Execute a recipe: compile to plan and run

Convenience function that compiles the recipe to an execution plan via recipe_to_plan and immediately executes it via ds.omop.plan.execute. Symbol names for server-side datasets are derived from the recipe's output result_symbol fields, or auto-generated as D_<name>.

Usage

recipe_execute(
  recipe,
  out = NULL,
  symbol = "omop",
  conns = NULL,
  output_mode = "memory",
  cohort = NULL,
  tables = NULL,
  combine = "union"
)

Arguments

recipe

An omop_recipe object.

out

Named character vector; output_name -> symbol_name mapping. If NULL, auto-generates symbol names from the recipe's output specifications.

symbol

Character; OMOP session symbol on the server (default "omop").

conns

DSI connections or NULL (uses active connections).

output_mode

Character; "memory" (default) or "staged". Passed through to ds.omop.plan.execute.

cohort

Optional recipe-level scope cohort applied at execution time: a dsomop_cohort_handle, a cohort_definition_id, or a server-side cohort table name. When supplied (with or without tables) it replaces any scope already on the recipe; NULL (the default) leaves the recipe's own scope untouched. Folded with tables by combine and intersected into every population (see omop_recipe).

tables

Optional character vector of omop.table symbol names to add to the execution-time scope (their distinct persons). May be combined with cohort.

combine

Character; how to fold the scope sources together: "union" (the default) or "intersect".

Value

Invisibly, the output symbol mapping (a named character vector). As with ds.omop.plan.execute, the produced symbols are recorded on the session so the manipulation wrappers can default to the last one.

See also

recipe_to_plan, ds.omop.plan.execute

Examples

if (FALSE) { # \dontrun{
recipe_execute(recipe)
recipe_execute(recipe, output_mode = "staged")
# Or with explicit symbol mapping:
recipe_execute(recipe, out = c(features_wide = "D_features"))
# Scope every population to a cohort intersected with a workspace table:
recipe_execute(recipe, cohort = my_cohort, tables = "inclusion_set",
               combine = "intersect")
} # }