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"title": "Compute Observed-Plus-Imputed Resistance Profile Probabilities", "topics": [ "compute_event_profile_probabilities" ] }, { "page": "compute_hospital_daly", "title": "Compute Hospital-Level DALY Breakdown", "topics": [ "compute_hospital_daly" ] }, { "page": "compute_marginal_resistance", "title": "Compute Marginal Resistance per Pathogen and Antibiotic Class", "topics": [ "compute_marginal_resistance" ] }, { "page": "compute_marginals_from_data", "title": "Compute Marginal Resistance Rates from Preprocessed Wide Data", "topics": [ "compute_marginals_from_data" ] }, { "page": "compute_pairwise_coresistance", "title": "Compute Pairwise Co-resistance Matrices per Pathogen", "topics": [ "compute_pairwise_coresistance" ] }, { "page": "compute_pairwise_from_data", "title": "Compute Pairwise Co-resistance Using Pearson Back-calculation", "topics": [ "compute_pairwise_from_data" ] }, { "page": "compute_posterior_predictive_status", "title": "Classify overall posterior predictive fit 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from deaths, CFR, and CR_L (formula-based)", "topics": [ "daly_calc_incidence_from_cfr" ] }, { "page": "daly_calc_infection_fraction", "title": "Calculate Infection Fraction of Deaths by Cause (S_J)", "topics": [ "daly_calc_infection_fraction" ] }, { "page": "daly_calc_paf_los", "title": "Compute PAF for length of stay per resistance profile", "topics": [ "daly_calc_paf_los" ] }, { "page": "daly_calc_paf_mortality", "title": "Compute Mortality Population Attributable Fraction per Resistance Profile", "topics": [ "daly_calc_paf_mortality" ] }, { "page": "daly_calc_pathogen_fraction_fatal", "title": "Calculate fatal pathogen distribution (P_{Lk})", "topics": [ "daly_calc_pathogen_fraction_fatal" ] }, { "page": "daly_calc_resistance_prevalence_fatal", "title": "Calculate Fatal Resistance Prevalence (R_k)", "topics": [ "daly_calc_resistance_prevalence_fatal" ] }, { "page": "daly_calc_syndrome_fraction", "title": "Calculate Infectious Syndrome Fraction (M_LJ)", "topics": [ 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"default_column_mappings", "title": "Default column name mappings for fuzzy matching", "topics": [ "default_column_mappings" ] }, { "page": "detect_preprocessing_capabilities", "title": "Detect Preprocessing Capabilities", "topics": [ "detect_preprocessing_capabilities" ] }, { "page": "eda_theme", "title": "EDA ggplot2 Theme", "topics": [ "eda_theme" ] }, { "page": "enumerate_binary_profiles", "title": "Enumerate All Binary Resistance Profiles for a Set of Antibiotic Classes", "topics": [ "enumerate_binary_profiles" ] }, { "page": "estimate_profiles_convex", "title": "Estimate Resistance Profile Probabilities via Convex Optimisation", "topics": [ "estimate_profiles_convex" ] }, { "page": "estimate_resistance_profiles", "title": "Estimate Resistance Profiles: Pathway 1 (Convex) or Pathway 2 (Bayesian)", "topics": [ "estimate_resistance_profiles" ] }, { "page": "export_report", "title": "Export Report to File", "topics": [ "export_report" ] }, { "page": "fit_bayesian_multivariate_probit", "title": "Fit Bayesian Hierarchical Multivariate Probit Model for Resistance Profiles", "topics": [ "fit_bayesian_multivariate_probit" ] }, { "page": "fit_distributions", "title": "Fit Multiple Distributions", "topics": [ "fit_distributions" ] }, { "page": "generate_preprocessing_report", "title": "Generate Preprocessing Report", "topics": [ "generate_preprocessing_report" ] }, { "page": "get_age_bins", "title": "Get Age Bin Labels", "topics": [ "get_age_bins" ] }, { "page": "get_los_by_resistance", "title": "Extract LOS Vectors by Resistance Status", "topics": [ "get_los_by_resistance" ] }, { "page": "hospital_display_label", "title": "Human-readable