Package 'OmopIndices'

Add Body Mass Index measurement

Description

Add Body Mass Index measurement

Usage

addBMI(
  x,
  conceptSet = getIndexCodelist("body_mass_index"),
  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 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 column named by appending ⁠_categories⁠ to nameStyle 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

addPolypharmacy(
  x,
  indexDate = "cohort_start_date",
  window = c(0, 0),
  overlap = TRUE,
  categories = NULL,
  nameStyle = "polypharmacy",
  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.
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 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 |>
  addPolypharmacy(window = c(-30, 0)) |>
  select(subject_id, cohort_start_date, polypharmacy) |>
  glimpse()

---

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

Description

Usage

addPolypharmacyCount(
  x,
  indexDate = "cohort_start_date",
  window = c(0, 0),
  overlap = TRUE,
  categories = NULL,
  nameStyle = "polypharmacy",
  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.
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.

Details

The function was renamed to addPolypharmacy()

Value

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

---

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()

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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()

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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")

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