From 43814f74bfe7559843a7e72fd3b7f3037bcf179d Mon Sep 17 00:00:00 2001
From: Douglas Bates <dmbates@gmail.com>
Date: Mon, 30 Oct 2017 16:06:20 -0500
Subject: [PATCH] Add profileBeta function

---
 src/profile.jl | 47 +++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 47 insertions(+)

diff --git a/src/profile.jl b/src/profile.jl
index 636c141dc..d4cff206d 100644
--- a/src/profile.jl
+++ b/src/profile.jl
@@ -12,5 +12,52 @@ function dropXcolumn(m::LinearMixedModel, i::Integer)
     A, L = createAL(trms)   
     osum = copy(m.optsum)
     copy!(osum.initial, m.optsum.final)
+    osum.initial_step .= osum.initial_step ./ 4.0
     LinearMixedModel(m.formula, trms, sqrtwts, A, LowerTriangular(L), osum)
 end
+
+struct ProfileSlice{T<:AbstractFloat}
+    zeta::Vector{T}
+    beta::Vector{T}
+    beta1::Matrix{T}
+    theta::Matrix{T}
+end
+
+struct Profile{T<:AbstractFloat}
+    beta::Vector{T}
+    sigma::Vector{T}
+    slices::Vector{ProfileSlice{T}}
+end
+
+function profileBeta(m::LinearMixedModel{T}) where T
+    X = m.trms[end - 1].x
+    beta = fixef(m)
+    se = stderr(m)
+    p = length(beta)
+    d0 = deviance(m)
+    y0 = copy(model_response(m))
+    slices = sizehint!(ProfileSlice{T}[], p)
+    zvals = -4.0:0.5:4.0
+    lzv = length(zvals)
+    for i in 1:p
+        m1 = dropXcolumn(m, i)
+        zeta = Vector{T}(lzv)
+        ff = Matrix{T}((p - 1), lzv)
+        th = Matrix{T}(sum(nθ, m.trms), lzv)
+        for (j, z) in enumerate(zvals)
+            if iszero(z)
+                zeta[j] = zero(T)
+                copy!(view(ff, :, j), deleteat!(copy(beta), i))
+                getθ!(view(th, :, j), m)
+            else
+                refit!(m1, y0 .- (beta[i] + z * se[i]) .* view(X, :, i))
+                zeta[j] = sign(z) * sqrt(deviance(m1) - d0)
+                fixef!(view(ff, :, j), m1)
+                getθ!(view(th, :, j), m1)
+            end
+        end
+        push!(slices, ProfileSlice(zeta, beta[i] .+ se[i] .* zvals, ff', th'))
+    end
+    slices
+end
+