Package {OmopIndices}

Type: Package
Title: Patient-Level Indices from the OMOP Common Data Model
Version: 0.1.0
Maintainer: Martí Català <marti.catalasabate@ndorms.ox.ac.uk>
Description: Provides tools to derive standardised, reproducible patient-level indices and covariates from Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) databases. Functions calculate comorbidity and frailty scores, including the Charlson Comorbidity Index, Electronic Frailty Index, and Hospital Frailty Risk Score, as well as body mass index, polypharmacy, ethnicity, location, and socioeconomic status measures.
License: Apache License (≥ 2)
Encoding: UTF-8
Suggests: CDMConnector, CodelistGenerator, CohortConstructor, DBI, duckdb, gt, here, htmltools, knitr, odbc, omock, PhenotypeR, rmarkdown, RPostgres, testthat, visOmopResults
URL: https://OHDSI.github.io/OmopIndices/
BugReports: https://github.com/OHDSI/OmopIndices/issues
Imports: cli, clock, dplyr, omopgenerics (≥ 1.4.0), PatientProfiles, purrr, rlang
Depends: R (≥ 4.1.0)
Config/roxygen2/version: 8.0.0
Config/Needs/website: rmarkdown
NeedsCompilation: no
Packaged: 2026-09-09 17:30:20 UTC; martics
Author: Martí Català ORCID iD [aut, cre], Marta Alcalde-Herraiz ORCID iD [aut], Maria T Sanchez-Santos ORCID iD [aut]
Repository: CRAN
Date/Publication: 2026-09-17 13:20:27 UTC

OmopIndices: Patient-Level Indices from the OMOP Common Data Model

Description

logo

Provides tools to derive standardised, reproducible patient-level indices and covariates from Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) databases. Functions calculate comorbidity and frailty scores, including the Charlson Comorbidity Index, Electronic Frailty Index, and Hospital Frailty Risk Score, as well as body mass index, polypharmacy, ethnicity, location, and socioeconomic status measures.

Author(s)

Maintainer: Martí Català marti.catalasabate@ndorms.ox.ac.uk (ORCID)

Authors:

See Also

Useful links:

Add Body Mass Index measurement

Description

Add Body Mass Index measurement

Usage

addBMI(
  x,
  conceptSet = NULL,
  indexDate = "cohort_start_date",
  window = c(-Inf, 0),
  order = "last",
  nameStyle = "bmi",
  categories = NULL,
  inObservation = TRUE,
  name = tableName(x)
)

Arguments

x

A cdm_table containing a person identifier column named person_id or subject_id.

conceptSet

A named concept set supplied as a codelist, codelist_with_details, concept_set_expression, or named list of concept IDs. It must contain obesity, bmi as concepts. By default, internal codelists are used.

indexDate

A character string naming the Date column in x that defines the index date.

window

A numeric vector of length two, c(min, max), defining the window for BMI in days relative to indexDate. Use -Inf or Inf for an unbounded lower or upper limit.

order

A character string specifying how to select among multiple BMI measurements within the window: last (latest), first (earliest), max (highest), or min (lowest).

nameStyle

A character string specifying the name of the new column.

categories

A named list of numeric vectors, each containing the lower and upper bounds of a BMI interval. An additional categorical column is added, and missing BMI values are labelled missing.

inObservation

Logical; whether to restrict records to the person's observation period.

name

A character string specifying the name of the output table. If NULL, a temporary table is created.

Value

The table x with a new column containing the selected BMI value.

Examples


library(omock)
library(duckdb)
library(OmopIndices)
library(dplyr)
library(CohortConstructor)

cdm <- mockCdmFromDataset(datasetName = "GiBleed", source = "duckdb")
cdm$cohort <- conceptCohort(
  cdm = cdm,
  conceptSet = list(sinusitis = c(257012L, 4283893L, 4294548L, 40481087L)),
  name = "cohort"
)

cdm$cohort |>
  addBMI(window = c(-365, 0), order = "last") |>
  select(subject_id, cohort_start_date, bmi) |>
  glimpse()

Add Charlson Comorbidity Index (CCI) value based on Charlson et al. (1987) (doi:10.1016/0021-9681(87)90171-8) and Charlson et al. (1994) (doi:10.1016/0895-4356(94)90129-5) (age-adjusted) version.

