diagnosed_placeholder: Diagnosis algorithms for selected diseases

In adamleejohnson/R-ukbiobank: UK Biobank Utilities

Diagnosis algorithms for selected diseases

Description

These convenience functions perform a combination of self-reported diagnosis lookups, ICD10 lookups, medication lookups, and lab/measurement value lookups in order to return a boolean vector indicating whether a diagnosis has been made within the provided instance ranges. The actual algorithm for each disease diagnosis (e.g. hypertension) is somewhat arbitrary, and (for example) is based on a selected list of medications, blood pressure measurements, ICD10 codes, etc. Users should construct their own algorithms to fit specific use-case scenarios.

Usage

diagnosed_chf(
  data,
  after_instance = default_after_inst(),
  up_to_instance = default_up_to_inst(),
  diagnosis_col = f.20002.0.0.Non_cancer_illness_code_self_reported
)

diagnosed_htn(
  data,
  after_instance = default_after_inst(),
  up_to_instance = default_up_to_inst(),
  diagnosis_col = f.20002.0.0.Non_cancer_illness_code_self_reported,
  min_sbp = 140,
  min_dbp = 90
)

diagnosed_hld(
  data,
  after_instance = default_after_inst(),
  up_to_instance = default_up_to_inst(),
  diagnosis_col = f.20002.0.0.Non_cancer_illness_code_self_reported
)

diagnosed_copd(
  data,
  after_instance = default_after_inst(),
  up_to_instance = default_up_to_inst(),
  diagnosis_col = f.20002.0.0.Non_cancer_illness_code_self_reported
)

diagnosed_pHTN(
  data,
  after_instance = default_after_inst(),
  up_to_instance = default_up_to_inst(),
  diagnosis_col = f.20002.0.0.Non_cancer_illness_code_self_reported
)

diagnosed_pulm_embolism(
  data,
  after_instance = default_after_inst(),
  up_to_instance = default_up_to_inst(),
  diagnosis_col = f.20002.0.0.Non_cancer_illness_code_self_reported
)

diagnosed_diabetes(
  data,
  after_instance = default_after_inst(),
  up_to_instance = default_up_to_inst(),
  diagnosis_col = f.20002.0.0.Non_cancer_illness_code_self_reported
)

Arguments

data	The primarydata frame. Thisdata frame includes all necessary columns required to perform look-ups (e.g. ICD10 code columns, medication code columns, age, sex, etc.).
after_instance	An integer specifying an instance number, or the name of the column (using <data-masking> rules) containing instance numbers to use as the minimum instance (non-inclusive). Used to include alldata after but NOT including the specified instance number. Defaults to default_after_inst(), which is typically -1 (i.e., include instances 0 and later).
up_to_instance	An integer specifying an instance number, or the name of the column (using <data-masking> rules) containing instance numbers to use as the maximum instance (inclusive). Used to include alldata up to and including the specified instance number. Defaults to default_up_to_inst(), which as of this writing returns 3.
diagnosis_col	Template column name for self-reported diagnosis codes. Default = f.20002.0.0.Non_cancer_illness_code_self_reported.
min_sbp	Minimum SBP for HTN diagnosis
min_dbp	Minimum DBP for HTN diagnosis

Instancing

The UK Biobank records visits as separate "instances." As of this writing, there are 4 instances labeled 0 through 3. At each instance, various information can be recorded or re-recorded. For example, blood pressure is typically recorded at most in-person evaluations. Therefore, there may be 4 separate columns for blood pressure recordings (actually, there could be more because the blood pressure may be recorded multiple times at each instance). Almost all of the functions in this package will utilize instance numbers to specify from which time pointsdata should be retrieved. For example, we may want to know the state of ICD10 diagnoses before instance 2. In this case, we would specify up_to_instance = 1 (search up to instance 1, inclusive) in functions that take this as an argument.

Arguments like up_to_instance and after_instance can take a constant instance number as their value. But they can also take the name of a column that contains an instance number, so that different instance limits can be used for each participant. For example, some participants undergo MRI at instance 2, and others at instance 3. If we want to know the state of a diagnosis up to and including the time of MRI, we would want to assign up_to_instance to the name of the column that specifies which instance the MRI occurred at. This column typically has to be generated by the user and attached to thedata frame beforehand.

Column names

Most functions in this package will take column names (*_col) as optional arguments (otherwise a default column names are used) which are then used as templates to find all other columns with the same field number, but different instance and array numbers. These functions will automatically find all matching instances (and arrays within each instance) within the specified parameters. Internally, a set of expand_instance_*() helper functions, which themselves rely on the column_expansion_helper() function, perform the work of searching for matching columns.

adamleejohnson/R-ukbiobank documentation built on April 25, 2022, 2:11 a.m.