library("knitr") knitr::opts_chunk$set( ) (load(system.file("testdata", "lmerperf.rda", package="lme4")))# 'ss' 'fitlist'

library("lme4")

In general `lme4`

's algorithms scale reasonably well with the number of observations
and the number of random effect levels. The biggest bottleneck is in the number of
*top-level parameters*, i.e. covariance parameters for
`lmer`

fits or `glmer`

fits with `nAGQ`

=0 [`length(getME(model, "theta"))`

],
covariance and fixed-effect parameters for `glmer`

fits with `nAGQ`

>0. `lme4`

does a derivative-free
(by default) nonlinear optimization step over the top-level parameters.

For this reason, "maximal" models involving interactions of factors with several levels each
(e.g. `(stimulus*primer | subject)`

) will be slow (as well as hard to estimate): if the two factors
have `f1`

and `f2`

levels respectively, then the corresponding `lmer`

fit will need to estimate
`(f1*f2)*(f1*f2+1)/2`

top-level parameters.

`lme4`

automatically constructs the random effects model matrix ($Z$) as a sparse matrix.
At present it does *not* allow an option for a sparse fixed-effects model matrix ($X$), which
is useful if the fixed-effect model includes factors with many levels. Treating such factors
as random effects instead, and using the modular framework (`?modular`

) to fix the variance
of this random effect at a large value, will allow it to be modeled using a sparse matrix.
(The estimates will converge to the fixed-effect case in the limit as the variance goes to infinity.)

`calc.derivs = FALSE`

After finding the best-fit model parameters (in most cases using *derivative-free*
algorithms such as Powell's BOBYQA or Nelder-Mead, `[g]lmer`

does a series of finite-difference
calculations to estimate the gradient and Hessian at the MLE. These are used to
try to establish whether the model has converged reliably, and (for `glmer`

) to
estimate the standard deviations of the fixed effect parameters (a less accurate
approximation is used if the Hessian estimate is not available. As currently implemented, this computation takes `2*n^2 - n + 1`

additional evaluations of the deviance,
where `n`

is the total number of top-level parameters. Using `control = [g]lmerControl(calc.derivs = FALSE)`

to turn off this calculation can speed up
the fit, e.g.

m0 <- lmer(y ~ service * dept + (1|s) + (1|d), InstEval, control = lmerControl(calc.derivs = FALSE))

## based on loaded lmerperf file t1 <- fitlist$basic$times[["elapsed"]] t2 <- fitlist$noderivs$times[["elapsed"]] pct <- round(100*(t1-t2)/t1) e1 <- fitlist$basic$optinfo$feval

Benchmark results for this run with and without derivatives show an
approximately `r pct`

% speedup (from `r round(t1)`

to `r round(t2)`

seconds on a Linux machine with
AMD Ryzen 9 2.2 GHz processors). This is a case with only 2 top-level
parameters, but the fit took only `r e1`

deviance function evaluations
(see `m0@optinfo$feval`

) to converge, so the effect of the additional 7 ($n^2 -n +1$)
function evaluations is noticeable.

gg <- glmerControl()$optimizer

`lmer`

uses the "`r lmerControl()$optimizer`

" optimizer by default;
`glmer`

uses a combination of `r gg[1]`

(`nAGQ=0`

stage) and `r gg[2]`

.
These are reasonably good choices, although switching `glmer`

fits to `nloptwrap`

for
both stages may be worth a try.

`allFits()`

gives an easy way to check the timings of a large range of optimizers:

tt <- sort(ss$times[,"elapsed"]) tt2 <- data.frame(optimizer = names(tt), elapsed = tt) rownames(tt2) <- NULL knitr::kable(tt2)

As expected, bobyqa - both the implementation in the `minqa`

package [`[g]lmerControl(optimizer="bobyqa")`

]
and the one in `nloptwrap`

[`optimizer="nloptwrap"`

or `optimizer="nloptwrap", optCtrl = list(algorithm = "NLOPT_LN_BOBYQA"`

] - are fastest.

Occasionally, the default optimizer stopping tolerances are unnecessarily strict.
These tolerances are specific to each optimizer, and can be set via the `optCtrl`

argument in `[g]lmerControl`

.
To see the defaults for `nloptwrap`

:

environment(nloptwrap)$defaultControl

## based on loaded lmerperf file t1 <- fitlist$basic$times[["elapsed"]] t2 <- fitlist$noderivs$times[["elapsed"]] t3 <- fitlist$nlopt_sloppy$times[["elapsed"]] pct <- round(100*(t1-t2)/t1) e1 <- fitlist$basic$optinfo$feval

In the particular case of the `InstEval`

example, this doesn't help much - loosening the tolerances
to `ftol_abs=1e-4`

, `xtol_abs=1e-4`

only saves 2 functional evaluations and a few seconds, while loosening
the tolerances still further gives convergence warnings.

There are not many options for parallelizing `lme4`

. Optimized BLAS does not seem to help much.

`glmmTMB`

may be faster than`lme4`

for GLMMs with large numbers of top-level parameters, especially for negative binomial models (i.e. compared to`glmer.nb`

)- the
`MixedModels.jl`

package in Julia may be*much*faster for some problems. You do need to install Julia. - see this short tutorial or this example (Jupyter notebook)
- the JellyMe4 and jglmm packages provide R interfaces

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