g3_leaveout: Leave-one-out analysis.
In gadget-framework/gadgetutils: Tools to create and maintain gadget3 models

g3_leaveout

R Documentation

Leave-one-out analysis.

Description

Perform a leave-one-out analysis. This involves running a set of optimisations, each one of which has a component (or set of components) turned off (i.e. weight = 0).

Usage

g3_leaveout(
  gd,
  outdir = "LOCV",
  model,
  params,
  grouping = list(),
  use_parscale = TRUE,
  method = "BFGS",
  control = list(),
  serial_compile = FALSE,
  mc.cores = parallel::detectCores()
)

Arguments

`gd`	Directory to store output
`outdir`	Directory name within gd to store run outputs
`model`	A G3 model, produced by g3_to_tmb() or g3_to_r()
`params`	Initial parameters to use with the model, this should be a TMB parameter template i.e. attr(tmb_model, 'parameter_template')
`grouping`	List of component names to group together. This allows you to leave out multiple components at a time, e.g. length and age-length distributions from a particular fleet
`use_parscale`	Logical indicating whether optim(control$parscale) should be used
`method`	The optimisation method, see `optim`
`control`	List of control options for optim, see `optim`
`serial_compile`	g3_tmb_adfun will be run in serial mode (i.e., not in parallel), potentially helping with memory issues
`mc.cores`	The number of cores to use, defaults to the number available