From e09073df622d9491ce88073d36b65bad27dc52a8 Mon Sep 17 00:00:00 2001 From: Douglas Bates Date: Thu, 17 Dec 2015 14:39:57 -0600 Subject: [PATCH 1/4] Sort random-effects terms by number of levels --- src/pls.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/pls.jl b/src/pls.jl index daf6b488c..3514ad54c 100644 --- a/src/pls.jl +++ b/src/pls.jl @@ -101,7 +101,7 @@ function lmm(f::Formula, fr::AbstractDataFrame; weights::Vector{Float64}=Float64 if length(retrms) ≤ 0 throw(ArgumentError("$f has no random-effects terms")) end - re = [remat(e,mf.df) for e in retrms] + re = sort!([remat(e,mf.df) for e in retrms]; by = nlevs, rev = true) LinearMixedModel(mf,re,map(LT,re),X.m,y,weights) end From e0381b15fbbae1ce75e2d25f5430c614e2788273 Mon Sep 17 00:00:00 2001 From: Douglas Bates Date: Thu, 17 Dec 2015 14:40:39 -0600 Subject: [PATCH 2/4] Add nlevs extractor for ReMat objects --- src/remat.jl | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/src/remat.jl b/src/remat.jl index a94f8948d..607b51e57 100644 --- a/src/remat.jl +++ b/src/remat.jl @@ -52,12 +52,14 @@ Base.eltype(R::ReMat) = eltype(R.z) vsize(A::ReMat) = isa(A,ScalarReMat) ? 1 : size(A.z,1) -Base.size(A::ReMat) = (length(A.f),vsize(A)*length(A.f.pool)) +nlevs(A::ReMat) = length(A.f.pool) + +Base.size(A::ReMat) = (length(A.f),vsize(A)*nlevs(A)) Base.size(A::ReMat,i::Integer) = i < 1 ? throw(BoundsError()) : i == 1 ? length(A.f) : - i == 2 ? vsize(A)*length(A.f.pool) : 1 + i == 2 ? vsize(A)*nlevs(A) : 1 ==(A::ReMat,B::ReMat) = (A.f == B.f) && (A.z == B.z) @@ -123,7 +125,7 @@ function Base.Ac_mul_B(A::ScalarReMat, B::ScalarReMat) Az = A.z Ar = A.f.refs if is(A,B) - v = zeros(eltype(Az),length(A.f.pool)) + v = zeros(eltype(Az),nlevs(A)) for i in eachindex(Ar) v[Ar[i]] += abs2(Az[i]) end @@ -138,7 +140,7 @@ function Base.Ac_mul_B(A::VectorReMat,B::VectorReMat) if is(A,B) l,n = size(Az) T = eltype(Az) - np = length(A.f.pool) + np = nlevs(A) a = zeros(T,(l,l,np)) for i in eachindex(Ar) Base.LinAlg.BLAS.syr!('L',one(T),sub(Az,:,i),sub(a,:,:,Ar[i])) From 365b1dda928de52d832a72a44f3cb21b45ffcf4e Mon Sep 17 00:00:00 2001 From: Douglas Bates Date: Thu, 17 Dec 2015 14:41:21 -0600 Subject: [PATCH 3/4] Add tests for getindex with HBlkDiag --- test/pls.jl | 2 ++ 1 file changed, 2 insertions(+) diff --git a/test/pls.jl b/test/pls.jl index d72d6e055..267503e46 100644 --- a/test/pls.jl +++ b/test/pls.jl @@ -57,6 +57,8 @@ fm3 = lmm(Reaction ~ 1+Days + (1+Days|Subject),slp) @test lowerbd(fm3) == [0.,-Inf,0.] @test isa(fm3.A[1,1],MixedModels.HBlkDiag{Float64}) @test size(fm3.A[1,1]) == (36,36) +@test fm3.A[1,1][1,1] == 10. +@test fm3.A[1,1][6,1] == 0. @test_throws BoundsError size(fm3.A[1,1],0) @test size(fm3.A[1,1],1) == 36 @test full(fm3.A[1,1])[1:2,1:2] == reshape([10.,45,45,285],(2,2)) From 4e52f94008aa5740b21889b32dc40dffcae50bd1 Mon Sep 17 00:00:00 2001 From: Douglas Bates Date: Thu, 17 Dec 2015 14:44:24 -0600 Subject: [PATCH 4/4] Update links to new commits --- docs/api/MixedModels.md | 122 ++++++++++++++++++++-------------------- 1 file changed, 61 insertions(+), 61 deletions(-) diff --git a/docs/api/MixedModels.md b/docs/api/MixedModels.md index eb5634712..f7286eed4 100644 --- a/docs/api/MixedModels.md +++ b/docs/api/MixedModels.md @@ -11,7 +11,7 @@ Akaike's Information Criterion *source:* -[MixedModels/src/pls.jl:215](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/pls.jl#L215) +[MixedModels/src/pls.jl:214](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/pls.jl#L214) --- @@ -21,7 +21,7 @@ Schwartz's Bayesian Information Criterion *source:* -[MixedModels/src/pls.jl:220](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/pls.jl#L220) +[MixedModels/src/pls.jl:219](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/pls.jl#L219) --- @@ -35,7 +35,7 @@ by each simulation. The original response is restored before returning. *source:* -[MixedModels/src/bootstrap.jl:8](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/bootstrap.jl#L8) +[MixedModels/src/bootstrap.jl:8](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/bootstrap.jl#L8) --- @@ -45,7 +45,7 @@ The fixed-effects parameter estimates *source:* -[MixedModels/src/pls.jl:238](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/pls.jl#L238) +[MixedModels/src/pls.jl:235](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/pls.jl#L235) --- @@ -55,7 +55,7 @@ Create a `LinearMixedModel` object from a formula and data frame *source:* -[MixedModels/src/pls.jl:95](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/pls.jl#L95) +[MixedModels/src/pls.jl:95](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/pls.jl#L95) --- @@ -65,7 +65,7 @@ lower bounds on the parameters (elements in the lower triangle) *source:* -[MixedModels/src/paramlowertriangular.jl:45](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/paramlowertriangular.jl#L45) +[MixedModels/src/paramlowertriangular.jl:45](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/paramlowertriangular.jl#L45) --- @@ -78,7 +78,7 @@ for the scale parameter, σ, that is profiled out. *source:* -[MixedModels/src/pls.jl:250](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/pls.jl#L250) +[MixedModels/src/pls.jl:247](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/pls.jl#L247) --- @@ -88,7 +88,7 @@ for the scale parameter, σ, that is profiled out. *source:* -[MixedModels/src/pls.jl:210](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/pls.jl#L210) +[MixedModels/src/pls.jl:209](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/pls.jl#L209) --- @@ -98,7 +98,7 @@ returns the penalized residual sum-of-squares *source:* -[MixedModels/src/pls.jl:280](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/pls.jl#L280) +[MixedModels/src/pls.jl:277](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/pls.jl#L277) --- @@ -109,7 +109,7 @@ returns the penalized residual sum-of-squares *source:* -[MixedModels/src/pls.jl:355](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/pls.jl#L355) +[MixedModels/src/pls.jl:352](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/pls.jl#L352) --- @@ -120,7 +120,7 @@ returns the penalized residual sum-of-squares *source:* -[MixedModels/src/pls.jl:355](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/pls.jl#L355) +[MixedModels/src/pls.jl:352](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/pls.jl#L352) --- @@ -130,7 +130,7 @@ refit the model `m` with response `y` *source:* -[MixedModels/src/bootstrap.jl:93](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/bootstrap.jl#L93) +[MixedModels/src/bootstrap.jl:93](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/bootstrap.jl#L93) --- @@ -143,7 +143,7 @@ A factory for `ReMat` objects constructed from a random-effects term and a *source:* -[MixedModels/src/remat.jl:37](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/remat.jl#L37) +[MixedModels/src/remat.jl:37](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/remat.jl#L37) --- @@ -153,7 +153,7 @@ A factory for `ReMat` objects constructed from a random-effects term and a *source:* -[MixedModels/src/pls.jl:395](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/pls.jl#L395) +[MixedModels/src/pls.jl:392](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/pls.jl#L392) --- @@ -163,7 +163,7 @@ A factory for `ReMat` objects constructed from a random-effects term and a *source:* -[MixedModels/src/pls.jl:395](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/pls.jl#L395) +[MixedModels/src/pls.jl:392](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/pls.jl#L392) --- @@ -175,7 +175,7 @@ returns `s`, the estimate of σ, the standard deviation of the per-observation n *source:* -[MixedModels/src/pls.jl:263](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/pls.jl#L263) +[MixedModels/src/pls.jl:260](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/pls.jl#L260) --- @@ -190,7 +190,7 @@ Simulate a response vector from model `m`, and refit `m`. *source:* -[MixedModels/src/bootstrap.jl:76](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/bootstrap.jl#L76) +[MixedModels/src/bootstrap.jl:76](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/bootstrap.jl#L76) --- @@ -200,7 +200,7 @@ returns s², the estimate of σ², the variance of the conditional distribution *source:* -[MixedModels/src/pls.jl:275](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/pls.jl#L275) +[MixedModels/src/pls.jl:272](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/pls.jl#L272) ## Types [Exported] @@ -220,7 +220,7 @@ Linear