Description

Add Charlson Comorbidity Index (CCI) value based on Charlson et al. (1987) (doi:10.1016/0021-9681(87)90171-8) and Charlson et al. (1994) (doi:10.1016/0895-4356(94)90129-5) (age-adjusted) version.

Usage

addCharlsonIndex(
  x,
  indexDate = "cohort_start_date",
  ageAdjusted = TRUE,
  conceptSet = getIndexCodelist("charlson"),
  nameStyle = "charlson",
  categories = NULL,
  name = tableName(x)
)

Arguments

x

A cdm_table containing a person identifier column named person_id or subject_id.

indexDate

A character string naming the Date column in x that defines the index date.

ageAdjusted

Logical; whether to include age adjustment in the Charlson Comorbidity Index.

conceptSet

A named concept set supplied as a codelist, codelist_with_details, concept_set_expression, or named list of concept IDs. It must contain myocardial_infarction, congestive_heart_failure, peripheral_vascular_disease, cerebrovascular_disease, dementia, chronic_pulmonary_disease, connective_tissue_disease, peptic_ulcer_disease, mild_liver_disease, diabetes_without_complication, hemiplegia, severe_chronic_kidney_disease, diabetes_with_complication, any_malignancy, moderate_or_severe_liver_disease, metastatic_solid_tumor, aids as concepts. By default, internal codelists are used.

nameStyle

A character string specifying the name of the new column.

categories

A named list of numeric vectors, each containing the lower and upper bounds of a score interval. An additional column with the suffix ⁠_categories⁠ is added. Intervals are evaluated in the order supplied, and missing scores are labelled missing.

name

A character string specifying the name of the output table. If NULL, a temporary table is created.

Value

The table x with a new column containing the Charlson Comorbidity Index value.

Examples


library(omock)
library(duckdb)
library(OmopIndices)
library(dplyr)
library(CohortConstructor)

cdm <- mockCdmFromDataset(datasetName = "GiBleed", source = "duckdb")
cdm$cohort <- conceptCohort(
  cdm = cdm,
  conceptSet = list(sinusitis = c(257012L, 4283893L, 4294548L, 40481087L)),
  name = "cohort"
)

# Using the internal concept sets:
cdm$cohort |>
  addCharlsonIndex(ageAdjusted = TRUE) |>
  select(subject_id, cohort_start_date, charlson) |>
  glimpse()

# This example uses custom concept sets.
customConceptSet <- list(
  myocardial_infarction = 329847L,
  congestive_heart_failure = 319835L,
  peripheral_vascular_disease = 321052L,
  cerebrovascular_disease = 381591L,
  dementia = 4182210L,
  chronic_pulmonary_disease = 255573L,
  connective_tissue_disease = 4134537L,
  peptic_ulcer_disease = 4027663L,
  mild_liver_disease = 194984L,
  moderate_or_severe_liver_disease = 4212540L,
  diabetes_without_complication = 201820L,
  diabetes_with_complication = 42538715L,
  hemiplegia = 374022L,
  severe_chronic_kidney_disease = 46271022L,
  any_malignancy = 4180914L,
  metastatic_solid_tumor = 432851L,
  aids = 4267414L
)

cdm$cohort |>
  addCharlsonIndex(
    conceptSet = customConceptSet,
    nameStyle = "charlson_custom"
  ) |>
  select(subject_id, cohort_start_date, charlson_custom) |>
  glimpse()

Add Electronic Frailty Index (eFI) value based on Clegg et al. (2016) (doi:10.1093/ageing/afw039)

Description

Add Electronic Frailty Index (eFI) value based on Clegg et al. (2016) (doi:10.1093/ageing/afw039)

Usage

addElectronicFrailtyIndex(
  x,
  indexDate = "cohort_start_date",
  conceptSet = getIndexCodelist("electronic_frailty_index"),
  categories = list(fit = c(0, 0.12), mild = c(0.12, 0.24), moderate = c(0.24, 0.36),
    severe = c(0.36, 1)),
  nameStyle = "efi",
  name = tableName(x)
)

