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 = NULL,
hai_cutoff = 2,
infer_department = TRUE,
event_gap_days = 14,
mortality_window = 14,
age_bins = "GBD_standard",
contaminant_method = "auto",
mdr_definition = "CDC",
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 NULL auto-detects date-like columns by name pattern.
- 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/XDR definition (used for both): "CDC", "WHO", or numeric threshold for number of resistant classes. Default "CDC".
- 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.