
 """
     insertionsort!(v::AbstractVector, lo::Integer, hi::Integer)
 
 Mutates `v` by sorting elements `x[lo:hi]` using the insertionsort algorithm. 
 This method is a copy-paste-edit of sort! in base/sort.jl (the method specialised on InsertionSortAlg),
-but amended to return the bubblesort distance.
+amended to return the bubblesort distance.
 """
 function insertionsort!(v::AbstractVector, lo::Integer, hi::Integer)
     if lo == hi return 0 end
@@ -192,4 +193,4 @@ function insertionsort!(v::AbstractVector, lo::Integer, hi::Integer)
         v[j] = x
     end
     return nswaps
-end
+end
\ No newline at end of file