Arguments

x

A cdm_table containing a person identifier column named person_id or subject_id.

indexDate

A character string naming the Date column in x that defines the index date.

conceptSet

A named concept set supplied as a codelist, codelist_with_details, concept_set_expression, or named list of concept IDs. It must contain activity_limitation, anemia, arthritis, atrial_fibrillation, cerebrovascular_disease, chronic_kidney_disease, diabetes, dizziness, dyspnea, falls, foot_problem, fragility_fracture, hearing_impairment, heart_failure, heart_valve_disorder, housebound, hypertension, hypotension_syncope, ischemic_heart_disease, memory_cognitive_disorder, mobility_problems, osteoporosis, parkinsonism_tremor, peptic_ulcer, peripheral_vascular_disease, care_requirement, respiratory_disease, skin_ulcer, sleep_disturbance, social_vulnerability, thyroid_disease, urinary_incontinence, urinary_system_disease, visual_impairment, weight_loss_anorexia as concepts. By default, internal codelists are used.

categories

A named list of numeric vectors, each containing the lower and upper bounds of a score interval. An additional column with the suffix ⁠_categories⁠ is added. Intervals are evaluated in the order supplied, and missing scores are labelled missing.

nameStyle

A character string specifying the name of the new column.

name

A character string specifying the name of the output table. If NULL, a temporary table is created.

Value

The table x with a new column containing the Electronic Frailty Index value.

Examples


library(omock)
library(duckdb)
library(OmopIndices)
library(dplyr)
library(CohortConstructor)

cdm <- mockCdmFromDataset(datasetName = "GiBleed", source = "duckdb")
cdm$cohort <- conceptCohort(
  cdm = cdm,
  conceptSet = list(sinusitis = c(257012L, 4283893L, 4294548L, 40481087L)),
  name = "cohort"
)

# Using the internal concept sets:
cdm$cohort |>
  addElectronicFrailtyIndex() |>
  select(subject_id, cohort_start_date, efi, efi_categories) |>
  glimpse()

# This example uses custom concept sets.
customConceptSet <- list(
  activity_limitation = 763723L,
  anemia = 439777L,
  arthritis = 4291025L,
  atrial_fibrillation = 313217L,
  chronic_kidney_disease = 46271022L,
  cerebrovascular_disease = 381591L,
  dizziness = 4223938L,
  dyspnea = 312437L,
  falls = 4059015L,
  foot_problem = 4101512L,
  fragility_fracture = 3170964L,
  hearing_impairment = 4234647L,
  heart_failure = 316139L,
  heart_valve_disorder = 4281749L,
  housebound = 4052962L,
  hypertension = 319826L,
  hypotension_syncope = 316447L,
  ischemic_heart_disease = 4185932L,
  memory_cognitive_disorder = 4304008L,
  mobility_problems = 4053076L,
  osteoporosis = 80502L,
  parkinsonism_tremor = 4140090L,
  peptic_ulcer = 4027663L,
  peripheral_vascular_disease = 321052L,
  care_requirement = 3661927L,
  respiratory_disease = 317009L,
  skin_ulcer = 4262920L,
  sleep_disturbance = 435524L,
  social_vulnerability = 4026161L,
  diabetes = 201820L,
  thyroid_disease = 4017052L,
  urinary_incontinence = 197672L,
  urinary_system_disease = 75865L,
  visual_impairment = 4265433L,
  weight_loss_anorexia = 436675L
)

cdm$cohort |>
  addElectronicFrailtyIndex(
    conceptSet = customConceptSet,
    nameStyle = "efi_custom"
  ) |>
  select(subject_id, cohort_start_date, efi_custom, efi_custom_categories) |>
  glimpse()

Add the ethnicity of a person to a table

Description

Add the ethnicity of a person to a table

Usage

addEthnicity(
  x,
  from = c("ethnicity_concept_id", "ethnicity_source_concept_id", "race_concept_id",
    "race_source_concept_id"),
  nameStyle = "ethnicity",
  name = tableName(x),
  missingEthnicityValue = "Missing"
)

Arguments

x

A cdm_table containing a person identifier column named person_id or subject_id.

from

A character vector specifying the ethnicity sources to try, in priority order. The first source that provides a value is used. Available options are:

  • ethnicity_concept_id to assign ethnicity using the concept_name associated with the ethnicity_concept_id column of the person table.

