Parametric bootstrap for linear mixed-effects models

Julia is well-suited to implementing bootstrapping and other simulation-based methods for statistical models. The bootstrap! function in the MixedModels package provides an efficient parametric bootstrap for linear mixed-effects models, assuming that the results of interest from each simulated response vector can be incorporated into a vector of floating-point values.

The parametric bootstrap

Bootstrapping is a family of procedures for generating sample values of a statistic, allowing for visualization of the distribution of the statistic or for inference from this sample of values.

A parametric bootstrap is used with a parametric model, m, that has been fitted to data. The procedure is to simulate n response vectors from m using the estimated parameter values and refit m to these responses in turn, accumulating the statistics of interest at each iteration.

The parameters of a linear mixed-effects model as fit by the lmm function are the fixed-effects parameters, β, the standard deviation, σ, of the per-observation noise, and the covariance parameter, θ, that defines the variance-covariance matrices of the random effects.

For example, a simple linear mixed-effects model for the Dyestuff data in the lme4 package for R is fit by

julia> using DataFrames, MixedModels, RData, Gadfly
Error: Failed to precompile Gadfly [c91e804a-d5a3-530f-b6f0-dfbca275c004] to /home/bates/.julia/compiled/v1.0/Gadfly/DvECm.ji.

julia> ds = names!(dat[:Dyestuff], [:Batch, :Yield])
30×2 DataFrames.DataFrame
│ Row │ Batch │ Yield  │
├─────┼───────┼────────┤
│ 1   │ A     │ 1545.0 │
│ 2   │ A     │ 1440.0 │
│ 3   │ A     │ 1440.0 │
│ 4   │ A     │ 1520.0 │
│ 5   │ A     │ 1580.0 │
│ 6   │ B     │ 1540.0 │
│ 7   │ B     │ 1555.0 │
│ 8   │ B     │ 1490.0 │
⋮
│ 22  │ E     │ 1630.0 │
│ 23  │ E     │ 1515.0 │
│ 24  │ E     │ 1635.0 │
│ 25  │ E     │ 1625.0 │
│ 26  │ F     │ 1520.0 │
│ 27  │ F     │ 1455.0 │
│ 28  │ F     │ 1450.0 │
│ 29  │ F     │ 1480.0 │
│ 30  │ F     │ 1445.0 │

julia> m1 = fit(LinearMixedModel, @formula(Yield ~ 1 + (1 | Batch)), ds)
Linear mixed model fit by maximum likelihood
 Formula: Yield ~ 1 + (1 | Batch)
   logLik   -2 logLik     AIC        BIC    
 -163.66353  327.32706  333.32706  337.53065

Variance components:
              Column    Variance  Std.Dev. 
 Batch    (Intercept)  1388.3333 37.260345
 Residual              2451.2500 49.510100
 Number of obs: 30; levels of grouping factors: 6

  Fixed-effects parameters:
             Estimate Std.Error z value P(>|z|)
(Intercept)    1527.5   17.6946  86.326  <1e-99

Now bootstrap the model parameters

julia> results = bootstrap(100_000, m1);
Error: UndefVarError: warn not defined

julia> showcompact(names(results))
Error: UndefVarError: results not defined

The results for each bootstrap replication are stored in the columns of the matrix passed in as the first argument. A density plot of the bootstrapped values of σ is created as


plot(results, x = :σ, Geom.density, Guide.xlabel("Parametric bootstrap estimates of σ"))

<pre class="julia-error"> ERROR: UndefVarError: Guide not defined </pre>

The distribution of the bootstrap samples of σ is a bit skewed but not terribly so. However, the distribution of the bootstrap samples of the estimate of σ₁ is highly skewed and has a spike at zero.