Function reference • RAMSES

Ramses object model S4 classes and methods handling `Ramses` objects
`RamsesObject-class`	An S4 virtual class for Ramses objects
`Patient()` `Patient.DBIConnection()` `Patient.RamsesObject()`	An S4 class to represent patients
`Encounter()`	An S4 class to represent inpatient encounters
`MedicationRequest()`	An S4 class to represent a drug-dose medication request
`TherapyEpisode()` `TherapyEpisode.DBIConnection()` `TherapyEpisode.MedicationRequest()`	An S4 class to represent episodes of antimicrobial therapy
`longitudinal_table()`	Get the longitudinal_table
`parenteral_changes()`	Get parenteral antimicrobial therapy sequences
`clinical_feature_interval()`	Clinical feature: number of clinical observations falling in an interval
`clinical_feature_last()`	Clinical feature: latest clinical observation value
`clinical_feature_mean()`	Clinical feature: running mean value of a clinical observation
`clinical_feature_ols_trend()`	Clinical feature: temporal trend of clinical observations
`collect()`	Retrieve the database record of a Ramses object
`compute()`	Compute the database records of a Ramses object
`therapy_timeline()`	Display an HTML antimicrobial therapy timeline
Transform and validate data Functions to enrich and validate data before loading into the warehouse.
`map_ICD10_CCS()` `map_ICD10_CCSR()`	Map ICD-10 codes to the Clinical Classifications Software (CCS)
`map_charlson_comorbidities()`	Map ICD-10 to Charlson comorbidities and weights
`map_infections_abx_indications()`	Map ICD-10 to common infections and antibiotic indications
`compute_DDDs()`	Compute Defined Daily Doses (DDDs)
`get_ATC_name()`	Look up ATC code name on the WHO website
`validate_inpatient_diagnoses()`	Validate inpatient diagnosis records
`validate_inpatient_episodes()`	Validate inpatient episode and ward movement records
`validate_prescriptions()`	Validate medication prescription records
`validate_administrations()`	Validate medication administration records
`validate_investigations()`	Validate records of observations & investigations
`validate_microbiology()`	Validate microbial isolates & susceptibility records
Load & link data Load records into the warehouse and create secondary information.
`load_inpatient_diagnoses()`	Load inpatient diagnosis records into the warehouse
`load_inpatient_episodes()`	Load episodes of care records into the warehouse
`load_inpatient_investigations()`	Load observations & investigations into the warehouse
`load_inpatient_microbiology()`	Load microbiology cultures and susceptibilities into the warehouse
`load_medications()`	Load drug prescription records into the warehouse
`transitive_closure_control()`	Set parameters for building combination therapy identifiers and therapy episode identifiers
Simulated sets of electronic health records
`patients`	Simulated patients
`inpatient_episodes`	Simulated episodes of inpatient care
`inpatient_wards`	Simulated hospital ward movements
`inpatient_diagnoses`	Simulated inpatient clinical diagnoses
`drug_prescriptions`	Simulated antimicrobial drug prescriptions
`drug_administrations`	Simulated antimicrobial drug administrations
`inpatient_microbiology`	Simulated microbial culture and susceptibility results
`inpatient_investigations`	Simulated clinical investigation results
Reference datasets Metadata provided with `Ramses`
`antibiotic_icd_indications`	Common infections and indications for antimicrobial therapy
`ccs`	Clinical Classifications Software (CCS): map to 4-character ICD codes
`ccsr`	Clinical Classifications Software Refined (CCSR): map to 4-character ICD codes
`download_icd10cm()`	Download the ICD-10-CM reference file by the US National Center for Health Statistics
`import_icd()`	Import the International Classification of Diseases from an archive
`reference_aware`	English Adaptation of the WHO AWaRe Index
`reference_drug_frequency`	Prescription frequency abbreviations
`reference_loinc`	LOINC codes for clinical investigations and observations
`reference_specimen_type`	Laboratory specimen type reference table (SNOMED CT concepts)
Database administration Functions to set up and manage the `Ramses` database
`connect_local_database()`	Connect to (or create) a local DuckDB database
`create_mock_database()`	Create a mock database for training/demonstration purposes
`bridge_spell_therapy_overlap()`	Create database bridge tables
`bridge_tables()` `bridge_episode_prescription_overlap()` `bridge_episode_prescription_initiation()` `bridge_encounter_therapy_overlap()`	Create database bridge tables
`create_therapy_episodes()`	Re-create therapy episodes and therapy combinations