  • ethnicity_source_concept_id to assign ethnicity using the concept_name associated with the ethnicity_source_concept_id column of the person table.

  • race_concept_id to assign ethnicity using the concept_name associated with the race_concept_id column of the person table.

  • race_source_concept_id to assign ethnicity using the concept_name associated with the race_source_concept_id column of the person table.

  • ethnicity_source_value to assign ethnicity using the value of the column ethnicity_source_value in the person table.

  • race_source_value to assign ethnicity using the value of the column race_source_value in the person table.

  • nhs-categories to assign ethnicity using NHS Ethnic Category.

  • nhs-groups to assign ethnicity using broad groups of NHS Ethnic Category as described in doi:10.1038/s41597-024-02958-1.

nameStyle

A character string specifying the name of the new column.

name

A character string specifying the name of the output table. If NULL, a temporary table is created.

missingEthnicityValue

A character string used to replace missing ethnicity values.

Value

The table x with a new column containing the patient's ethnicity.

Examples


library(omock)
library(duckdb)
library(OmopIndices)
library(dplyr)
library(CohortConstructor)

cdm <- mockCdmFromDataset(datasetName = "GiBleed", source = "duckdb")
cdm$cohort <- conceptCohort(
  cdm = cdm,
  conceptSet = list(sinusitis = c(257012L, 4283893L, 4294548L, 40481087L)),
  name = "cohort"
)

cdm$cohort |>
  addEthnicity() |>
  select(subject_id, cohort_start_date, ethnicity) |>
  glimpse()

Add the hospital frailty risk score as defined in Gilbert et al. (2018) (doi:10.1016/S0140-6736(18)30668-8)

Description

Add the hospital frailty risk score as defined in Gilbert et al. (2018) (doi:10.1016/S0140-6736(18)30668-8)

Usage

addHospitalFrailtyRiskScore(
  x,
  indexDate = "cohort_start_date",
  conceptSet = getIndexCodelist("hospital_frailty_risk_score"),
  categories = list(low = c(0, 5), intermediate = c(5, 15), high = c(15, Inf)),
  nameStyle = "hfrs",
  name = tableName(x)
)

Arguments

x

A cdm_table containing a person identifier column named person_id or subject_id.

indexDate

A character string naming the Date column in x that defines the index date.