mixed-effects model representation *source:* -[MixedModels/src/pls.jl:26](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/pls.jl#L26) +[MixedModels/src/pls.jl:26](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/pls.jl#L26) --- @@ -230,7 +230,7 @@ Linear mixed-effects model representation *source:* -[MixedModels/src/remat.jl:4](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/remat.jl#L4) +[MixedModels/src/remat.jl:4](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/remat.jl#L4) --- @@ -242,7 +242,7 @@ The matrix is represented by the grouping factor, `f`, and a vector `z`. *source:* -[MixedModels/src/remat.jl:11](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/remat.jl#L11) +[MixedModels/src/remat.jl:11](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/remat.jl#L11) --- @@ -255,7 +255,7 @@ The main purpose is to isolate the logic in the show method. *source:* -[MixedModels/src/pls.jl:442](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/pls.jl#L442) +[MixedModels/src/pls.jl:439](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/pls.jl#L439) --- @@ -268,7 +268,7 @@ model matrix, `z`. *source:* -[MixedModels/src/remat.jl:24](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/remat.jl#L24) +[MixedModels/src/remat.jl:24](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/remat.jl#L24) ## Methods [Internal] @@ -281,7 +281,7 @@ model matrix, `z`. *source:* -[MixedModels/src/logdet.jl:4](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/logdet.jl#L4) +[MixedModels/src/logdet.jl:4](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/logdet.jl#L4) --- @@ -294,7 +294,7 @@ and initialized to the identity. *source:* -[MixedModels/src/paramlowertriangular.jl:96](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/paramlowertriangular.jl#L96) +[MixedModels/src/paramlowertriangular.jl:96](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/paramlowertriangular.jl#L96) --- @@ -304,7 +304,7 @@ An instance of the canonical Link type for a distribution in the exponential fam *source:* -[MixedModels/src/GLMM/glmtools.jl:52](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/GLMM/glmtools.jl#L52) +[MixedModels/src/GLMM/glmtools.jl:52](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/GLMM/glmtools.jl#L52) --- @@ -317,7 +317,7 @@ Uses `inject!` (as opposed to `copy!`), `downdate!` (as opposed to `syrk!` *source:* -[MixedModels/src/cfactor.jl:7](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/cfactor.jl#L7) +[MixedModels/src/cfactor.jl:7](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/cfactor.jl#L7) --- @@ -328,7 +328,7 @@ errors being thrown when `R` is computationally singular *source:* -[MixedModels/src/cfactor.jl:34](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/cfactor.jl#L34) +[MixedModels/src/cfactor.jl:34](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/cfactor.jl#L34) --- @@ -338,7 +338,7 @@ Convert a lower Cholesky factor to a correlation matrix *source:* -[MixedModels/src/pls.jl:290](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/pls.jl#L290) +[MixedModels/src/pls.jl:287](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/pls.jl#L287) --- @@ -348,7 +348,7 @@ Condition numbers for blocks of Λ *source:* -[MixedModels/src/pls.jl:285](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/pls.jl#L285) +[MixedModels/src/pls.jl:282](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/pls.jl#L282) --- @@ -362,7 +362,7 @@ A no-op for other matrix types. *source:* -[MixedModels/src/densify.jl:8](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/densify.jl#L8) +[MixedModels/src/densify.jl:8](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/densify.jl#L8) --- @@ -376,7 +376,7 @@ A no-op for other matrix types. *source:* -[MixedModels/src/densify.jl:8](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/densify.jl#L8) +[MixedModels/src/densify.jl:8](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/densify.jl#L8) --- @@ -386,7 +386,7 @@ describe the blocks of the A and R matrices *source:* -[MixedModels/src/pls.jl:509](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/pls.jl#L509) +[MixedModels/src/pls.jl:506](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/pls.jl#L506) --- @@ -396,7 +396,7 @@ Evaluate the squared deviance residual for a distribution instance and values of *source:* -[MixedModels/src/GLMM/glmtools.jl:74](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/GLMM/glmtools.jl#L74) +[MixedModels/src/GLMM/glmtools.jl:74](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/GLMM/glmtools.jl#L74) --- @@ -406,7 +406,7 @@ Subtract, in place, A'A or A'B from C *source:* -[MixedModels/src/cfactor.jl:48](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/cfactor.jl#L48) +[MixedModels/src/cfactor.jl:48](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/cfactor.jl#L48) --- @@ -418,7 +418,7 @@ Optimize the objective using an NLopt optimizer. *source:* -[MixedModels/src/pls.jl:148](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/pls.jl#L148) +[MixedModels/src/pls.jl:148](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/pls.jl#L148) --- @@ -430,7 +430,7 @@ Optimize the objective using an NLopt optimizer. *source:* -[MixedModels/src/pls.jl:148](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/pls.jl#L148) +[MixedModels/src/pls.jl:148](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/pls.jl#L148) --- @@ -442,7 +442,7 @@ Optimize the objective using an NLopt optimizer. *source:* -[MixedModels/src/pls.jl:148](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/pls.jl#L148) +[MixedModels/src/pls.jl:148](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/pls.jl#L148) --- @@ -452,7 +452,7 @@ Overwrite `v` with the fixed-effects coefficients of model `m` *source:* -[MixedModels/src/pls.jl:230](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/pls.jl#L230) +[MixedModels/src/pls.jl:227](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/pls.jl#L227) --- @@ -462,7 +462,7 @@ Overwrite `v` with the fixed-effects coefficients of model `m` *source:* -[MixedModels/src/pls.jl:313](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/pls.jl#L313) +[MixedModels/src/pls.jl:310](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/pls.jl#L310) --- @@ -472,7 +472,7 @@ return the lower triangle as a vector (column-major ordering) *source:* -[MixedModels/src/paramlowertriangular.jl:7](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/paramlowertriangular.jl#L7) +[MixedModels/src/paramlowertriangular.jl:7](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/paramlowertriangular.jl#L7) --- @@ -482,7 +482,7 @@ return the lower triangle as a vector (column-major ordering) *source:* -[MixedModels/src/pls.jl:318](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/pls.jl#L318) +[MixedModels/src/pls.jl:315](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/pls.jl#L315) --- @@ -495,7 +495,7 @@ behavior on the `HBlkDiag` type. *source:* -[MixedModels/src/inflate.jl:7](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/inflate.jl#L7) +[MixedModels/src/inflate.jl:7](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/inflate.jl#L7) --- @@ -505,7 +505,7 @@ like `copy!` but allowing for heterogeneous matrix types *source:* -[MixedModels/src/inject.jl:4](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/inject.jl#L4) +[MixedModels/src/inject.jl:4](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/inject.jl#L4) --- @@ -515,7 +515,7 @@ Predicate - whether or not the model has been fit. *source:* -[MixedModels/src/pls.jl:324](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/pls.jl#L324) +[MixedModels/src/pls.jl:321](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/pls.jl#L321) --- @@ -525,7 +525,7 @@ returns `log(det(Λ'Z'ZΛ + I))` *source:* -[MixedModels/src/logdet.jl:35](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/logdet.jl#L35) +[MixedModels/src/logdet.jl:35](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/logdet.jl#L35) --- @@ -535,7 +535,7 @@ Likelihood ratio test of one or more models *source:* -[MixedModels/src/pls.jl:331](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/pls.jl#L331) +[MixedModels/src/pls.jl:328](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/pls.jl#L328) --- @@ -547,7 +547,7 @@ In Julia 0.5 this can be a one-liner `m.trms[end][:,end]` *source:* -[MixedModels/src/bootstrap.jl:103](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/bootstrap.jl#L103) +[MixedModels/src/bootstrap.jl:103](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/bootstrap.jl#L103) --- @@ -557,7 +557,7 @@ In-place modification of μ to starting values from d, y and wt *source:* -[MixedModels/src/GLMM/glmtools.jl:92](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/GLMM/glmtools.jl#L92) +[MixedModels/src/GLMM/glmtools.jl:92](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/GLMM/glmtools.jl#L92) --- @@ -567,7 +567,7 @@ Initial μ value from the response and the weight *source:* -[MixedModels/src/GLMM/glmtools.jl:83](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/GLMM/glmtools.jl#L83) +[MixedModels/src/GLMM/glmtools.jl:83](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/GLMM/glmtools.jl#L83) --- @@ -579,7 +579,7 @@ This should be called after updating parts of `m.trms[end]`, typically the respo *source:* -[MixedModels/src/bootstrap.jl:25](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/bootstrap.jl#L25) +[MixedModels/src/bootstrap.jl:25](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/bootstrap.jl#L25) --- @@ -589,7 +589,7 @@ Reset the value of `m.θ` to the initial values *source:* -[MixedModels/src/bootstrap.jl:37](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/bootstrap.jl#L37) +[MixedModels/src/bootstrap.jl:37](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/bootstrap.jl#L37) --- @@ -601,7 +601,7 @@ used in `chol2cor` *source:* -[MixedModels/src/paramlowertriangular.jl:63](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/paramlowertriangular.jl#L63) +[MixedModels/src/paramlowertriangular.jl:63](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/paramlowertriangular.jl#L63) --- @@ -611,7 +611,7 @@ set the lower triangle of A to v using column-major ordering *source:* -[MixedModels/src/paramlowertriangular.jl:23](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/paramlowertriangular.jl#L23) +[MixedModels/src/paramlowertriangular.jl:23](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/paramlowertriangular.jl#L23) --- @@ -623,7 +623,7 @@ This is the bottom right element of the bottom right block of m.R *source:* -[MixedModels/src/pls.jl:270](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/pls.jl#L270) +[MixedModels/src/pls.jl:267](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/pls.jl#L267) --- @@ -633,7 +633,7 @@ This is the bottom right element of the bottom right block of m.R *source:* -[MixedModels/src/pls.jl:434](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/pls.jl#L434) +[MixedModels/src/pls.jl:431](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/pls.jl#L431) --- @@ -643,7 +643,7 @@ scale B using the implicit expansion of A to a homogeneous block diagonal *source:* -[MixedModels/src/paramlowertriangular.jl:71](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/paramlowertriangular.jl#L71) +[MixedModels/src/paramlowertriangular.jl:71](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/paramlowertriangular.jl#L71) --- @@ -653,7 +653,7 @@ Add unscaled random effects to y *source:* -[MixedModels/src/bootstrap.jl:47](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/bootstrap.jl#L47) +[MixedModels/src/bootstrap.jl:47](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/bootstrap.jl#L47) --- @@ -663,7 +663,7 @@ returns the estimated variance-covariance matrix of the fixed-effects estimator *source:* -[MixedModels/src/pls.jl:501](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/pls.jl#L501) +[MixedModels/src/pls.jl:498](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/pls.jl#L498) --- @@ -673,7 +673,7 @@ Evaluate `y*log(y/μ)` with the correct limit as `y` approaches zero from above *source:* -[MixedModels/src/GLMM/glmtools.jl:67](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/GLMM/glmtools.jl#L67) +[MixedModels/src/GLMM/glmtools.jl:67](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/GLMM/glmtools.jl#L67) ## Types [Internal] @@ -685,5 +685,5 @@ Summary of an NLopt optimization *source:* -[MixedModels/src/pls.jl:4](https://github.com/dmbates/MixedModels.jl/tree/f42452aa03213ace2d9d898088abbfeb5b9ee850/src/pls.jl#L4) +[MixedModels/src/pls.jl:4](https://github.com/dmbates/MixedModels.jl/tree/365b1dda928de52d832a72a44f3cb21b45ffcf4e/src/pls.jl#L4)