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Hua-ZhouHua-Zhou
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accomodate Julia v0.6
1 parent a9327f1 commit a6940da

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+20
-24
lines changed

‎.travis.yml‎

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@@ -4,8 +4,8 @@ os:
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- linux
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- osx
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julia:
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- 0.4
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- 0.5
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- 0.6
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- nightly
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matrix:
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allow_failures:
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notifications:
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email:
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on_success: change
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on_failure: always
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on_failure: always
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recipients:
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- esobel@ucla.edu

‎README.md‎

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@@ -17,7 +17,7 @@ Within Julia, use the package manager to install VarianceComponentModels:
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Pkg.clone("https://github.com/OpenMendel/VarianceComponentModels.jl.git")
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This package supports Julia v0.4 and v0.5.
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This package supports Julia v0.5 and v0.6.
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## Citation
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‎REQUIRE‎

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@@ -1,4 +1,4 @@
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julia 0.4
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julia 0.5
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Compat
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MathProgBase

‎appveyor.yml‎

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@@ -1,9 +1,9 @@
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environment:
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matrix:
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- JULIAVERSION: "julialang/bin/winnt/x86/0.4/julia-0.4-latest-win32.exe"
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- JULIAVERSION: "julialang/bin/winnt/x64/0.4/julia-0.4-latest-win64.exe"
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- JULIAVERSION: "julialang/bin/winnt/x86/0.5/julia-0.5-latest-win32.exe"
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- JULIAVERSION: "julialang/bin/winnt/x64/0.5/julia-0.5-latest-win64.exe"
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- JULIAVERSION: "julialang/bin/winnt/x86/0.4/julia-0.5-latest-win32.exe"
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- JULIAVERSION: "julialang/bin/winnt/x64/0.4/julia-0.5-latest-win64.exe"
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- JULIAVERSION: "julialang/bin/winnt/x86/0.5/julia-0.6-latest-win32.exe"
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- JULIAVERSION: "julialang/bin/winnt/x64/0.5/julia-0.6-latest-win64.exe"
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#- JULIAVERSION: "julianightlies/bin/winnt/x86/julia-latest-win32.exe"
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#- JULIAVERSION: "julianightlies/bin/winnt/x64/julia-latest-win64.exe"
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‎src/VarianceComponentModels.jl‎

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@@ -122,7 +122,7 @@ function TwoVarCompModelRotate{T, BT, ΣT}(
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λ = convert(Vector{T}, F.values)
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Φ = convert(Matrix{T}, F.vectors)
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# correct negative eigenvalues due to roundoff
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map!(x -> max(x, zero(T)), λ)
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@compat map!(x -> max(x, zero(T)), λ, λ)
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Brot = isempty(vcm.B) ? Array{T}(size(vcm.B)) : vcm.B * Φ
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logdetΣ2 = convert(T, logdet(vcm.Σ[2]))
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TwoVarCompModelRotate{T, BT}(Brot, λ, Φ, logdetΣ2)

‎src/two_variance_component.jl‎

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Original file line numberDiff line numberDiff line change
@@ -904,11 +904,11 @@ function mle_fs!{T1<:VarianceComponentModel, T2<:TwoVarCompVariateRotate}(
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Bcov = zeros(T, nmean, nmean)
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Bcov = pinv(fisher_B(vcmodel, vcdatarot, dd.vcaux))
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Bse = similar(vcmodel.B)
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copy!(Bse, sqrt(diag(Bcov)))
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copy!(Bse, sqrt.(diag(Bcov)))
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Σcov = pinv(fisher_Σ(vcmodel, vcdatarot))
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Σse = (zeros(T, d, d), zeros(T, d, d))
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copy!(Σse[1], sqrt(diag(view(Σcov, 1:d^2, 1:d^2))))
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copy!(Σse[2], sqrt(diag(view(Σcov, d^2+1:2d^2, d^2+1:2d^2))))
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copy!(Σse[1], sqrt.(diag(view(Σcov, 1:d^2, 1:d^2))))
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copy!(Σse[2], sqrt.(diag(view(Σcov, d^2+1:2d^2, d^2+1:2d^2))))
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# output
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maxlogl, vcmodel, Σse, Σcov, Bse, Bcov
@@ -1105,11 +1105,11 @@ function mle_mm!{T1 <: VarianceComponentModel, T2 <: TwoVarCompVariateRotate}(
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# standard errors
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Bcov = pinv(fisher_B(vcm, vcdatarot, vcaux))
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Bse = similar(vcm.B)
1108-
copy!(Bse, sqrt(diag(Bcov)))
1108+
copy!(Bse, sqrt.(diag(Bcov)))
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Σcov = pinv(fisher_Σ(vcm, vcdatarot))
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Σse = (zeros(T, d, d), zeros(T, d, d))
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copy!(Σse[1], sqrt(diag(view(Σcov, 1:d^2, 1:d^2))))
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copy!(Σse[2], sqrt(diag(view(Σcov, d^2+1:2d^2, d^2+1:2d^2))))
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copy!(Σse[1], sqrt.(diag(view(Σcov, 1:d^2, 1:d^2))))
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copy!(Σse[2], sqrt.(diag(view(Σcov, d^2+1:2d^2, d^2+1:2d^2))))
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# output
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logl, vcm, Σse, Σcov, Bse, Bcov
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# standard errors and covariance of mean parameters
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Bcov = inv(fisher_B(vcmodel, vcdatarot, vcaux))
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Bse = similar(vcmodel.B)
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copy!(Bse, sqrt(diag(Bcov)))
1243+
copy!(Bse, sqrt.(diag(Bcov)))
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# output
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logpdf(vcmodel, vcdatarot), vcmodel, Σse, Σcov, Bse, Bcov

‎test/REQUIRE‎

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BaseTestNext

‎test/multivariate_calculus_test.jl‎

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@@ -1,7 +1,6 @@
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module MultivariateCalculusTest
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using VarianceComponentModels
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using BaseTestNext
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using VarianceComponentModels, Base.Test
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srand(123)
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@@ -102,7 +101,7 @@ end
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dX2[i, j] = vecdot(Y, M[(i-1)*p+1:i*p, (j-1)*r+1:j*r])
103102
end
104103
end
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@test_approx_eq_eps vecnorm(dX1 - vec(dX2)) 0.0 1.0e-8
104+
@test vecnorm(dX1 - vec(dX2)) < 1e-8
106105
end
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# test duplication

‎test/two_variance_component_test.jl‎

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@@ -1,7 +1,6 @@
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module TwoVarianceComponentTest
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using VarianceComponentModels, MathProgBase, Ipopt
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using BaseTestNext
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using VarianceComponentModels, MathProgBase, Ipopt, Base.Test
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srand(123)
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‎test/variance_component_models_test.jl‎

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module VarianceComponentTypeTest
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using VarianceComponentModels, MathProgBase, Ipopt
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using BaseTestNext
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using VarianceComponentModels, MathProgBase, Ipopt, Base.Test
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srand(123)
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