conceptSet

A named concept set supplied as a codelist, codelist_with_details, concept_set_expression, or named list of concept IDs. It must contain abnormal_results_of_function_studies, abnormalities_of_gait_and_mobility, abnormalities_of_heart_beat, acute_renal_failure, agent_resistant_to_penicillin_and_related_antibiotics, alzheimers_disease, artificial_opening_status, blindness_and_low_vision, calculus_of_kidney_and_ureter, care_involving_use_of_rehabilitation_procedures, carrier_of_infectious_disease, cellulitis, cerebral_infarction, cerebral_ischaemic_attacks, chronic_renal_failure, cognitive_functions_and_awareness, convulsions_not_elsewhere_classified, decubitus_ulcer, deficiency_of_other_b_group_vitamins, degenerative_diseases_of_nervous_system, delirium, dementia_in_alzheimers_disease, dependence_on_enabling_machines_and_devices, depressive_episode, diarrhoea_and_gastroenteritis, disorders_of_kidney_and_ureter, disorders_of_mineral_metabolism, duodenal_ulcer, dysphagia, epilepsy, exposure_to_unspecified_factor, fall, fall_involving_bed, fall_on_and_from_stairs_and_steps, fever_of_unknown_origin, fluid_electrolyte_and_acid_base_balance, fracture_of_femur, fracture_of_lumbar_spine_and_pelvis, fracture_of_ribs_sternum_and_thoracic_spine, fracture_of_shoulder_and_upper_arm, gangrene_not_elsewhere_classified, general_sensations_and_perceptions, hemiplegia, hypotension, infections_of_skin, intracranial_injury, mental_and_behavioural_disorders_due_to_use_of_alcohol, nausea_and_vomiting, nervous_and_musculoskeletal_systems_r_29_6_tendency_to_fall, nosocomial_condition, open_wound_of_forearm, open_wound_of_head, osteoporosis_with_pathological_fracture, osteoporosis_without_pathological_fracture, other_abnormal_findings_of_blood_chemistry, other_anaemias, other_and_unspecified_injuries_of_head, other_arthrosis, other_bacterial_agents, other_bacterial_intestinal_infections, other_cerebrovascular_diseases, other_diseases_of_digestive_system, other_disorders_of_pancreatic_internal_secretion, other_disorders_of_urinary_system, other_fall_on_same_level, other_functional_intestinal_disorders, other_hearing_loss, other_joint_disorders_not_elsewhere_classified, other_medical_procedures, other_noninfective_gastroenteritis_and_colitis, other_septicaemia, other_soft_tissue_disorders_not_elsewhere_classified, parkinsons_disease, personal_history_of_other_diseases_and_conditions, personal_history_of_risk_factors, pneumonia_organism_unspecified, pneumonitis_due_to_solids_and_liquids, polyarthrosis, problems_related_to_care_provider_dependency, problems_related_to_life_management_difficulty, problems_related_to_medical_facilities_and_other_health_care, problems_related_to_social_environment, prosthetic_devices_implants, respiratory_failure_not_elsewhere_classified, retention_of_urine, scoliosis, senility, sequelae_of_cerebrovascular_disease, somnolence_stupor_and_coma, speech_disturbances_not_elsewhere_classified, spinal_stenosis_secondary_code_only, streptococcus_and_staphylococcus, superficial_injury_of_head, superficial_injury_of_lower_leg, symptoms_and_signs_concerning_food_and_fluid_intake, symptoms_and_signs_involving_emotional_state, syncope_and_collapse, thyrotoxicosis_hyperthyroidism, ulcer_of_lower_limb_not_elsewhere_classified, unknown_and_unspecified_causes_of_morbidity, unspecified_acute_lower_respiratory_infection, unspecified_dementia, unspecified_fall, unspecified_haematuria, unspecified_renal_failure, unspecified_urinary_incontinence, vascular_dementia, vitamin_d_deficiency, volume_depletion as concepts. By default, internal codelists are used.

categories

A named list of numeric vectors, each containing the lower and upper bounds of a score interval. An additional column with the suffix ⁠_categories⁠ is added. Intervals are evaluated in the order supplied, and missing scores are labelled missing.

nameStyle

A character string specifying the name of the new column.

name

A character string specifying the name of the output table. If NULL, a temporary table is created.

Value

The table x with a new column containing the Hospital Frailty Risk Score value.

Examples


library(omock)
library(duckdb)
library(OmopIndices)
library(dplyr)
library(CohortConstructor)

cdm <- mockCdmFromDataset(datasetName = "GiBleed", source = "duckdb")
cdm$cohort <- conceptCohort(
  cdm = cdm,
  conceptSet = list(sinusitis = c(257012L, 4283893L, 4294548L, 40481087L)),
  name = "cohort"
)

cdm$cohort |>
  addHospitalFrailtyRiskScore() |>
  select(subject_id, cohort_start_date, hfrs, hfrs_categories) |>
  glimpse()

Add socioeconomic status as a column to a table using the Index of Multiple Deprivation

Description

Add socioeconomic status as a column to a table using the Index of Multiple Deprivation

Usage

addIndexOfMultipleDeprivation(
  x,
  indexDate = "cohort_start_date",
  window = c(-Inf, Inf),
  order = "last",
  nameStyle = "socio_economic_status",
  name = tableName(x),
  missingSocioEconomicStatusValue = "Missing"
)

Arguments

x

A cdm_table containing a person identifier column named person_id or subject_id.

indexDate

A character string naming the Date column in x that defines the index date.

window

A numeric vector of length two, c(min, max), defining the window for socio_economic_status in days relative to indexDate. Use -Inf or Inf for an unbounded lower or upper limit.

order

A character string specifying which record to select when multiple records are found: first or last.

nameStyle

A character string specifying the name of the new column.

name

A character string specifying the name of the output table. If NULL, a temporary table is created.

missingSocioEconomicStatusValue

A character string used to replace missing socioeconomic status values.

