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

# \donttest{
library(omock)
library(duckdb)
library(OmopIndices)
library(dplyr)
library(CohortConstructor)

cdm <- mockCdmFromDataset(datasetName = "GiBleed", source = "duckdb")
#> ℹ Loading bundled GiBleed tables from package data.
#> ℹ Adding drug_strength table.
#> ℹ Creating local <cdm_reference> object.
#> ℹ Inserting <cdm_reference> into duckdb.
#> duckdb keeps downloaded extensions and secrets in a temporary directory:
#> ℹ /tmp/Rtmplwnqmn/duckdb
#> This is removed when the R session ends.
#> • Extensions are re-downloaded each session.
#> • Secrets are lost.
#> ℹ Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
#> ℹ Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
#> ℹ See ?duckdb_storage for details and alternatives.
cdm$cohort <- conceptCohort(
  cdm = cdm,
  conceptSet = list(sinusitis = c(257012L, 4283893L, 4294548L, 40481087L)),
  name = "cohort"
)
#> ℹ Subsetting table condition_occurrence using 4 concepts with domain:
#>   condition.
#> ℹ Combining tables.
#> ℹ Creating cohort attributes.
#> ℹ Applying cohort requirements.
#> ℹ Merging overlapping records.
#> ✔ Cohort cohort created.

cdm$cohort |>
  addHospitalFrailtyRiskScore() |>
  select(subject_id, cohort_start_date, hfrs, hfrs_categories) |>
  glimpse()
#> Warning: 669 unique codelist concept IDs are not present in `cdm$concept`.
#> Warning: 669 unique codelist concept IDs are not present in `cdm$concept`.
#> ! 703 concept(s) from domain NA eliminated as it is not supported.
#> ℹ Supported domains are: device, specimen, measurement, drug, condition,
#>   observation, procedure, episode, and visit.
#> Your SQL query is over 20,000 characters which can cause issues on some database platforms!
#> Try calling computeQuery earlier in your pipeline.
#> Rows: ??
#> Columns: 4
#> $ subject_id        <int> 4382, 2776, 2776, 304, 3676, 5255, 727, 2260, 2830, …
#> $ cohort_start_date <date> 1994-09-03, 2014-10-22, 2016-01-04, 1957-06-07, 197…
#> $ hfrs              <dbl> 1.5, 2.3, 2.3, 1.8, 2.3, 1.5, 1.4, 1.5, 1.5, 1.5, 1.…
#> $ hfrs_categories   <chr> "low", "low", "low", "low", "low", "low", "low", "lo…
# }