Covariance-related functions for general AbstractArray #599
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| @@ -87,27 +100,32 @@ weight_funcs = (weights, aweights, fweights, pweights) | |||
| @testset "Mean and covariance" begin | |||
| (m, C) = mean_and_cov(X; corrected=false) | |||
| @test m == mean(X, dims=1) | |||
| @test C == cov(X, dims=1, corrected=false) | |||
| @test C ≈ cov(X, dims=1, corrected=false) | |||
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Any reason to use ≈ rather than isequal?
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Strict equality fails for sparse matrices because cov is specialized for SparseMatrixCSC in Statistics (https://github.com/JuliaLang/Statistics.jl/blob/b384104d35ff0e7cf311485607b177223ed72b9a/src/Statistics.jl#L1058), but mean_and_cov uses covm rather than cov.
I think if we want to achieve strict equality here, the fix should be in Statistics (specializing covm rather than cov)
| @inbounds for i in CartesianIndices(size(C)) | ||
| si = s[i[1]] * s[i[2]] | ||
| # the covariance is 0 when si==0, although C[i] is NaN in this case | ||
| C[i] = iszero(si) ? zero(eltype(C)) : C[i] * si |
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In case eltype(C) isn't a concrete type:
| C[i] = iszero(si) ? zero(eltype(C)) : C[i] * si | |
| Ci = C[i] | |
| C[i] = iszero(si) ? zero(Ci) : Ci * si |
Can you explain a bit more what happens here?
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If one of the variables has zero variance, its covariance with any other variable is 0, but the correlation is undefined, and the result of cor would have NaN in that element. In that case Ci == NaN, si == 0, but the correct output is 0, not NaN.
For example,
X = [1:3 ones(3)]
cov(X) == [1 0; 0 0]
cor(X) == [1 NaN; NaN 1]
cor2cov(cor(X), std.(eachcol(X))) # previously [1 NaN; NaN 0], which is incorrect
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This is mostly changing
DenseMatrixin method signatures toAbstractMatrix, and running the tests also on a sparse array and a custom-typed array.Other changes:
_symmetrize!for sparse matricescor2cov!discovered when testing with sparse matrixmean_and_cov(vector). I didn't addmean_and_cov(vector, weights)since that would need a fix to cov(x, w::AbstractWeights) dispatches on cov(X, Y) fallback #409, which has a long discussion pointing to JuliaLang/Statistics.jl#2