The AMD pipeline as planned, without fitting anything

Description

Returns the steps [ferx_amd](ferx_amd.qmd) would run for this space and this model, in order, each either runnable or skipped with the reason - the plan the engine computes before its first fit, so it is the same list the run itself walks rather than a second derivation of it.

Usage

ferx_amd_plan(
  model = NULL,
  data = NULL,
  search_space = NULL,
  config = NULL,
  strategy = NULL,
  retries_on = NULL,
  skip = NULL
)

Arguments

  • model: Path to a .ferx model, or a ferx_model object. Omit when config is given.
  • data: Path to the dataset. Defaults to the model’s [data] block. Names the dataset the pipeline runs on, so like model it cannot be given beside config.
  • search_space: MFL search space, as a string or a character vector of lines. Required in the inline form.
  • config: Path to a .ferxsearch file. Mutually exclusive with the arguments that state the search.
  • strategy: Step order: "default", "reevaluation", "SIR", "SRI" or "RSI". NULL keeps the engine default ("default").
  • retries_on: Which selected models get the perturbed-restart pass: "all_final", "final" or "skip". NULL keeps the engine default ("all_final").
  • skip: Steps left out of the pipeline, any of "structural", "iivsearch", "residual", "iovsearch", "allometry", "covariates". A step the space says nothing about is skipped anyway; this is for one the space does describe.

Details

The model and the dataset are read (a step is skipped when the starting model declares no iov_column, which only the model says), but nothing is fitted.

Seealso

[ferx_amd](ferx_amd.qmd)Other search: [ferx_allometry](ferx_allometry.qmd), [ferx_amd](ferx_amd.qmd), [ferx_covsearch](ferx_covsearch.qmd), [ferx_globalsearch](ferx_globalsearch.qmd), [ferx_iivsearch](ferx_iivsearch.qmd), [ferx_iovsearch](ferx_iovsearch.qmd), [ferx_modelsearch](ferx_modelsearch.qmd), [ferx_ruvsearch](ferx_ruvsearch.qmd), [ferx_search_config](ferx_search_config.qmd), [ferx_search_coverage](ferx_search_coverage.qmd), [ferx_search_results](ferx_search_results.qmd), [ferx_search_space](ferx_search_space.qmd)

Concept

search

Value

A data frame with one row per planned step: index, step, tool, rerun, directory (the name the step’s files would go under) and skipped (the reason, or NAwhen the step will run). The options as the engine read them are attached as the options attribute.

Examples

ex <- ferx_example("warfarin_amd")
ferx_amd_plan(config = ex$search)
ferx_amd_plan(model = ex$model, data = ex$data,
              search_space = "IIV?(@PK, exp)", strategy = "SIR")