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Create AMR Preprocessing Configuration

Source: R/config.R
amr_config.Rd

Creates a configuration object that controls the behavior of the preprocessing pipeline. Users can override default settings for their specific use case.

Usage

amr_config(
  column_mappings = NULL,
  fuzzy_match = TRUE,
  strict_validation = FALSE,
  date_columns = c("date_of_admission", "date_of_culture", "date_of_final_outcome",
    "DOB"),
  hai_cutoff = 2,
  infer_department = TRUE,
  event_gap_days = 14,
  mortality_window = 14,
  age_bins = "GBD_standard",
  contaminant_method = "auto",
  mdr_definition = "CDC",
  xdr_definition = "CDC",
  map_icd10 = TRUE,
  rr_table = "GBD_2021",
  organism_map = "default",
  antibiotic_map = "WHO_2023",
  intermediate_as_resistant = TRUE,
  verbose = TRUE
)

Arguments

column_mappings

Named list of column name mappings. Default uses default_column_mappings.

fuzzy_match

Logical. Enable fuzzy matching for column names. Default TRUE.

strict_validation

Logical. If TRUE, stops execution if required fields are missing. If FALSE, issues warnings. Default FALSE.

date_columns

Character vector of date column names to parse. Default includes standard date fields.

hai_cutoff

Numeric. Number of days after admission to classify as Hospital-Acquired Infection (HAI). Default 2.

infer_department

Logical. Attempt to infer hospital department from other variables if missing. Default TRUE.

event_gap_days

Numeric. Minimum days between events to create new event_id. Default 14.

mortality_window

Numeric. Days after culture to classify death as infection-related. Default 14.

age_bins

Character. Age binning strategy: "GBD_standard", "pediatric", or "geriatric". Can also be a custom vector. Default "GBD_standard".

contaminant_method

Character. Method for contaminant classification: "auto" (cascade through available methods), "device_based", "heuristic", "provided". Default "auto".

mdr_definition

Character or numeric. MDR definition: "CDC", "WHO", or numeric threshold for number of resistant classes. Default "CDC".

xdr_definition

Character or numeric. XDR definition. Default "CDC".

map_icd10

Logical. Attempt ICD-10 code mapping. Default TRUE.

rr_table

Character. Name of built-in RR table to use, or path to custom RR table. Default "GBD_2021".

organism_map

Character or named vector. "default" for built-in mapping, or custom named vector. Default "default".

antibiotic_map

Character. Built-in antibiotic classification: "WHO_2023" or path to custom. Default "WHO_2023".

intermediate_as_resistant

Logical. Treat Intermediate (I) as Resistant (R) except for special cases like Colistin. Default TRUE.

verbose

Logical. Print progress messages during processing. Default TRUE.

Value

An amr_config object (list with class)

Examples

if (FALSE) { # \dontrun{
# Use defaults
config <- amr_config()

# Customize for specific hospital
config <- amr_config(
  hai_cutoff = 3,
  mdr_definition = 5,
  strict_validation = FALSE
)
} # }