glmmTMBControl: Control parameters for glmmTMB optimization

Description Usage Arguments Details Examples

View source: R/glmmTMB.R

Description

Control parameters for glmmTMB optimization

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
glmmTMBControl(
  optCtrl = NULL,
  optArgs = list(),
  optimizer = nlminb,
  profile = FALSE,
  collect = FALSE,
  parallel = getOption("glmmTMB.cores", 1L),
  eigval_check = TRUE,
  zerodisp_val = log(sqrt(.Machine$double.eps)),
  start_method = list(method = NULL, jitter.sd = 0)
)

Arguments

optCtrl

Passed as argument control to optimizer. Default value (if default nlminb optimizer is used): list(iter.max=300, eval.max=400)

optArgs

additional arguments to be passed to optimizer function (e.g.: list(method="BFGS") when optimizer=optim)

optimizer

Function to use in model fitting. See Details for required properties of this function.

profile

(logical) Experimental option to improve speed and robustness when a model has many fixed effects

collect

(logical) Experimental option to improve speed by recognizing duplicated observations.

parallel

(integer) Set number of OpenMP threads to evaluate the negative log-likelihood in parallel. The default is to evaluate models serially (i.e. single-threaded); users can set a default value for an R session via options(glmmTMB.cores=<value>). At present reduced-rank models (i.e., a covariance structure using rr(...)) cannot be fitted in parallel; the number of threads will be automatically set to 1, with a warning if this overrides the user-specified value.

eigval_check

Check eigenvalues of variance-covariance matrix? (This test may be very slow for models with large numbers of fixed-effect parameters.)

zerodisp_val

value of the dispersion parameter when dispformula=~0 is specified

start_method

(list) Options to initialize the starting values when fitting models with reduced-rank (rr) covariance structures; jitter.sd adds variation to the starting values of latent variables when method = "res".

Details

By default, glmmTMB uses the nonlinear optimizer nlminb for parameter estimation. Users may sometimes need to adjust optimizer settings in order to get models to converge. For instance, the warning ‘iteration limit reached without convergence’ may be fixed by increasing the number of iterations using (e.g.)

glmmTMBControl(optCtrl=list(iter.max=1e3,eval.max=1e3)).

Setting profile=TRUE allows glmmTMB to use some special properties of the optimization problem in order to speed up estimation in cases with many fixed effects.

Control parameters may depend on the model specification. The value of the controls is evaluated inside an R object that is derived from the output of the mkTMBStruc function. For example, to specify that profile should be enabled if the model has more than 5 fixed-effect parameters, specify

profile=quote(length(parameters$beta)>=5)

The optimizer argument can be any optimization (minimizing) function, provided that:

Examples

1
2
3
4
5
6
## fit with default (nlminb) and alternative (optim/BFGS) optimizer
m1 <- glmmTMB(count~ mined, family=poisson, data=Salamanders)
m1B <- update(m1, control=glmmTMBControl(optimizer=optim,
               optArgs=list(method="BFGS")))
## estimates are *nearly* identical:
all.equal(fixef(m1), fixef(m1B))

Example output

[1] "Component “cond”: Mean relative difference: 2.66761e-06"

glmmTMB documentation built on July 20, 2021, 9:06 a.m.