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Define a list of control parameters. Note that the format of this input is likely to change more rapidly than that of phylosem

Usage

phylosem_control(
  nlminb_loops = 1,
  newton_loops = 1,
  trace = 0,
  eval.max = 1000,
  iter.max = 1000,
  getsd = TRUE,
  quiet = FALSE,
  run_model = TRUE,
  getJointPrecision = FALSE
)

Arguments

nlminb_loops

Integer number of times to call nlminb.

newton_loops

Integer number of Newton steps to do after running nlminb.

trace

Parameter values are printed every `trace` iteration for the outer optimizer. Passed to `control` in nlminb.

eval.max

Maximum number of evaluations of the objective function allowed. Passed to `control` in nlminb.

iter.max

Maximum number of iterations allowed. Passed to `control` in nlminb.

getsd

Boolean indicating whether to call sdreport

quiet

Boolean indicating whether to run model printing messages to terminal or not;

run_model

Boolean indicating whether to estimate parameters (the default), or instead to return the model inputs and compiled TMB object without running;

getJointPrecision

whether to get the joint precision matrix. Passed to sdreport.

Value

An S3 object of class "phylosem_control" that specifies detailed model settings, allowing user specification while also specifying default values