phylosem_control {phylosem}

Detailed control for phylosem structure

Description

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