Add AGQ for GLMMs, update docs

JuliaStats · Jun 13, 2018 · 16092dc · 16092dc
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diff --git a/docs/jmd/constructors.jmd b/docs/jmd/constructors.jmd
@@ -146,10 +146,10 @@ deviance(fm1)
 
 The value optimized when fitting a `GeneralizedLinearMixedModel` is the Laplace approximation to the deviance.
 ```@docs
-LaplaceDeviance
+deviance!
 ```
 ```{julia;term=true}
-LaplaceDeviance(gm1)
+MixedModels.deviance!(gm1)
 ```
 
 ## Fixed-effects parameter estimates

diff --git a/docs/jmd/optimization.jmd b/docs/jmd/optimization.jmd
@@ -276,7 +276,7 @@ pirls!(mdl, true, true)
 ```
 
 ```{julia;term=true}
-LaplaceDeviance(mdl)
+deviance(mdl)
 ```
 
 ```{julia;term=true}

diff --git a/docs/src/MultipleTerms.md b/docs/src/MultipleTerms.md
@@ -195,7 +195,7 @@ A bootstrap simulation of the model
 
 ````julia
 julia> @time penmbstp = bootstrap(10000, penm);
- 13.155906 seconds (16.06 M allocations: 786.972 MiB, 2.41% gc time)
+ 12.957938 seconds (16.06 M allocations: 786.972 MiB, 3.24% gc time)
 
 ````
 
@@ -394,7 +394,7 @@ confirm this impression in that all the prediction intervals for the random effe
 julia> srand(4321234);
 
 julia> @time pstsbstp = bootstrap(10000, pstsm);
-  9.528515 seconds (12.30 M allocations: 635.462 MiB, 2.33% gc time)
+  9.419357 seconds (12.30 M allocations: 635.462 MiB, 2.34% gc time)
 
 ````
 
@@ -535,7 +535,7 @@ A bootstrap sample
 
 ````julia
 julia> @time psts1bstp = bootstrap(10000, pstsm1);
-  3.816650 seconds (5.36 M allocations: 263.656 MiB, 3.11% gc time)
+  3.810468 seconds (5.36 M allocations: 263.656 MiB, 2.88% gc time)
 
 ````
 
@@ -630,7 +630,7 @@ At this point we will fit models that have random effects for student, instructo
 
 ````julia
 julia> @time instm = fit(LinearMixedModel, @formula(Y ~ 1 + A + (1|G) + (1|H) + (1|I)), dat[:InstEval])
-  2.366413 seconds (155.16 k allocations: 197.943 MiB, 1.60% gc time)
+  2.669603 seconds (206.36 k allocations: 200.873 MiB, 1.62% gc time)
 Linear mixed model fit by maximum likelihood
  Formula: Y ~ 1 + A + (1 | G) + (1 | H) + (1 | I)
      logLik        -2 logLik          AIC             BIC       

diff --git a/docs/src/assets/MultipleTerms_10_1.svg b/docs/src/assets/MultipleTerms_10_1.svg