Pipeline

Main preprocessing pipeline and configuration

amr_preprocess(): AMR Data Preprocessing Pipeline
amr_config(): Create AMR Preprocessing Configuration
validate_config(): Validate AMR Configuration
print(<amr_config>): Print AMR Configuration
print(<amr_result>): Print Method for AMR Preprocessing Results
summary(<amr_result>): Summary Method for AMR Preprocessing Results
print(<amr_preprocessing_report>): Print Preprocessing Report

Normalization

Standardize column names, organisms, antibiotics, and specimens

standardize_column_names(): Standardize Column Names to Package Convention
normalize_organism(): Normalize Organism Names
normalize_antibiotic(): Normalize Antibiotic Names
normalize_specimen(): Normalize Specimen/Sample Type
standardize_gender(): Standardize Gender Values
standardize_outcome(): Standardize Outcome Values
standardize_susceptibility(): Standardize Susceptibility Values
recode_intermediate(): Recode Intermediate (I) Susceptibility Values
clean_antibiotic_values(): Clean Antibiotic Susceptibility Values
parse_dates(): Parse Dates Safely

Classification

MDR/XDR classification, organism grouping, and AWaRe

classify_mdr(): Classify MDR (Multidrug Resistant)
classify_xdr(): Classify XDR (Extensively Drug Resistant)
classify_org_group(): Classify Organism Group
classify_aware(): Classify AWaRe Category
classify_antibiotic_class(): Classify Antibiotic to WHO Class
classify_mortality(): Classify Infection-Related Mortality
derive_infection_type(): Derive Infection Type (HAI / CAI) per Patient
derive_infection_type_for_mortality(): Derive Infection Type (HAI / CAI) for Mortality RR Model

Enrichment

Derive missing variables from existing data

enrich_age(): Enrich Age
enrich_los(): Enrich Length of Stay
enrich_infection_type(): Enrich Infection Type
enrich_hospital_department(): Enrich Hospital Department
assign_age_bins(): Assign Age Bins
derive_age(): Derive Age from Date of Birth

Deduplication and collapsing

Event IDs, deduplication, and data reshaping

create_event_ids(): Create Event IDs from Patient-Level Data
deduplicate_events(): Deduplicate Events
flag_contaminants(): Flag Contaminant Organisms
flag_polymicrobial(): Flag Polymicrobial Infections (No Specimen Type, No Episode ID)
collapse_to_antibiotic_level(): Collapse to Antibiotic Level (OPTIONAL - Run When YOU Decide)
collapse_to_class_level(): Collapse to Class Level
create_wide_format(): Create Wide Format Dataset
pivot_wide_to_long(): Convert Wide Format to Long Format
create_resistance_profile(): Create Resistance Profile
compute_polymicrobial_weight(): Compute Polymicrobial Weights

Resistance profiles

Marginal resistance, coresistance, and profile computation

compute_R_kd_fatal(): Compute Fatal Prevalence of Resistance (R_kd)
compute_base_yll_from_dl(): Compute Base YLL Block from a Scalar D_L (Steps 1-3)
compute_fatal_resistance_prevalence(): Compute Per-Profile Fatal Prevalence of Resistance R_Kdelta* (Eq. 13)
compute_fraction_associated(): Compute Associated-Burden Fractions per Resistance Profile
compute_hospital_daly(): Compute Hospital-Level DALY Breakdown
compute_marginal_resistance(): Compute Marginal Resistance per Pathogen and Antibiotic Class
compute_p0(): Compute Baseline Mortality Rate Among Fully Susceptible Patients (p0)
compute_paf_los(): Compute LOS Population Attributable Fraction per Resistance Profile
compute_paf_rr_mortality(): Compute Mortality Population Attributable Fraction per Resistance Profile
compute_pairwise_coresistance(): Compute Pairwise Co-resistance Matrices per Pathogen
compute_patient_los(): Compute Patient-Level Post-Infection LOS
compute_polymicrobial_weight(): Compute Polymicrobial Weights
compute_processing_statistics(): Compute Processing Statistics
compute_resistance_profiles(): Compute Resistance Profile Probabilities per Pathogen
compute_yld_associated(): Compute YLDs Associated with Resistance
compute_yld_attributable(): Compute YLDs Attributable to Resistance
compute_yll_associated(): Compute YLL Associated with AMR (Patient-Level, Facility-Direct)
compute_yll_attributable(): Compute YLL Attributable to AMR
select_resistance_class(): Select Resistance Class
prioritize_resistance(): Prioritize Resistance

Burden estimation (YLL/YLD)

GBD-methodology burden calculations

calculate_CR_L(): Calculate the CFR adjustment factor (CR_L)
calculate_P_Lk(): Calculate Fatal Pathogen Distribution (P_{LK})
calculate_P_Lk_fatal(): Calculate fatal pathogen distribution (P_{Lk})
calculate_P_Lk_prime(): Calculate non-fatal pathogen distribution (P'_{Lk})
calculate_Rkd_prime(): Calculate non-fatal prevalence of resistance (R'_{k,d})
calculate_YLD(): Calculate YLD per pathogen
calculate_cfr_lk(): Calculate case fatality ratio by syndrome and pathogen (CFR_{Lk})
calculate_deaths_by_cause(): Calculate Deaths by Underlying Cause (D_J)
calculate_distance_matrix(): Calculate Distance Matrix Between Locations
calculate_incidence_L(): Calculate syndrome incidence from deaths, CFR, and CR_L (formula-based)
calculate_infection_fraction(): Calculate Infection Fraction of Deaths by Cause (S_J)
calculate_los(): Calculate Length of Stay
calculate_spatial_autocorrelation(): Calculate Spatial Autocorrelation (Moran's I)
calculate_spatial_metrics(): Calculate AMR Metrics by Geographic Unit
calculate_syndrome_deaths(): Calculate Deaths by Infectious Syndrome (D_L)
calculate_syndrome_fraction(): Calculate Infectious Syndrome Fraction (M_LJ)
fit_distributions(): Fit Multiple Distributions
fit_los_rr_distribution(): Estimate Per-Class LOS Relative Risk via Parametric Distribution Fitting
fit_los_rr_nima(): Estimate Per-Profile LOS Relative Risk via Distribution Fitting (Nima Procedure)
fit_los_rr_poisson(): Estimate Per-Class LOS Relative Risk via Quasi-Poisson Regression
fit_mortality_rr_logistic(): Estimate Per-Class Mortality Odds Ratio via Mixed-Effects Logistic Regression
assign_rr_to_profiles(): Assign Per-Class LOS RR to Resistance Profiles (Max Rule)
convert_or_to_rr(): Convert Odds Ratios to Relative Risks Using Baseline Mortality (p0)
count_incident_cases(): Count incident cases by syndrome from facility data
filter_profiles_to_rr_classes(): Filter Profiles to Classes with Actual RR Estimates
get_top_pathogens(): Identify top N pathogens by occurrence
load_rr_reference(): Load RR (Relative Risk) Reference Data
lookup_rr(): Lookup Relative Risk Values
add_rr_mappings(): Add RR Pathogen and Drug Mappings
map_class_to_rr(): Map Antibiotic Class to RR Drug Category
map_to_rr_pathogen(): Map Organism to RR Pathogen Category

LOS modeling

Length-of-stay distribution fitting and comparison

safe_fit(): Safely Fit a Distribution
fit_distributions(): Fit Multiple Distributions
compare_distribution_aic(): Compare Distribution Fits by AIC
summarise_distribution(): Summarise a Fitted Distribution
plot_los_distributions(): Plot LOS Distribution with Fitted Overlays
prepare_los_data(): Prepare LOS Dataset
get_los_by_resistance(): Extract LOS Vectors by Resistance Status

Burden plots

GBD-style and hospital-level burden visualizations

compute_hospital_daly(): Compute Hospital-Level DALY Breakdown
plot_gbd_fig4(): GBD Figure 4 – Deaths by Organism Group (Overlapping Bars)
plot_gbd_fig6(): GBD Figure 6 – Attributable Deaths Heatmap (Pathogen x Drug Class)
plot_burden_comparison(): Burden Comparison Bar Plot
plot_burden_heatmap(): Burden Heatmap Across Hospitals
plot_daly_lollipop(): DALY Lollipop Plot
plot_resistance_fraction(): Resistance Fraction Stacked Bar

Visualization

Generic AMR plotting utilities

amr_theme(): AMR Theme for ggplot2
get_amr_palette(): Get Color Palette
plot_bar(): Generic Bar Plot
plot_grouped_bar(): Grouped (Dodged) Bar Plot
plot_stacked_bar(): Stacked Bar Plot
plot_heatmap(): Heatmap
plot_histogram(): Histogram
plot_line(): Line Chart
plot_proportion(): Proportion Bar Plot
plot_resistance_heatmap(): Resistance Pattern Heatmap

Spatial analysis

Spatial metrics and mapping

create_spatial_object(): Create Spatial Object from AMR Data
create_choropleth_map(): Create Choropleth Map
create_interactive_map(): Create Interactive Leaflet Map
calculate_spatial_autocorrelation(): Calculate Spatial Autocorrelation (Moran's I)
calculate_spatial_metrics(): Calculate AMR Metrics by Geographic Unit
calculate_distance_matrix(): Calculate Distance Matrix Between Locations
detect_hotspots(): Detect Spatial Hotspots (Getis-Ord Gi*)

Validation and reporting

Data quality checks and reports

validate_data_quality(): Validate Data Quality
validate_required_fields(): Validate Required Fields
check_logical_consistency(): Check Logical Consistency
summarize_column_mapping(): Summarize Column Mapping
summarize_data_quality(): Summarize Data Quality
summarize_raw_data(): Summarize Raw Data
summarize_transformations(): Summarize Data Transformations
generate_preprocessing_report(): Generate Preprocessing Report
export_report(): Export Report to File

Utilities

Helper functions

round_to_sum(): Largest-Remainder Rounding
shorten_drug_class(): Shorten Antibiotic Class Names
default_column_mappings: Default Column Name Mappings
get_age_bins(): Standard Age Bins (GBD Compatible)
get_antimicrobial_categories(): Get Antimicrobial Categories for MDR/XDR Classification
get_beta_lactam_hierarchy(): Beta-Lactam Class Hierarchy
get_contaminant_list(): Get Contaminant List from Reference File
get_magiorakos_thresholds(): Get Magiorakos MDR/XDR Thresholds
is_contaminant(): Check if Organism is a Contaminant
groom_optional_columns(): Groom Optional Columns
remove_duplicate_rows(): Remove Duplicate Rows
extract_genus(): Extract Genus from Organism Name
extract_species(): Extract Species from Organism Name

Package index