Generic function for running a pharmpy tool, like bootstrap, or modelsearch. A separate function is available for fit()

Generic function for running a pharmpy tool, like bootstrap, or modelsearch. A separate function is available for fit()

Usage

call_pharmpy_tool(
  id,
  model = NULL,
  results = NULL,
  tool = NULL,
  folder = NULL,
  clean = TRUE,
  verbose = TRUE,
  force = FALSE,
  options = list(),
  remove_tables = TRUE
)

Arguments

id: model id. Optional. If not specified, will generate random modelfit id. The id will be used to create the run folder.
model: Pharmpy model object, preferably created using create_model().
results: TODO
tool: TODO
folder: TODO
clean: if one or more run folders exists for the tool, do we want to remove them first?
verbose: verbose output?
force: TODO
options: list of arguments pass on to tool as argument. Documentation for available arguments for each Pharmpy tool can be found here: https://pharmpy.github.io/latest/mfl.html.
remove_tables: if TRUE (default), removes all $TABLE records from the model before passing it to the Pharmpy tool.

Value

fit object

Examples

if (FALSE) { # \dontrun{
# Run 200 bootstrap samples on a fitted model
bs <- call_pharmpy_tool(
  id      = "run1",
  model   = model,
  results = results,
  tool    = "bootstrap",
  options = list(samples = 200)
)

# Inspect parameter estimates (one row per sample)
head(as.data.frame(bs$parameter_estimates))

# Plot distributions and overlay original estimates
orig <- setNames(results$parameter_estimates$estimates,
                 results$parameter_estimates$parameter)
plot_bootstrap(bs, original_estimates = orig)
} # }