Index All functions in alphabetical order
`Encounter()`	An S4 class to represent inpatient encounters
`MedicationRequest()`	An S4 class to represent a drug-dose medication request
`Patient()` `Patient.DBIConnection()` `Patient.RamsesObject()`	An S4 class to represent patients
`RamsesObject-class`	An S4 virtual class for Ramses objects
`TherapyEpisode()` `TherapyEpisode.DBIConnection()` `TherapyEpisode.MedicationRequest()`	An S4 class to represent episodes of antimicrobial therapy
`antibiotic_icd_indications`	Common infections and indications for antimicrobial therapy
`bridge_spell_therapy_overlap()`	Create database bridge tables
`bridge_tables()` `bridge_episode_prescription_overlap()` `bridge_episode_prescription_initiation()` `bridge_encounter_therapy_overlap()`	Create database bridge tables
`ccs`	Clinical Classifications Software (CCS): map to 4-character ICD codes
`ccsr`	Clinical Classifications Software Refined (CCSR): map to 4-character ICD codes
`clinical_feature_interval()`	Clinical feature: number of clinical observations falling in an interval
`clinical_feature_last()`	Clinical feature: latest clinical observation value
`clinical_feature_mean()`	Clinical feature: running mean value of a clinical observation
`clinical_feature_ols_trend()`	Clinical feature: temporal trend of clinical observations
`collect()`	Retrieve the database record of a Ramses object
`compute()`	Compute the database records of a Ramses object
`compute_DDDs()`	Compute Defined Daily Doses (DDDs)
`connect_local_database()`	Connect to (or create) a local DuckDB database
`create_mock_database()`	Create a mock database for training/demonstration purposes
`create_therapy_episodes()`	Re-create therapy episodes and therapy combinations
`download_icd10cm()`	Download the ICD-10-CM reference file by the US National Center for Health Statistics
`drug_administrations`	Simulated antimicrobial drug administrations
`drug_prescriptions`	Simulated antimicrobial drug prescriptions
`get_ATC_name()`	Look up ATC code name on the WHO website
`import_icd()`	Import the International Classification of Diseases from an archive
`inpatient_diagnoses`	Simulated inpatient clinical diagnoses
`inpatient_episodes`	Simulated episodes of inpatient care
`inpatient_investigations`	Simulated clinical investigation results
`inpatient_microbiology`	Simulated microbial culture and susceptibility results
`inpatient_wards`	Simulated hospital ward movements
`load_inpatient_diagnoses()`	Load inpatient diagnosis records into the warehouse
`load_inpatient_episodes()`	Load episodes of care records into the warehouse
`load_inpatient_investigations()`	Load observations & investigations into the warehouse
`load_inpatient_microbiology()`	Load microbiology cultures and susceptibilities into the warehouse
`load_medications()`	Load drug prescription records into the warehouse
`longitudinal_table()`	Get the longitudinal_table
`map_ICD10_CCS()` `map_ICD10_CCSR()`	Map ICD-10 codes to the Clinical Classifications Software (CCS)
`map_charlson_comorbidities()`	Map ICD-10 to Charlson comorbidities and weights
`map_infections_abx_indications()`	Map ICD-10 to common infections and antibiotic indications
`parenteral_changes()`	Get parenteral antimicrobial therapy sequences
`patients`	Simulated patients
`reference_aware`	English Adaptation of the WHO AWaRe Index
`reference_drug_frequency`	Prescription frequency abbreviations
`reference_loinc`	LOINC codes for clinical investigations and observations
`reference_specimen_type`	Laboratory specimen type reference table (SNOMED CT concepts)
`show(<RamsesObject>)` `show(<Encounter>)` `show(<TherapyEpisode>)` `show(<MedicationRequest>)`	Show a Ramses object
`therapy_table()`	Get the therapy table (DEPRECATED)
`therapy_timeline()`	Display an HTML antimicrobial therapy timeline
`transitive_closure_control()`	Set parameters for building combination therapy identifiers and therapy episode identifiers
`validate_administrations()`	Validate medication administration records
`validate_inpatient_diagnoses()`	Validate inpatient diagnosis records
`validate_inpatient_episodes()`	Validate inpatient episode and ward movement records
`validate_investigations()`	Validate records of observations & investigations
`validate_microbiology()`	Validate microbial isolates & susceptibility records
`validate_prescriptions()`	Validate medication prescription records

Reference

Ramses object model

Transform and validate data

Load & link data

Simulated sets of electronic health records

Reference datasets

Database administration

Index