Validate Pre-computed Aggregate Marginal Inputs

Validates a pre-computed marginal resistance table (e.g. from GBD or a surveillance network) before it is passed to estimate_profiles_convex(). Checks prevalence bounds, duplicate rows, zero-denominator cells, impossible pairwise values, and minimum class counts per pathogen.

Usage

validate_aggregate_inputs(
  marginals,
  pairwise = NULL,
  pathogen_col = "pathogen",
  class_col = "antibiotic_class",
  rate_col = "marginal_resistance",
  n_tested_col = "n_tested",
  n_resistant_col = "n_resistant",
  class1_col = "antibiotic_class_1",
  class2_col = "antibiotic_class_2",
  pairwise_rate_col = "pairwise_resistance_prevalence",
  min_classes_per_pathogen = 2L
)

Arguments

marginals

Data frame with at minimum columns pathogen_col, class_col, and rate_col. Optionally also n_tested_col and n_resistant_col.

pairwise

Data frame or NULL. Pairwise co-resistance table with columns pathogen_col, class1_col, class2_col, and pairwise_rate_col. Default NULL.

pathogen_col

Character. Default "pathogen".

class_col

Character. Default "antibiotic_class".

rate_col

Character. Marginal resistance rate column. Default "marginal_resistance".

n_tested_col

Character or NULL. Default "n_tested".

n_resistant_col

Character or NULL. Default "n_resistant".

class1_col

Character. Default "antibiotic_class_1".

class2_col

Character. Default "antibiotic_class_2".

pairwise_rate_col

Character. Default "pairwise_resistance_prevalence".

min_classes_per_pathogen

Integer. Pathogens with fewer classes are flagged. Default 2L.

Value

Tibble of check results (same schema as validate_profile_inputs()). Stops on any "fail".