egf_control function

Define Control Parameters

Set parameters controlling the behaviour of egf.

egf_control(outer_optimizer = egf_optimizer(nlminb),
            inner_optimizer = egf_optimizer(newton),
            trace = FALSE, profile = FALSE, sparse_X = FALSE,
            omp_num_threads = getOption("egf.cores", 1L))

Arguments

• outer_optimizer, inner_optimizer: egf_optimizer objects specifying outer and inner optimization methods.
• trace: an integer determining the amount of tracing performed; see Details .
• profile: a logical. If TRUE, then fixed effect coefficients are profiled out of the likelihood, which may stabilize optimization for models with many fixed effects. This feature should be considered experimental, and in fact it may destabilize optimization, as it relies on assumptions about the optimization problem that are not necessarily satisfied by the nonlinear mixed effects models fit by egf.
• sparse_X: a logical. If TRUE, then the fixed effects design matrix is represented as a (sparse) dgCMatrix , rather than as a traditional (dense) matrix.
• omp_num_threads: an integer indicating a number of OpenMP threads to be used when evaluating the objective function, provided that epigrowthfit was compiled with OpenMP support.

Returns

A list inheriting from class egf_control containing the validated arguments.

Details

trace affects the amount of information printed during likelihood evaluations:

• 0: likelihood evaluations are always silent.
• 1: a message is printed whenever a negative log marginal likelihood term is NaN or exceeds 1e+09.
• 2: all negative log marginal likelihood terms are printed.

egf passes silent = trace == 0L to MakeADFun. A corollary is that nonzero values of trace have a number of additional side effects:

• error messages are printed during function and gradient evaluations;
• the maximum absolute gradient element is printed with each gradient evaluation; and
• trace flags set by config are turned on.

Warning

Setting trace > 0L and omp_num_threads > 0L simultaneously should be avoided, because tracing messages are printed using API functions that are not thread-safe.

Examples

control <- egf_control()
str(control)