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PharmCat · Jan 10, 2021 · b979ca6 · b979ca6
1 parent 41eab05
commit b979ca6
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Showing 7 changed files with 10 additions and 9 deletions.
diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "Metida"
 uuid = "a1dec852-9fe5-11e9-361f-8d9fde67cfa2"
 authors = ["Vladimir Arnautov <[email protected]>"]
-version = "0.1.10"
+version = "0.1.11"
 
 [deps]
 CategoricalArrays = "324d7699-5711-5eae-9e2f-1d82baa6b597"

diff --git a/src/Metida.jl b/src/Metida.jl
@@ -44,6 +44,8 @@ function _precompile_()
     precompile(Tuple{typeof(Metida.ffxpone), Int64})
 
     precompile(Tuple{typeof(Metida.reml_sweep_β), Metida.LMM{Float64}, Array{Float64, 1}})
+    precompile(Tuple{typeof(Metida.reml_sweep_β3), Metida.LMM{Float64}, Array{Float64, 1}})
+
     precompile(Tuple{typeof(Metida.rholinkpsigmoid), Float64})
 
     precompile(Tuple{typeof(Metida.varlinkvecapply!), Array{Float64, 1}, Array{Function, 1}})

diff --git a/src/fit.jl b/src/fit.jl
@@ -55,7 +55,6 @@ function fit!(lmm::LMM{T}; verbose::Symbol = :auto, varlinkf = :exp, rholinkf =
         grf(x) = optfunc(lmm, x)[1]
         ai = ForwardDiff.hessian(aif, θ)
         gr = ForwardDiff.gradient(grf, θ)
-    #println("vec: ", θ)
         try
             θ .-= (inv(ai) ./4 )*gr
         catch
@@ -73,7 +72,7 @@ function fit!(lmm::LMM{T}; verbose::Symbol = :auto, varlinkf = :exp, rholinkf =
                 if θ[i] > initθ*1.25 θ[i] = initθ*1.25 end
             end
         end
-        push!(lmm.log, "First step with AI like method, θ: "*string(θ))
+        push!(lmm.log, "First step with AI-like method, θ: "*string(θ))
     end
     #println("new: ", θ)
     #varlinkvecapply!(θ, fvr)

diff --git a/src/reml.jl b/src/reml.jl
@@ -136,7 +136,7 @@ function reml_sweep_β2(lmm::LMM{T2}, @nospecialize θ::Vector{T}) where T <: Nu
         Vpv .= Vi
         Vx   = view(Vp, 1:q, q+1:q+lmm.rankx)
         #Vxt  = view(Vp,  N+1:qswm, 1:N)
-        Vx  .= view(lmm.data.xv,  lmm.data.block[i],:)
+        Vx  .= view(lmm.data.xv, lmm.data.block[i], :)
 
         sweep!(Vp, 1:q)
         V⁻¹[i] = Symmetric(utriaply!(x -> -x, Vpv))

diff --git a/src/utils.jl b/src/utils.jl
@@ -65,10 +65,11 @@ function intersectdf(df, s)::Vector
     end
     for i2 = 1:size(u, 1)
         for i = 1:length(s)
-            v2[i] = sort!(v[i][u[i2, i]])
+            v2[i] = v[i][u[i2, i]]
         end
         res[i2] = collect(intersect(Set.(v2)...))
         #res[i2] = intersect(v2...)
+        sort!(res[i2])
     end
     res
 end

diff --git a/src/varstruct.jl b/src/varstruct.jl
@@ -236,7 +236,6 @@ struct CovStructure{T} <: AbstractCovarianceStructure
             end
         end
         view(rcnames, tr[end]) .= rcoefnames(schema[end], t[end], Val{repeated.covtype.s}())
-
             for i = 1:length(blocks)
                 sblock[i] = Vector{Vector{Vector{UInt32}}}(undef, alleffl)
                 for s = 1:alleffl

diff --git a/test/ar.jl b/test/ar.jl
@@ -16,14 +16,14 @@ transform!(df, :Day => categorical, renamecols=false)
     subject = :Time
     )
     Metida.fit!(lmm)
-    @test lmm.result.reml ≈ 451.06614967014093 atol=1E-6
+    @test lmm.result.reml ≈ 453.3395435627574 atol=1E-6
 
     lmm = Metida.LMM(@formula(Pulse~1), df;
     repeated = Metida.VarEffect(Metida.@covstr(1), Metida.AR),
     subject = :Time
     )
     Metida.fit!(lmm)
-    @test lmm.result.reml ≈ 463.9964183016498 atol=1E-6
+    @test lmm.result.reml ≈ 471.85107712169827 atol=1E-6
 end
 
 #=
@@ -44,7 +44,7 @@ transform!(df, :Diet => categorical, renamecols=false)
     subject = :Chick
     )
     Metida.fit!(lmm)
-    @test lmm.result.reml ≈ 5451.857613990478 atol=1E-6
+    @test lmm.result.reml ≈ 4439.254893054906 atol=1E-6
 
     lmm = Metida.LMM(@formula(weight~1 + Diet & Time), df;
     random = Metida.VarEffect(Metida.@covstr(Diet), Metida.ARH),