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optimise ExactPermutationTest. #225

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optimise ExactPermutationTest. #225

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7 changes: 5 additions & 2 deletions src/permutation.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -21,8 +21,11 @@ that `f(x)` is equal to `f(y)`. All possible permutations are sampled.
function ExactPermutationTest(x::AbstractVector{R}, y::AbstractVector{S},
f::Function) where {R<:Real,S<:Real}
xy, rx, ry = ptstats(x,y)
P = permutations(xy)
samples = [f(view(p,rx)) - f(view(p,ry)) for p in P]
rxry = [rx;ry]
P = combinations(rxry,rx[end])
# check the length of the output before allocating memory (10^9 is time consuming, but feasible)
@assert binomial(big(length(rxry)),rx[end])<10^9 "Performing the exact test is computionally expensive, you may use the ApproximatePermutationTest function instead."
samples = [f(view(xy,p)) - f(view(xy,setdiff(rxry,p))) for p in P]
PermutationTest(f(x) - f(y), samples)
end

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