Examining the stability of diagnostic coding across the transition from the DNPR2 to the DNPR3 for a publication

Preprint here.

The repo is split into multiple directories:

1. doc/validation – where we check assumptions about the data which have been questioned during our analyses
2. rmd - where we perform data management and analyses
3. src - for functions used in the analyses
4. tests - testing of functions

Each of these folders are "self-contained" in the sense that all variables used in a file is either defined in the same file, or in a previous file from the same folder.

In general, code uses lpr3 for the DNPR3 and lpr2 for the DNPR2. This is to conform with the naming scheme in the Central Denmark Region Business Intelligence Office, which is where the data comes from.

Results are generated in Render.rmd.

Brief explanation of analyses:

1. individual_unique_diagnoses - within-quarter incident number of unique diagnoses. Calculated for two approaches to determining whether a sequence of visits is from the same treatment course:
   • seq_responsibility_id: Visits are considered part of the same treatment course if they share a sequence responsibility identifier (DNPR3 "forløbsansvar"), specified further in the print table S1
   • same_clinic: Visits are considered part of the same treatment course if they are from the same patient in the same clinic
2. diagnostic_stability_in_course - to which extent does the first diagnosis and the last diagnosis in a treatment course match?
   • seq_responsibility_id: Visits are considered part of the same treatment course if they share a sequence responsibility identifier (DNPR3 "forløbsansvar"), specified further in the print table S1
   • same_clinic: Visits are considered part of the same treatment course if they are from the same patient in the same clinic
3. subchapter_props - is the proportion of visits within each ICD-10 subchapter stable (e.g. the proportion of all visits within a quarter that are coded as F3)
   • seq_responsibility_id: Visits are considered part of the same treatment course if they share a sequence responsibility identifier (DNPR3 "forløbsansvar"), specified further in the print table S1
   • same_clinic: Visits are considered part of the same treatment course if they are from the same patient in the same clinic