Value

The table x with a new column containing the Index of Multiple Deprivation value.

Examples


library(omock)
library(duckdb)
library(OmopIndices)
library(dplyr)
library(CohortConstructor)

cdm <- mockCdmFromDataset(datasetName = "GiBleed", source = "duckdb")
cdm$cohort <- conceptCohort(
  cdm = cdm,
  conceptSet = list(sinusitis = c(257012L, 4283893L, 4294548L, 40481087L)),
  name = "cohort"
)

cdm$cohort |>
  addIndexOfMultipleDeprivation() |>
  select(subject_id, cohort_start_date, socio_economic_status) |>
  glimpse()

Add the location to a table

Description

Add the location to a table

Usage

addLocation(
  x,
  from = c("location_id", "care_site_id"),
  nameStyle = "location",
  name = tableName(x),
  locationSource = "location_source_value",
  missingLocationValue = "Missing"
)

Arguments

x

A cdm_table containing a person identifier column named person_id or subject_id.

from

A character vector specifying the location sources to try, in priority order. The first source that provides a location is used. Supported values are location_id and care_site_id.

nameStyle

A character string specifying the name of the new column.

name

A character string specifying the name of the output table. If NULL, a temporary table is created.

locationSource

A character string specifying the column to retrieve from the location table. Supported values include location_source_value, city, state, zip, county, country_concept_id, and country_source_value.

missingLocationValue

A character string used to replace missing location values.

Value

The table x with a new column containing the patient's location.

Examples


library(omock)
library(duckdb)
library(OmopIndices)
library(dplyr)
library(CohortConstructor)

cdm <- mockCdmFromDataset(datasetName = "GiBleed", source = "duckdb")
cdm$cohort <- conceptCohort(
  cdm = cdm,
  conceptSet = list(sinusitis = c(257012L, 4283893L, 4294548L, 40481087L)),
  name = "cohort"
)

cdm$cohort |>
  addLocation() |>
  select(subject_id, cohort_start_date, location) |>
  glimpse()

Add the maximum number of ingredients to which an individual is simultaneously exposed within a specified window

Description

Add the maximum number of ingredients to which an individual is simultaneously exposed within a specified window

Usage

addPolypharmacyCount(
  x,
  indexDate = "cohort_start_date",
  window = c(0, 0),
  overlap = TRUE,
  nameStyle = "polypharmacy_count",
  name = tableName(x)
)

Arguments

x

A cdm_table containing a person identifier column named person_id or subject_id.

indexDate

A character string naming the Date column in x that defines the index date.

window

A numeric vector of length two, c(min, max), defining the window for polypharmacy in days relative to indexDate. Use -Inf or Inf for an unbounded lower or upper limit.

overlap

Logical; if TRUE, count drug eras that overlap in time. If FALSE, count drug eras that occur within the window without requiring them to overlap one another.

nameStyle

A character string specifying the name of the new column.

name

A character string specifying the name of the output table. If NULL, a temporary table is created.

Value

The table x with a new column containing the maximum number of simultaneous ingredients in the window of interest.

Examples


library(omock)
library(duckdb)
library(OmopIndices)
library(dplyr)
library(CohortConstructor)

cdm <- mockCdmFromDataset(datasetName = "GiBleed", source = "duckdb")
cdm$cohort <- conceptCohort(
  cdm = cdm,
  conceptSet = list(sinusitis = c(257012L, 4283893L, 4294548L, 40481087L)),
  name = "cohort"
)

cdm$cohort |>
  addPolypharmacyCount(window = c(-30, 0)) |>
  select(subject_id, cohort_start_date, polypharmacy_count) |>
  glimpse()

Add socioeconomic status as a column to a table

Description

Add socioeconomic status as a column to a table

Usage

addSocioEconomicStatus(
  x,
  indexDate = "cohort_start_date",
  window = c(-Inf, Inf),
  order = "last",
  from = c("imd", "townsend"),
  nameStyle = "socio_economic_status",
  name = tableName(x),
  missingSocioEconomicStatusValue = "Missing"
)

Arguments

x

A cdm_table containing a person identifier column named person_id or subject_id.

indexDate

A character string naming the Date column in x that defines the index date.

window

A numeric vector of length two, c(min, max), defining the window for socio_economic_status in days relative to indexDate. Use -Inf or Inf for an unbounded lower or upper limit.

order

A character string specifying which record to select when multiple records are found: first or last.

from

A character vector specifying the socioeconomic status sources to try, in priority order. Supported values are imd, for the Index of Multiple Deprivation, and townsend, for the Townsend deprivation index.

nameStyle

A character string specifying the name of the new column.

name

A character string specifying the name of the output table. If NULL, a temporary table is created.

missingSocioEconomicStatusValue

A character string used to replace missing socioeconomic status values.

Value

The table x with a new column containing the patient's socioeconomic status.

Examples


library(omock)
library(duckdb)
library(OmopIndices)
library(dplyr)
library(CohortConstructor)

cdm <- mockCdmFromDataset(datasetName = "GiBleed", source = "duckdb")
cdm$cohort <- conceptCohort(
  cdm = cdm,
  conceptSet = list(sinusitis = c(257012L, 4283893L, 4294548L, 40481087L)),
  name = "cohort"
)

cdm$cohort |>
  addSocioEconomicStatus() |>
  select(subject_id, cohort_start_date, socio_economic_status) |>
  glimpse()

Add socioeconomic status as a column to a table using the Townsend deprivation index

Description

Add socioeconomic status as a column to a table using the Townsend deprivation index

Usage

addTownsend(
  x,
  indexDate = "cohort_start_date",
  window = c(-Inf, Inf),
  order = "last",
  nameStyle = "socio_economic_status",
  name = tableName(x),
  missingSocioEconomicStatusValue = "Missing"
)

Arguments

x

A cdm_table containing a person identifier column named person_id or subject_id.

indexDate

A character string naming the Date column in x that defines the index date.

window

A numeric vector of length two, c(min, max), defining the window for socio_economic_status in days relative to indexDate. Use -Inf or Inf for an unbounded lower or upper limit.

order

A character string specifying which record to select when multiple records are found: first or last.

nameStyle

A character string specifying the name of the new column.

name

A character string specifying the name of the output table. If NULL, a temporary table is created.

missingSocioEconomicStatusValue

A character string used to replace missing socioeconomic status values.

Value

The table x with a new column containing the Townsend deprivation index.

Examples


library(omock)
library(duckdb)
library(OmopIndices)
library(dplyr)
library(CohortConstructor)

cdm <- mockCdmFromDataset(datasetName = "GiBleed", source = "duckdb")
cdm$cohort <- conceptCohort(
  cdm = cdm,
  conceptSet = list(sinusitis = c(257012L, 4283893L, 4294548L, 40481087L)),
  name = "cohort"
)

cdm$cohort |>
  addTownsend() |>
  select(subject_id, cohort_start_date, socio_economic_status) |>
  glimpse()

Add Updated Charlson Comorbidity Index (CCI) value based on Quan et al. (2011) (doi:10.1093/aje/kwq433)

Description

Add Updated Charlson Comorbidity Index (CCI) value based on Quan et al. (2011) (doi:10.1093/aje/kwq433)

Usage

addUpdatedCharlsonIndex(
  x,
  indexDate = "cohort_start_date",
  ageAdjusted = TRUE,
  conceptSet = getIndexCodelist("updated_charlson"),
  nameStyle = "updated_charlson",
  categories = NULL,
  name = tableName(x)
)

Arguments

x

A cdm_table containing a person identifier column named person_id or subject_id.

indexDate

A character string naming the Date column in x that defines the index date.

ageAdjusted

Logical; whether to include age adjustment in the updated Charlson Comorbidity Index.

conceptSet

A named concept set supplied as a codelist, codelist_with_details, concept_set_expression, or named list of concept IDs. It must contain congestive_heart_failure, dementia, chronic_pulmonary_disease, connective_tissue_disease, mild_liver_disease, hemiplegia, severe_chronic_kidney_disease, diabetes_with_complication, any_malignancy, moderate_or_severe_liver_disease, metastatic_solid_tumor, aids as concepts. By default, internal codelists are used.

nameStyle

A character string specifying the name of the new column.

categories

A named list of numeric vectors, each containing the lower and upper bounds of a score interval. An additional column with the suffix ⁠_categories⁠ is added. Intervals are evaluated in the order supplied, and missing scores are labelled missing.

name

A character string specifying the name of the output table. If NULL, a temporary table is created.

