Shared fit driver for the nlm-family estimation methods

Usage

.nlmFamilyFitGeneric(
  env,
  method,
  fitModel,
  getTheta,
  controlToFocei,
  returnFlag,
  objective = NULL,
  message = function(fit) fit$message,
  emitFitWarnings = TRUE,
  extra = "",
  adjustOutput = TRUE,
  postSetup = NULL
)

Arguments

env: dispatch environment (provides `ui`, `control`, `data`, `table`)
method: estimation-method string; also the slot the raw fit is stored under (e.g. `"nlm"` -> `.ret[["nlm"]]`)
fitModel: `function(ui, dataSav)` running the optimizer
getTheta: `function(fit, ui)` returning the full theta vector, or the name of the optimizer's estimates in the fit (e.g. `"par"`), which `.nlmFamilyGetTheta()` completes with the fixed thetas
controlToFocei: `function(env)` translating the control to a focei-style control for output assembly
returnFlag: rxode2 control flag name that short-circuits and returns the raw optimizer result (e.g. `"returnNlm"`)
objective: optional `function(fit)` returning the raw objective, or the name of the fit's minimized -log-likelihood, which is doubled; when `NULL` the driver does not set `$objective` (a `postSetup` closure did)
message: `function(fit)` returning the `$message` (default `fit$message`)
emitFitWarnings: when TRUE (the default), re-emit the warnings collected from `fitModel` (the optimizer, the covariance step and `nlmWarnings()`) via `warning()`, so they reach the fit's `$runInfo`; `FALSE` drops them
extra: `$extra` print string, or a `function(control)` returning it
adjustOutput: when TRUE, run `.nlmFamilyAdjustOutput()`
postSetup: optional `function(ret, ui, fitList)` returning a modified `ret`, run right after the raw fit is stored and before `.nlmFamilyAdjustOutput()` (for methods that set cov/covMethod/objective with custom values)

Value

the assembled nlmixr2 fit (or the raw optimizer result if `returnFlag`)

Author

Matthew L. Fidler