R6 class for medical condition code specifications

Stores the code sets and narrative algorithm description for a single version of a medical condition definition. Each version is a distinct object (e.g., spec_acei_v1, spec_acei_v2).

The spec stores:

defs: named list with elements condition and outcome, each holding a narrative algorithm description string (or NULL if not defined).
codes: named list of key-level lists keyed by {code_type}_{encounter} (e.g., dx_icd9). Each key-level list has:
- codes: character vector of exact short-format codes (no periods).
- condition: logical vector parallel to codes; TRUE if the code belongs to the condition/history definition.
- outcome: logical vector parallel to codes; TRUE if the code belongs to the outcome definition.
- definitions: optional character vector of code definitions, parallel to codes.
- exclusions: optional character string describing codes to exclude.

Active bindings

condition: Short condition identifier (read-only).
version: Version label, e.g. "v1" (read-only).
label: Human-readable condition label (read-only).

Methods

`CodeSpec$new()`

Create a new CodeSpec.

Usage

CodeSpec$new(
  condition,
  label,
  defs = NULL,
  codes = NULL,
  version = NULL,
  versions = NULL
)

Arguments

condition: Short identifier string, e.g. "htn".
label: Human-readable label, e.g. "Hypertension".
defs: Named list with elements condition and outcome (character strings or NULL).
codes: Named list of key-level lists. See class description.
version: Optional version label string, e.g. "v1".
versions: Deprecated. Use defs/codes/version directly.

`CodeSpec$print()`

Print a summary of the spec.

Usage

CodeSpec$print(...)

`CodeSpec$keys()`

Return code-set keys.

Usage

CodeSpec$keys()

Returns

Character vector of keys like "dx_icd9".

`CodeSpec$get_codes()`

Retrieve codes from the spec as a tidy data frame.

Usage

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

Arguments

code_type: Optional character vector of code types to return. Valid values: "dx_icd9", "dx_icd10", "proc_icd9", "proc_icd10", "hcpcs", "cpt", "rev". NULL returns all.
variable_type: "condition" (default) or "outcome". If the spec has no codes flagged for "outcome", falls back to "condition".
periods: Logical. If TRUE, return codes with decimal periods (e.g., "401.0"). Default FALSE returns short format ("4010").
priority: Integer vector subsetting confidence tiers to include (1 = core, 2 = probable, 3 = cautious). Default 1.

Returns

A tibble with columns type, code, priority, version, and definition.

`CodeSpec$get_defs()`

Retrieve the narrative algorithm description.

Usage

CodeSpec$get_defs(variable_type = c("condition", "outcome"))

Arguments

variable_type: "condition" (default) or "outcome".

Returns

Character string, or NULL if no definition exists for that variable type.

`CodeSpec$clone()`

The objects of this class are cloneable with this method.

Usage

CodeSpec$clone(deep = FALSE)

Arguments

deep: Whether to make a deep clone.