Value

The table x with a new column containing the updated Charlson Comorbidity Index value.

Examples


library(omock)
library(duckdb)
library(OmopIndices)
library(dplyr)
library(CohortConstructor)

cdm <- mockCdmFromDataset(datasetName = "GiBleed", source = "duckdb")
cdm$cohort <- conceptCohort(
  cdm = cdm,
  conceptSet = list(sinusitis = c(257012L, 4283893L, 4294548L, 40481087L)),
  name = "cohort"
)

# Using the internal concept sets:
cdm$cohort |>
  addUpdatedCharlsonIndex(ageAdjusted = TRUE) |>
  select(subject_id, cohort_start_date, updated_charlson) |>
  glimpse()

# This example uses custom concept sets.
customConceptSet <- list(
  congestive_heart_failure = 319835L,
  dementia = 4182210L,
  chronic_pulmonary_disease = 255573L,
  connective_tissue_disease = 4134537L,
  mild_liver_disease = 194984L,
  moderate_or_severe_liver_disease = 4212540L,
  diabetes_with_complication = 42538715L,
  hemiplegia = 374022L,
  severe_chronic_kidney_disease = 46271022L,
  any_malignancy = 4180914L,
  metastatic_solid_tumor = 432851L,
  aids = 4267414L
)

cdm$cohort |>
  addUpdatedCharlsonIndex(
    conceptSet = customConceptSet,
    nameStyle = "updated_charlson_custom"
  ) |>
  select(subject_id, cohort_start_date, updated_charlson_custom) |>
  glimpse()

Helper for consistent documentation of categories argument

Description

Helper for consistent documentation of categories argument

Arguments

categories

A named list of numeric vectors, each containing the lower and upper bounds of a score interval. An additional column with the suffix ⁠_categories⁠ is added. Intervals are evaluated in the order supplied, and missing scores are labelled missing.

Get the codelists used for a specified index calculation

Description

Get the codelists used for a specified index calculation

Usage

getIndexCodelist(index)

Arguments

index

A character string identifying the index for which to retrieve internal codelists. Supported values are "body_mass_index", "charlson", "electronic_frailty_index", "hospital_frailty_risk_score", and "updated_charlson".

Value

A codelist containing the concepts used for the selected index.

Examples

library(OmopIndices)

getIndexCodelist("charlson")

Helper for consistent documentation of inObservation argument

Description

Helper for consistent documentation of inObservation argument

Arguments

inObservation

Logical; whether to restrict records to the person's observation period.

Helper for consistent documentation of indexDate argument

Description

Helper for consistent documentation of indexDate argument

Arguments

indexDate

A character string naming the Date column in x that defines the index date.

Helper for consistent documentation of index argument

Description

Helper for consistent documentation of index argument

Arguments

index

A character string identifying the index for which to retrieve internal codelists. Supported values are "body_mass_index", "charlson", "electronic_frailty_index", "hospital_frailty_risk_score", and "updated_charlson".

Helper for consistent documentation of name argument

Description

Helper for consistent documentation of name argument

Arguments

name

A character string specifying the name of the output table. If NULL, a temporary table is created.

Helper for consistent documentation of nameStyle argument

Description

Helper for consistent documentation of nameStyle argument

Arguments

nameStyle

A character string specifying the name of the new column.

Objects exported from other packages

Description

These objects are imported from other packages. Follow the links below to see their documentation.

omopgenerics

tableName()

Helper for consistent documentation of x argument

Description

Helper for consistent documentation of x argument

Arguments

x

A cdm_table containing a person identifier column named person_id or subject_id.