Keeps records that meet the full burden-analysis readiness criteria:
Patient ID present
Culture date present
Organism name present and standardized
Antibiotic name present and standardized
Harmonized AST value in S/I/R
Not flagged as a contaminant (if column present)
Usage
prep_filter_analysis_ready(
data,
patient_col = "patient_id",
culture_date_col = "culture_date",
organism_col = "organism_name",
antibiotic_col = "antibiotic_name",
ast_col = "ast_value_harmonized",
exclude_contaminants = TRUE,
contaminant_col = "contaminant_flag"
)Arguments
- data
Data frame after preprocessing.
- patient_col
Character. Patient ID column. Default "patient_id".
- culture_date_col
Character. Culture date column. Default "culture_date".
- organism_col
Character. Organism column. Default "organism_name".
- antibiotic_col
Character. Antibiotic column. Default "antibiotic_name".
- ast_col
Character. Harmonized AST column. Default "ast_value_harmonized".
- exclude_contaminants
Logical. Exclude rows flagged as contaminants. Default TRUE.
- contaminant_col
Character. Contaminant flag column. Default "contaminant_flag".