R6 class for composite condition code specifications

A CompositeCodeSpec is a composition of all versioned condition components that collectively define a composite endpoint (e.g., ASCVD). Unlike CodeSpec, it does not store codes directly — instead it holds references to specific versioned CodeSpec leaf objects, accessible by name via the component argument.

The components list is a flat named list mapping "name_vX" keys to CodeSpec objects, e.g.:

components = list(
  chd_v1           = spec_chd_v1,
  stroke_v1        = spec_stroke_v1,
  cerebrovasc_disease_v1 = spec_cerebrovasc_disease_v1
)

The component argument is optional when calling get_codes() or get_defs(); omitting it (or passing "all") returns every component. The variable_type argument is forwarded to the component spec, so both condition and outcome codes are accessible.

Active bindings

condition: Short condition identifier (read-only).
version: Version label (read-only; NULL for composites).
label: Human-readable label (read-only).

Methods

`CompositeCodeSpec$new()`

Create a new CompositeCodeSpec.

Usage

CompositeCodeSpec$new(
  condition,
  label,
  defs = NULL,
  components = list(),
  version = NULL,
  components_by_variable_type = NULL
)

Arguments

condition: Short identifier string, e.g. "ascvd".
label: Human-readable label.
defs: Character string describing the composite definition.
components: Named list of CodeSpec objects, keyed by "name_vX" strings.
version: Optional version label (typically NULL for composites).
components_by_variable_type: Optional named list with elements condition and/or outcome, each a character vector of component names (keys of components) to use as the default set when component is omitted (or "all") for that variable_type. Lets a composite's default component set differ between the condition and outcome definitions (e.g. ASCVD's condition definition uses cerebrovascular disease while its outcome definition uses stroke instead). Explicitly naming component always bypasses this filter. NULL (default) means every component is used regardless of variable_type.

`CompositeCodeSpec$print()`

Print a summary of the composite spec.

Usage

CompositeCodeSpec$print(...)

`CompositeCodeSpec$components()`

Return the flat named component list.

Usage

CompositeCodeSpec$components()

Returns

Named list of CodeSpec objects.

`CompositeCodeSpec$keys()`

Return the code-set keys available across all components.

Usage

CompositeCodeSpec$keys()

Returns

Character vector of unique key strings.

`CompositeCodeSpec$get_codes()`

Retrieve codes from one or more components as a tidy data frame.

Usage

CompositeCodeSpec$get_codes(
  component = NULL,
  code_type = NULL,
  variable_type = c("condition", "outcome"),
  periods = FALSE,
  priority = 1L
)

Arguments

component: Optional component name(s), e.g. "chd_v1". NULL (default) or "all" returns every component that applies to variable_type (see components_by_variable_type in $new()), with a class column distinguishing them.
code_type: Optional character vector of code types to filter.
variable_type: "condition" (default) or "outcome".
periods: Logical. FALSE (default) = short format.
priority: Integer vector subsetting confidence tiers to include. Default 1.

Returns

A tibble with columns type, code, priority, version, and class (the component's own condition identifier, e.g. "chd" – not the versioned component key, since version already captures that).

`CompositeCodeSpec$get_defs()`

Retrieve the narrative algorithm description from one or more components.

Usage

CompositeCodeSpec$get_defs(
  component = NULL,
  variable_type = c("condition", "outcome")
)

Arguments

component: Optional component name. NULL (default) or "all" renders every component that applies to variable_type (see components_by_variable_type in $new()).
variable_type: "condition" (default) or "outcome".

Returns

Character string, or (for "all"/NULL) an invisible named list rendered to the console.

`CompositeCodeSpec$clone()`

The objects of this class are cloneable with this method.

Usage

CompositeCodeSpec$clone(deep = FALSE)

Arguments

deep: Whether to make a deep clone.