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Validate Inputs for Resistance Profile Estimation (Pathway 1)

Source: R/daly_resistance_profiles.R
validate_profile_inputs.Rd

Checks that all mandatory columns exist, detects long vs wide format, validates AST content, and verifies that columns required for any requested stratification are present. Returns a tibble of check results and stops on any failed mandatory check.

Usage

validate_profile_inputs(
  data,
  col_map = list(isolate_col = "isolate_id", pathogen_col = "pathogen", ast_col =
    "ast_value", patient_col = "patient_id", date_col = "date_of_culture", geography_col
    = "state", specimen_col = "specimen_type", age_col = "age", dob_col = "dob",
    antibiotic_col = "antibiotic_name", class_col = "antibiotic_class", location_col =
    NULL, outcome_col = NULL),
  stratify_by = NULL,
  outcome_col = NULL
)

Arguments

data

Data frame to validate.

col_map

Named list mapping logical roles to actual column names. Defaults use standard package column names. Set any entry to NULL to skip that check (only valid for optional roles).

stratify_by

Character vector or NULL. Requested stratification dimensions. Accepted values: "geography", "year", "outcome". Triggers additional column checks for each dimension. Default NULL.

outcome_col

Character or NULL. Outcome column name. Required when "outcome" is in stratify_by. Can also be supplied via col_map$outcome_col. Default NULL.

Value

A tibble with columns check_name, status ("pass" / "warn" / "fail"), message, and n_affected. The attribute detected_format ("long" or "wide") is attached. Stops with an informative message if any mandatory check fails.

Details

Mandatory columns (always):

  • isolate_col – unique isolate identifier; the counting unit for all resistance statistics. One patient may have multiple isolates.

  • pathogen_col – organism / pathogen name.

  • ast_col – susceptibility result; must contain S / I / R.

  • patient_col – patient identifier (retained for context, not counted).

  • date_col – culture date; used to derive year when "year" is in stratify_by.

  • geography_col – geographic unit (state / district).

  • specimen_col – specimen type (blood, urine, etc.).

  • age_col OR dob_col – at least one must be present.

Mandatory in long format only:

  • antibiotic_col – antibiotic / drug name column.

Optional (warn if absent, do not stop):

  • class_col – antibiotic class; derived from antibiotic_col via WHO AWaRe reference if absent.

  • location_col – ward / ICU / OPD; retained for subgroup outputs.

  • outcome_col – patient outcome; required for outcome stratification.

Examples

if (FALSE) { # \dontrun{
report <- validate_profile_inputs(
  data        = my_ast_data,
  col_map     = list(
    isolate_col   = "isolate_id",
    pathogen_col  = "organism",
    ast_col       = "result",
    patient_col   = "pid",
    date_col      = "culture_date",
    geography_col = "state",
    specimen_col  = "specimen",
    age_col       = "age_years",
    dob_col       = NULL,
    antibiotic_col = "drug_name",
    class_col     = NULL,
    location_col  = "ward",
    outcome_col   = "discharge_status"
  ),
  stratify_by = c("geography", "year"),
  outcome_col = "discharge_status"
)
} # }