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.
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:
prepare_lpr2()prepare_lpr3()keep_pregnancy_dates()keep_diabetes_diagnoses()add_t1d_diagnoses_cols()keep_podiatrist_services()keep_hba1c()keep_gld_purchases()drop_pcos()drop_pregnancies()add_insulin_purchases_cols()keep_two_earliest_events()join_inclusions()create_inclusion_dates()classify_t1d()