hospital/site display label", "topics": [ "hospital_display_label" ] }, { "page": "infer_patient_syndrome_wide", "title": "Assign Syndrome from Wide-Format Syndrome Flags", "topics": [ "infer_patient_syndrome_wide" ] }, { "page": "mask_and_validate_ast", "title": "Masked-AST Holdout Validation", "topics": [ "mask_and_validate_ast" ] }, { "page": "plot_abx_complex_heatmap", "title": "Plot Antibiotic Resistance ComplexHeatmap", "topics": [ "plot_abx_complex_heatmap" ] }, { "page": "plot_abx_heatmap", "title": "Plot Antibiotic Resistance Heatmap", "topics": [ "plot_abx_heatmap" ] }, { "page": "plot_abx_susceptibility", "title": "Plot Antibiotic Susceptibility Pattern (Stacked R/S Bars)", "topics": [ "plot_abx_susceptibility" ] }, { "page": "plot_age_ridge", "title": "Ridge / Density Plot of Patient Age", "topics": [ "plot_age_ridge" ] }, { "page": "plot_burden_by_hospital", "title": "Plot YLL or YLD Associated vs Attributable per Hospital", "topics": [ "plot_burden_by_hospital" ] }, { "page": "plot_burden_by_organism", "title": "Plot YLL or YLD Associated vs Attributable by Organism", "topics": [ "plot_burden_by_organism" ] }, { "page": "plot_death_discharged", "title": "Plot Death vs Discharged Counts for Top Pathogens", "topics": [ "plot_death_discharged" ] }, { "page": "plot_hai_cai_by_facility", "title": "Plot HAI vs CAI Infection Distribution by Facility", "topics": [ "plot_hai_cai_by_facility" ] }, { "page": "plot_infection_type_by_location", "title": "Plot Infection Type (HAI/CAI) by Location (ICU/Ward), Faceted by Hospital", "topics": [ "plot_infection_type_by_location" ] }, { "page": "plot_location_by_facility", "title": "Plot Patient Distribution by Location Type Across Facilities", "topics": [ "plot_location_by_facility" ] }, { "page": "plot_los_by_agebin", "title": "Boxplot of Length of Stay by Age Group", "topics": [ "plot_los_by_agebin" ] }, { "page": "plot_los_distributions", "title": "Plot LOS Distribution with Fitted Overlays", "topics": [ "plot_los_distributions" ] }, { "page": "plot_los_ridge", "title": "Ridge / Density Plot of Length of Stay (LOS)", "topics": [ "plot_los_ridge" ] }, { "page": "plot_mono_poly_by_facility", "title": "Plot Mono vs Polymicrobial Infections by Facility", "topics": [ "plot_mono_poly_by_facility" ] }, { "page": "plot_omega_convergence_heatmap", "title": "Sampling-diagnostic (Rhat) heatmap for Omega", "topics": [ "plot_omega_convergence_heatmap" ] }, { "page": "plot_omega_correlation_heatmap", "title": "Posterior-median latent cross-class correlation heatmap (Omega)", "topics": [ "plot_omega_correlation_heatmap" ] }, { "page": "plot_omega_degeneracy_diagnostic", "title": "Near-degeneracy diagnostic for the posterior Omega correlation matrix", "topics": [ "plot_omega_degeneracy_diagnostic" ] }, { "page": "plot_omega_summary_table", "title": "Full per-pair Omega summary table (rho, 95% CrI, Rhat, ESS bulk/tail)", "topics": [ "plot_omega_summary_table" ] }, { "page": "plot_outcome_by_agebin", "title": "Plot Final Outcome Proportions by Age Bin", "topics": [ "plot_outcome_by_agebin" ] }, { "page": "plot_outcome_by_organism", "title": "Plot Final Outcome Proportions for Resistant or Susceptible Patients", "topics": [ "plot_outcome_by_organism" ] }, { "page": "plot_outcome_by_year", "title": "Plot Distribution of Final Outcomes by Year", "topics": [ "plot_outcome_by_year" ] }, { "page": "plot_outcome_distribution", "title": "Plot Distribution of Final Outcomes", "topics": [ "plot_outcome_distribution" ] }, { "page": "plot_patients_by_hospital", "title": "Plot Unique Patient Count by Hospital", "topics": [ "plot_patients_by_hospital" ] }, { "page": "plot_probit_beta_family_diagnostics", "title": "Fixed-effect convergence broken out by source of variation", "topics": [ "plot_probit_beta_family_diagnostics" ] }, { "page": "plot_probit_diagnostics", "title": "Generate diagnostic plots for a fitted Bayesian multivariate probit model", "topics": [ "plot_probit_diagnostics" ] }, { "page": "plot_probit_fixed_effect_diagnostics", "title": "Fixed-effect coefficient diagnostics, split by contrast type and faceted by antimicrobial class", "topics": [ "plot_probit_fixed_effect_diagnostics" ] }, { "page": "plot_probit_posterior_predictive_checks", "title": "Plot posterior predictive checks for a fitted probit model", "topics": [ "plot_probit_posterior_predictive_checks" ] }, { "page": "plot_probit_worst_offender_diagnostics", "title": "Trace and rank plots for the worst-converging structural parameters", "topics": [ "plot_probit_worst_offender_diagnostics" ] }, { "page": "plot_probit_worst_parameters", "title": "Human-readable worst-converging structural parameters", "topics": [ "plot_probit_worst_parameters" ] }, { "page": "plot_resistance_by_agebin", "title": "Resistance proportion by age group", "topics": [ "plot_resistance_by_agebin" ] }, { "page": "plot_resistance_by_organism", "title": "Resistance proportion for top N organisms", "topics": [ "plot_resistance_by_organism" ] }, { "page": "plot_resistance_by_sample", "title": "Plot Distribution of Antibiotic Resistance Across Sample Types", "topics": [ "plot_resistance_by_sample" ] }, { "page": "plot_syndrome_distribution", "title": "Plot Syndrome Distribution", "topics": [ "plot_syndrome_distribution" ] }, { "page": "plot_top_organisms", "title": "Plot Top Pathogens by Unique Patients", "topics": [ "plot_top_organisms" ] }, { "page": "plot_yld_heatmap", "title": "Heatmap of YLD per 1 000 Admissions by Organism Group", "topics": [ "plot_yld_heatmap" ] }, { "page": "plot_yll_heatmap", "title": "Heatmap of YLL per 1 000 Admissions by Resistance Class and Pathogen Group", "topics": [ "plot_yll_heatmap" ] }, { "page": "prep_apply_column_map", "title": "Apply Column Map to Rename Columns", "topics": [ "prep_apply_column_map" ] }, { "page": "prep_assert_standard_names", "title": "Assert Standard Names Are Present", "topics": [ "prep_assert_standard_names" ] }, { "page": "prep_assign_age_bins", "title": "Assign Age Bins", "topics": [ "prep_assign_age_bins" ] }, { "page": "prep_assign_facility_type", "title": "Assign a facility type / sector column from a user-supplied mapping", "topics": [ "prep_assign_facility_type" ] }, { "page": "prep_assign_organism_group", "title": "Assign Organism Group", "topics": [ "prep_assign_organism_group" ] }, { "page": "prep_assign_patient_syndrome", "title": "Assign One Syndrome Per Patient or Event", "topics": [ "prep_assign_patient_syndrome" ] }, { "page": "prep_attrition_flow", "title": "Track Attrition Through the Pipeline", "topics": [ "prep_attrition_flow" ] }, { "page": "prep_build_column_map", "title": "Build and Validate a Column Map Against a Dataset", "topics": [ "prep_build_column_map" ] }, { "page": "prep_build_fatal_cohort", "title": "Build Fatal Cohort", "topics": [ "prep_build_fatal_cohort" ] }, { "page": "prep_build_nonfatal_cohort", "title": "Build Non-Fatal Cohort", "topics": [ "prep_build_nonfatal_cohort" ] }, { "page": "prep_check_columns", "title": "Check required columns exist and report types", "topics": [ "prep_check_columns" ] }, { "page": "prep_check_keys", "title": "Check join key quality", "topics": [ "prep_check_keys" ] }, { "page": "prep_check_organism_ast_consistency", "title": "Check Organism-AST Consistency", "topics": [ "prep_check_organism_ast_consistency" ] }, { "page": "prep_classify_antibiotic_class", "title": "Classify Antibiotic to WHO Class", "topics": [ "prep_classify_antibiotic_class" ] }, { "page": "prep_classify_aware", "title": "Classify AWaRe Category", "topics": [ "prep_classify_aware" ] }, { "page": "prep_classify_mdr_xdr", "title": "Classify MDR and XDR", "topics": [ "prep_classify_mdr_xdr" ] }, { "page": "prep_classify_mortality", "title": "Classify Infection-Related Mortality", "topics": [ "prep_classify_mortality" ] }, { "page": "prep_classify_readmission", "title": "Classify Readmission Type", "topics": [ "prep_classify_readmission" ] }, { "page": "prep_clean_ast_values", "title": "Clean Antibiotic Susceptibility Values", "topics": [ "prep_clean_ast_values" ] }, { "page": "prep_clean_optional_columns", "title": "Clean Optional Columns", "topics": [ "prep_clean_optional_columns" ] }, { "page": "prep_coerce_dates", "title": "Detect and convert all date-like columns in a table", "topics": [ "prep_coerce_dates" ] }, { "page": "prep_collapse_class_level", "title": "Collapse to Class Level", "topics": [ "prep_collapse_class_level" ] }, { "page": "prep_compute_poly_weights", "title": "Compute Polymicrobial Weights", "topics": [ "compute_polymicrobial_weight", "prep_compute_poly_weights" ] }, { "page": "prep_create_event_ids", "title": "Create Event IDs from Patient-Level Data", "topics": [ "prep_create_event_ids" ] }, { "page": "prep_create_resistance_profile", "title": "Create Resistance Profile", "topics": [ "prep_create_resistance_profile" ] }, { "page": "prep_create_wide_ast_matrix", "title": "Create Wide Format AST Matrix", "topics": [ "prep_create_wide_ast_matrix" ] }, { "page": "prep_decode_antibiotic_code", "title": "Decode Antibiotic Short Codes to Full Names", "topics": [ "prep_decode_antibiotic_code" ] }, { "page": "prep_deduplicate_ast", "title": "Handle Duplicate AST Results", "topics": [ "prep_deduplicate_ast" ] }, { "page": "prep_deduplicate_events", "title": "Deduplicate Events", "topics": [ "prep_deduplicate_events" ] }, { "page": "prep_derive_dob_from_components", "title": "Derive Date of Birth from Age Components", "topics": [ "prep_derive_dob_from_components" ] }, { "page": "prep_derive_hai_cai", "title": "Derive HAI/CAI Infection Type", "topics": [ "prep_derive_hai_cai" ] }, { "page": "prep_derive_icu_flag", "title": "Derive ICU Flag", "topics": [ "prep_derive_icu_flag" ] }, { "page": "prep_derive_los_from_dates", "title": "Derive Length of Stay from Date Columns", "topics": [ "prep_derive_los_from_dates" ] }, { "page": "prep_detect_schema_drift", "title": "Detect Schema Drift Across Centres", "topics": [ "prep_detect_schema_drift" ] }, { "page": "prep_diagnosis_text", "title": "Prepare Diagnosis Text", "topics": [ "prep_diagnosis_text" ] }, { "page": "prep_extract_genus", "title": "Extract Genus from Organism Name", "topics": [ "prep_extract_genus" ] }, { "page": "prep_extract_species", "title": "Extract Species from Organism Name", "topics": [ "prep_extract_species" ] }, { "page": "prep_fill_age", "title": "Fill Missing Age Values", "topics": [ "prep_fill_age" ] }, { "page": "prep_filter_analysis_ready", "title": "Filter Analysis-Ready Records", "topics": [ "prep_filter_analysis_ready" ] }, { "page": "prep_filter_fungal", "title": "Filter Fungal Organisms", "topics": [ "prep_filter_fungal" ] }, { "page": "prep_filter_minimally_usable", "title": "Filter Minimally Usable Records", "topics": [ "prep_filter_minimally_usable" ] }, { "page": "prep_flag_contaminants", "title": "Flag Contaminant Organisms", "topics": [ "prep_flag_contaminants" ] }, { "page": "prep_flag_hai_inferred", "title": "Flag HAI Inferred vs Observed", "topics": [ "prep_flag_hai_inferred" ] }, { "page": "prep_flag_invalid_ast", "title": "Flag Invalid AST Values", "topics": [ "prep_flag_invalid_ast" ] }, { "page": "prep_flag_organism_unmatched", "title": "Flag Organisms Unmatched in Reference", "topics": [ "prep_flag_organism_unmatched" ] }, { "page": "prep_flag_polymicrobial", "title": "Flag Polymicrobial Infections", "topics": [ "flag_polymicrobial", "prep_flag_polymicrobial" ] }, { "page": "prep_flag_readmission", "title": "Flag and Classify Readmissions", "topics": [ "prep_flag_readmission" ] }, { "page": "prep_get_contaminant_list", "title": "Get Contaminant List from Reference File", "topics": [ "prep_get_contaminant_list" ] }, { "page": "prep_harmonize_ast", "title": "Harmonize AST Values", "topics": [ "prep_harmonize_ast" ] }, { "page": "prep_infer_department", "title": "Infer Hospital Department", "topics": [ "prep_infer_department" ] }, { "page": "prep_inventory_columns", "title": "Inventory Columns", "topics": [ "prep_inventory_columns" ] }, { "page": "prep_is_contaminant", "title": "Check if Organism is a Contaminant", "topics": [ "prep_is_contaminant" ] }, { "page": "prep_log_source", "title": "Log Data Source Provenance", "topics": [ "prep_log_source" ] }, { "page": "prep_map_diagnosis_to_icd", "title": "Map Diagnosis Text to ICD Candidates", "topics": [ "prep_map_diagnosis_to_icd" ] }, { "page": "prep_map_icd_to_syndrome", "title": "Map ICD Codes to Infectious Syndromes", "topics": [ "prep_map_icd_to_syndrome" ] }, { "page": "prep_missingness_report", "title": "Missingness Report", "topics": [ "prep_missingness_report" ] }, { "page": "prep_parse_date_column", "title": "Detect and decode encrypted or non-standard date columns", "topics": [ "prep_parse_date_column" ] }, { "page": "prep_pivot_ast_wide_to_long", "title": "Convert Wide Format to Long Format", "topics": [ "prep_pivot_ast_wide_to_long" ] }, { "page": "prep_recode_intermediate_ast", "title": "Recode Intermediate (I) Susceptibility Values", "topics": [ "prep_recode_intermediate_ast" ] }, { "page": "prep_reconcile_hai_observed_inferred", "title": "Reconcile Observed and Inferred HAI/CAI Classification", "topics": [ "prep_reconcile_hai_observed_inferred" ] }, { "page": "prep_report_capabilities", "title": "Report Preprocessing Capabilities", "topics": [ "prep_report_capabilities" ] }, { "page": "prep_split_poly_episode", "title": "Split Polymicrobial Episodes by Strategy", "topics": [ "prep_split_poly_episode" ] }, { "page": "prep_standardize_antibiotics", "title": "Normalize Antibiotic Names", "topics": [ "prep_standardize_antibiotics" ] }, { "page": "prep_standardize_column_names", "title": "Standardize Column Names to Package Convention", "topics": [ "prep_standardize_column_names" ] }, { "page": "prep_standardize_final_outcome", "title": "Standardize Final Outcome Column", "topics": [ "prep_standardize_final_outcome" ] }, { "page": "prep_standardize_infection_type", "title": "Standardize Infection Type Column", "topics": [ "prep_standardize_infection_type" ] }, { "page": "prep_standardize_organisms", "title": "Normalize Organism Names", "topics": [ "prep_standardize_organisms" ] }, { "page": "prep_standardize_outcome", "title": "Standardize Outcome Values (deprecated)", "topics": [ "prep_standardize_outcome" ] }, { "page": "prep_standardize_sex", "title": "Standardize Sex Values", "topics": [ "prep_standardize_sex" ] }, { "page": "prep_standardize_specimens", "title": "Normalize Specimen/Sample Type", "topics": [ "prep_standardize_specimens" ] }, { "page": "prep_validate_analysis_ready", "title": "Validate Analysis-Ready Dataset", "topics": [ "prep_validate_analysis_ready" ] }, { "page": "prep_validate_date_logic", "title": "Validate Date Logic", "topics": [ "prep_validate_date_logic" ] }, { "page": "prep_validate_table", "title": "Run all pre-join sanity checks for one table", "topics": [ "prep_validate_table" ] }, { "page": "prepare_los_data", "title": "Prepare LOS Dataset", "topics": [ "prepare_los_data" ] }, { "page": "prepare_random_effects", "title": "Build the generic random-effect representation for an arbitrary number of blocks", "topics": [ "prepare_random_effects" ] }, { "page": "preprocess_for_profiles", "title": "Preprocess AST Data for Resistance Profile Estimation (Pathway 1)", "topics": [ "preprocess_for_profiles" ] }, { "page": "print.amr_config", "title": "Print AMR Configuration", "topics": [ "print.amr_config" ] }, { "page": "print.amr_preprocessing_report", "title": "Print Preprocessing Report", "topics": [ "print.amr_preprocessing_report" ] }, { "page": "print.amr_result", "title": "Print Method for AMR Preprocessing Results", "topics": [ "print.amr_result" ] }, { "page": "re_contribution", "title": "Compute each event's total random-effect contribution from a flattened re_effect[D, total_re_levels] matrix (as emitted by the generic Stan models' generated re_effect, or reconstructed R-side from posterior draws of z_re/tau_re/L_corr_re). This is the SINGLE generic helper every downstream mu-reconstruction site should call instead of hand-summing hospital_effect/patient_effect/admission_effect.", "topics": [ "re_contribution" ] }, { "page": "round_to_sum", "title": "Largest-Remainder Rounding", "topics": [ "round_to_sum" ] }, { "page": "run_preprocess", "title": "AMR Data Preprocessing Pipeline", "topics": [ "run_preprocess" ] }, { "page": "safe_fit", "title": "Safely Fit a Distribution", "topics": [ "safe_fit" ] }, { "page": "select_resistance_class", "title": "Select Resistance Class for Burden Attribution", "topics": [ "select_resistance_class" ] }, { "page": "shorten_drug_class", "title": "Shorten Antibiotic Class Names", "topics": [ "shorten_drug_class" ] }, { "page": "simulate_probit_mixed_predictive", "title": "Simulate mixed predictive replicate datasets: new random-effect levels for a requested block, retaining fitted hyperparameters", "topics": [ "simulate_probit_mixed_predictive" ] }, { "page": "simulate_probit_posterior_predictive", "title": "Simulate posterior predictive replicate datasets from a fitted probit model", "topics": [ "simulate_probit_posterior_predictive" ] }, { "page": "simulate_probit_prior_predictive", "title": "Simulate prior predictive replicate datasets for a probit model", "topics": [ "simulate_probit_prior_predictive" ] }, { "page": "summarise_distribution", "title": "Summarise a Fitted Distribution", "topics": [ "summarise_distribution" ] }, { "page": "summarize_column_mapping", "title": "Summarize Column Mapping", "topics": [ "summarize_column_mapping" ] }, { "page": "summarize_data_quality", "title": "Summarize Data Quality", "topics": [ "summarize_data_quality" ] }, { "page": "summarize_fit_correlation_matrix", "title": "Summarize a posterior D x D correlation matrix from stored fit draws", "topics": [ "summarize_fit_correlation_matrix" ] }, { "page": "summarize_raw_data", "title": "Summarize Raw Data", "topics": [ "summarize_raw_data" ] }, { "page": "summarize_transformations", "title": "Summarize Data Transformations", "topics": [ "summarize_transformations" ] }, { "page": "summary.amr_result", "title": "Summary Method for AMR Preprocessing Results", "topics": [ "summary.amr_result" ] }, { "page": "validate_aggregate_inputs", "title": "Validate Pre-computed Aggregate Marginal Inputs", "topics": [ "validate_aggregate_inputs" ] }, { "page": "validate_complete_profile_calibration", "title": "Observed-versus-Model Complete-Profile Validation", "topics": [ "validate_complete_profile_calibration" ] }, { "page": "validate_compute_backend", "title": "Validate a selectable Stan compute backend configuration", "topics": [ "validate_compute_backend" ] }, { "page": "validate_config", "title": "Validate AMR Configuration", "topics": [ "validate_config" ] }, { "page": "validate_data_quality", "title": "Validate Data Quality", "topics": [ "validate_data_quality" ] }, { "page": "validate_marginal_calibration", "title": 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