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Internal function flow

Source: vignettes/function-flow.qmd

This document describes the flow of functions and objects within the package, specifically within the main exposed function classify_diabetes(). It shows the data sources and how they enter or are used in the function as well as how the different internal functions and logic are connected to each other. A high-level overview of the flow is shown in the diagram below.

flowchart TD
  subgraph data_sources["Data sources"]
    lpr_diag[("lpr_diag")]
    lpr_adm[("lpr_adm")]
    kontakter[("kontakter")]
    diagnoser[("diagnoser")]
    sysi[("sysi")]
    sssy[("sssy")]
    lmdb[("lmdb")]
    lab_forsker[("lab_forsker")]
    bef[("bef")]
  end

  subgraph classify_diabetes["classify_diabetes()"]

    lpr_diag --> prepare_lpr2["prepare_lpr2()"]
    lpr_adm --> prepare_lpr2

    kontakter --> prepare_lpr3["prepare_lpr3()"]
    diagnoser --> prepare_lpr3

    prepare_lpr2 --> keep_pregnancy_dates["keep_pregnancy_dates()"]
    prepare_lpr3 --> keep_pregnancy_dates

    %% Keep
    sysi --> keep_podiatrist_services["keep_podiatrist_services()"]:::keep
    sssy --> keep_podiatrist_services

    prepare_lpr2 --> keep_diabetes_diagnoses["keep_diabetes_diagnoses()"]:::keep
    prepare_lpr3 --> keep_diabetes_diagnoses
    keep_diabetes_diagnoses --> add_t1d_diagnoses_cols["add_t1d_diagnoses_cols()"]

    lmdb --> keep_gld_purchases["keep_gld_purchases()"]:::keep

    lab_forsker --> keep_hba1c["keep_hba1c()"]:::keep

    %% Drop
    keep_gld_purchases --> drop_pcos["drop_pcos()"]:::drop
    bef --> drop_pcos

    drop_pcos --> drop_pregnancies["drop_pregnancies()"]:::drop
    keep_pregnancy_dates --> drop_pregnancies
    keep_hba1c --> drop_pregnancies
    drop_pregnancies --> add_insulin_purchases_cols["add_insulin_purchases_cols()"]

    %% Join and classify
    add_t1d_diagnoses_cols --> keep_two_earliest_events["keep_two_earliest_events()"]
    keep_podiatrist_services --> keep_two_earliest_events
    add_insulin_purchases_cols --> keep_two_earliest_events

    keep_two_earliest_events --> join_inclusions["join_inclusions()"]
    join_inclusions --> create_inclusion_dates["create_inclusion_dates()"]
    create_inclusion_dates --> classify_t1d["classify_t1d()"]

    keep_pregnancy_dates ~~~ drop_pcos

  end

  %% Styling
  classDef default fill:#EEEEEE, color:#000000, stroke:#000000
  classDef keep fill:lightblue
  classDef drop fill:orange
  style classify_diabetes fill:#FFFFFF, color:#000000
  style data_sources fill:#FFFFFF, color:#000000, stroke-width:0px

Flow of functions in, as well as their required input registers, in the classify_diabetes() function used for classifying diabetes status using the osdc package. Light blue and orange boxes represent filtering functions (keep_* and drop_*, respectively).

The sections below are split into functions for keeping and dropping events as well as functions for determining the final diagnosis date and eventual classification of type 1 and type 2 diabetes.

For more details and descriptions about the individual steps within the algorithm, see the documentation on the internal functions: